GEO_accession	GEO_ID	sample_ID	data_type	tissue	age	stimulus	genotype	title	sequencer	Treatment_protocol
GSE92835	GSM2437889	SRR5126147	paired-end	root	7_day_old	mock,1_day	Nipponbare	Regulation of gene expression during formation of nodule-like structures (NLS) in rice root	Illumina HiSeq 2500	Seven-day-old whole plants of rice, grown on Fahraeus medium plates under controlled conditions as discussed above were soaked in 50μM of 2,4-D solution for one hour. Ten ml of 2,4-D solution was used per plant for treatment solution. Following this treatment, the plants were transferred to 15-cm petri plates containing low-N Fahraeus medium. All plants were grown in a Percival growth chamber (Model #: CU-22L, Iowa, USA) with a 16-h, 22C day and 8-h, 24C night cycle and 150 to 200 μmol m–2s–1 light intensity at 65% relative humidity. Plants were phenotypically scored for NLS formation after 1, 7, and 14 days post treatment. Non-treated (mock) rice plants were cultivated similarly except 2,4-D was not included in the treatment solution to be used as controls for our studies.
GSE92835	GSM2437890	SRR5126148	paired-end	root	7_day_old	mock,1_day	Nipponbare	Regulation of gene expression during formation of nodule-like structures (NLS) in rice root	Illumina HiSeq 2500	Seven-day-old whole plants of rice, grown on Fahraeus medium plates under controlled conditions as discussed above were soaked in 50μM of 2,4-D solution for one hour. Ten ml of 2,4-D solution was used per plant for treatment solution. Following this treatment, the plants were transferred to 15-cm petri plates containing low-N Fahraeus medium. All plants were grown in a Percival growth chamber (Model #: CU-22L, Iowa, USA) with a 16-h, 22C day and 8-h, 24C night cycle and 150 to 200 μmol m–2s–1 light intensity at 65% relative humidity. Plants were phenotypically scored for NLS formation after 1, 7, and 14 days post treatment. Non-treated (mock) rice plants were cultivated similarly except 2,4-D was not included in the treatment solution to be used as controls for our studies.
GSE92835	GSM2437891	SRR5126149	paired-end	root	7_day_old	mock,1_day	Nipponbare	Regulation of gene expression during formation of nodule-like structures (NLS) in rice root	Illumina HiSeq 2500	Seven-day-old whole plants of rice, grown on Fahraeus medium plates under controlled conditions as discussed above were soaked in 50μM of 2,4-D solution for one hour. Ten ml of 2,4-D solution was used per plant for treatment solution. Following this treatment, the plants were transferred to 15-cm petri plates containing low-N Fahraeus medium. All plants were grown in a Percival growth chamber (Model #: CU-22L, Iowa, USA) with a 16-h, 22C day and 8-h, 24C night cycle and 150 to 200 μmol m–2s–1 light intensity at 65% relative humidity. Plants were phenotypically scored for NLS formation after 1, 7, and 14 days post treatment. Non-treated (mock) rice plants were cultivated similarly except 2,4-D was not included in the treatment solution to be used as controls for our studies.
GSE92835	GSM2437892	SRR5126150	paired-end	root	7_day_old	auxin(50CM_2,4_D),1_day	Nipponbare	Regulation of gene expression during formation of nodule-like structures (NLS) in rice root	Illumina HiSeq 2500	Seven-day-old whole plants of rice, grown on Fahraeus medium plates under controlled conditions as discussed above were soaked in 50μM of 2,4-D solution for one hour. Ten ml of 2,4-D solution was used per plant for treatment solution. Following this treatment, the plants were transferred to 15-cm petri plates containing low-N Fahraeus medium. All plants were grown in a Percival growth chamber (Model #: CU-22L, Iowa, USA) with a 16-h, 22C day and 8-h, 24C night cycle and 150 to 200 μmol m–2s–1 light intensity at 65% relative humidity. Plants were phenotypically scored for NLS formation after 1, 7, and 14 days post treatment. Non-treated (mock) rice plants were cultivated similarly except 2,4-D was not included in the treatment solution to be used as controls for our studies.
GSE92835	GSM2437893	SRR5126151	paired-end	root	7_day_old	auxin(50CM_2,4_D),1_day	Nipponbare	Regulation of gene expression during formation of nodule-like structures (NLS) in rice root	Illumina HiSeq 2500	Seven-day-old whole plants of rice, grown on Fahraeus medium plates under controlled conditions as discussed above were soaked in 50μM of 2,4-D solution for one hour. Ten ml of 2,4-D solution was used per plant for treatment solution. Following this treatment, the plants were transferred to 15-cm petri plates containing low-N Fahraeus medium. All plants were grown in a Percival growth chamber (Model #: CU-22L, Iowa, USA) with a 16-h, 22C day and 8-h, 24C night cycle and 150 to 200 μmol m–2s–1 light intensity at 65% relative humidity. Plants were phenotypically scored for NLS formation after 1, 7, and 14 days post treatment. Non-treated (mock) rice plants were cultivated similarly except 2,4-D was not included in the treatment solution to be used as controls for our studies.
GSE92835	GSM2437894	SRR5126152	paired-end	root	7_day_old	auxin(50CM_2,4_D),1_day	Nipponbare	Regulation of gene expression during formation of nodule-like structures (NLS) in rice root	Illumina HiSeq 2500	Seven-day-old whole plants of rice, grown on Fahraeus medium plates under controlled conditions as discussed above were soaked in 50μM of 2,4-D solution for one hour. Ten ml of 2,4-D solution was used per plant for treatment solution. Following this treatment, the plants were transferred to 15-cm petri plates containing low-N Fahraeus medium. All plants were grown in a Percival growth chamber (Model #: CU-22L, Iowa, USA) with a 16-h, 22C day and 8-h, 24C night cycle and 150 to 200 μmol m–2s–1 light intensity at 65% relative humidity. Plants were phenotypically scored for NLS formation after 1, 7, and 14 days post treatment. Non-treated (mock) rice plants were cultivated similarly except 2,4-D was not included in the treatment solution to be used as controls for our studies.
GSE92835	GSM2437895	SRR5126153	paired-end	root	7_day_old	mock,7_days	Nipponbare	Regulation of gene expression during formation of nodule-like structures (NLS) in rice root	Illumina HiSeq 2500	Seven-day-old whole plants of rice, grown on Fahraeus medium plates under controlled conditions as discussed above were soaked in 50μM of 2,4-D solution for one hour. Ten ml of 2,4-D solution was used per plant for treatment solution. Following this treatment, the plants were transferred to 15-cm petri plates containing low-N Fahraeus medium. All plants were grown in a Percival growth chamber (Model #: CU-22L, Iowa, USA) with a 16-h, 22C day and 8-h, 24C night cycle and 150 to 200 μmol m–2s–1 light intensity at 65% relative humidity. Plants were phenotypically scored for NLS formation after 1, 7, and 14 days post treatment. Non-treated (mock) rice plants were cultivated similarly except 2,4-D was not included in the treatment solution to be used as controls for our studies.
GSE92835	GSM2437895	SRR5126154	paired-end	root	7_day_old	mock,7_days	Nipponbare	Regulation of gene expression during formation of nodule-like structures (NLS) in rice root	Illumina HiSeq 2500	Seven-day-old whole plants of rice, grown on Fahraeus medium plates under controlled conditions as discussed above were soaked in 50μM of 2,4-D solution for one hour. Ten ml of 2,4-D solution was used per plant for treatment solution. Following this treatment, the plants were transferred to 15-cm petri plates containing low-N Fahraeus medium. All plants were grown in a Percival growth chamber (Model #: CU-22L, Iowa, USA) with a 16-h, 22C day and 8-h, 24C night cycle and 150 to 200 μmol m–2s–1 light intensity at 65% relative humidity. Plants were phenotypically scored for NLS formation after 1, 7, and 14 days post treatment. Non-treated (mock) rice plants were cultivated similarly except 2,4-D was not included in the treatment solution to be used as controls for our studies.
GSE92835	GSM2437896	SRR5126155	paired-end	root	7_day_old	mock,7_days	Nipponbare	Regulation of gene expression during formation of nodule-like structures (NLS) in rice root	Illumina HiSeq 2500	Seven-day-old whole plants of rice, grown on Fahraeus medium plates under controlled conditions as discussed above were soaked in 50μM of 2,4-D solution for one hour. Ten ml of 2,4-D solution was used per plant for treatment solution. Following this treatment, the plants were transferred to 15-cm petri plates containing low-N Fahraeus medium. All plants were grown in a Percival growth chamber (Model #: CU-22L, Iowa, USA) with a 16-h, 22C day and 8-h, 24C night cycle and 150 to 200 μmol m–2s–1 light intensity at 65% relative humidity. Plants were phenotypically scored for NLS formation after 1, 7, and 14 days post treatment. Non-treated (mock) rice plants were cultivated similarly except 2,4-D was not included in the treatment solution to be used as controls for our studies.
GSE92835	GSM2437896	SRR5126156	paired-end	root	7_day_old	mock,7_days	Nipponbare	Regulation of gene expression during formation of nodule-like structures (NLS) in rice root	Illumina HiSeq 2500	Seven-day-old whole plants of rice, grown on Fahraeus medium plates under controlled conditions as discussed above were soaked in 50μM of 2,4-D solution for one hour. Ten ml of 2,4-D solution was used per plant for treatment solution. Following this treatment, the plants were transferred to 15-cm petri plates containing low-N Fahraeus medium. All plants were grown in a Percival growth chamber (Model #: CU-22L, Iowa, USA) with a 16-h, 22C day and 8-h, 24C night cycle and 150 to 200 μmol m–2s–1 light intensity at 65% relative humidity. Plants were phenotypically scored for NLS formation after 1, 7, and 14 days post treatment. Non-treated (mock) rice plants were cultivated similarly except 2,4-D was not included in the treatment solution to be used as controls for our studies.
GSE92835	GSM2437897	SRR5126157	paired-end	root	7_day_old	mock,7_days	Nipponbare	Regulation of gene expression during formation of nodule-like structures (NLS) in rice root	Illumina HiSeq 2500	Seven-day-old whole plants of rice, grown on Fahraeus medium plates under controlled conditions as discussed above were soaked in 50μM of 2,4-D solution for one hour. Ten ml of 2,4-D solution was used per plant for treatment solution. Following this treatment, the plants were transferred to 15-cm petri plates containing low-N Fahraeus medium. All plants were grown in a Percival growth chamber (Model #: CU-22L, Iowa, USA) with a 16-h, 22C day and 8-h, 24C night cycle and 150 to 200 μmol m–2s–1 light intensity at 65% relative humidity. Plants were phenotypically scored for NLS formation after 1, 7, and 14 days post treatment. Non-treated (mock) rice plants were cultivated similarly except 2,4-D was not included in the treatment solution to be used as controls for our studies.
GSE92835	GSM2437897	SRR5126158	paired-end	root	7_day_old	mock,7_days	Nipponbare	Regulation of gene expression during formation of nodule-like structures (NLS) in rice root	Illumina HiSeq 2500	Seven-day-old whole plants of rice, grown on Fahraeus medium plates under controlled conditions as discussed above were soaked in 50μM of 2,4-D solution for one hour. Ten ml of 2,4-D solution was used per plant for treatment solution. Following this treatment, the plants were transferred to 15-cm petri plates containing low-N Fahraeus medium. All plants were grown in a Percival growth chamber (Model #: CU-22L, Iowa, USA) with a 16-h, 22C day and 8-h, 24C night cycle and 150 to 200 μmol m–2s–1 light intensity at 65% relative humidity. Plants were phenotypically scored for NLS formation after 1, 7, and 14 days post treatment. Non-treated (mock) rice plants were cultivated similarly except 2,4-D was not included in the treatment solution to be used as controls for our studies.
GSE92835	GSM2437898	SRR5126159	paired-end	root	7_day_old	auxin(50CM_2,4_D),7_days	Nipponbare	Regulation of gene expression during formation of nodule-like structures (NLS) in rice root	Illumina HiSeq 2500	Seven-day-old whole plants of rice, grown on Fahraeus medium plates under controlled conditions as discussed above were soaked in 50μM of 2,4-D solution for one hour. Ten ml of 2,4-D solution was used per plant for treatment solution. Following this treatment, the plants were transferred to 15-cm petri plates containing low-N Fahraeus medium. All plants were grown in a Percival growth chamber (Model #: CU-22L, Iowa, USA) with a 16-h, 22C day and 8-h, 24C night cycle and 150 to 200 μmol m–2s–1 light intensity at 65% relative humidity. Plants were phenotypically scored for NLS formation after 1, 7, and 14 days post treatment. Non-treated (mock) rice plants were cultivated similarly except 2,4-D was not included in the treatment solution to be used as controls for our studies.
GSE92835	GSM2437898	SRR5126160	paired-end	root	7_day_old	auxin(50CM_2,4_D),7_days	Nipponbare	Regulation of gene expression during formation of nodule-like structures (NLS) in rice root	Illumina HiSeq 2500	Seven-day-old whole plants of rice, grown on Fahraeus medium plates under controlled conditions as discussed above were soaked in 50μM of 2,4-D solution for one hour. Ten ml of 2,4-D solution was used per plant for treatment solution. Following this treatment, the plants were transferred to 15-cm petri plates containing low-N Fahraeus medium. All plants were grown in a Percival growth chamber (Model #: CU-22L, Iowa, USA) with a 16-h, 22C day and 8-h, 24C night cycle and 150 to 200 μmol m–2s–1 light intensity at 65% relative humidity. Plants were phenotypically scored for NLS formation after 1, 7, and 14 days post treatment. Non-treated (mock) rice plants were cultivated similarly except 2,4-D was not included in the treatment solution to be used as controls for our studies.
GSE92835	GSM2437899	SRR5126161	paired-end	root	7_day_old	auxin(50CM_2,4_D),7_days	Nipponbare	Regulation of gene expression during formation of nodule-like structures (NLS) in rice root	Illumina HiSeq 2500	Seven-day-old whole plants of rice, grown on Fahraeus medium plates under controlled conditions as discussed above were soaked in 50μM of 2,4-D solution for one hour. Ten ml of 2,4-D solution was used per plant for treatment solution. Following this treatment, the plants were transferred to 15-cm petri plates containing low-N Fahraeus medium. All plants were grown in a Percival growth chamber (Model #: CU-22L, Iowa, USA) with a 16-h, 22C day and 8-h, 24C night cycle and 150 to 200 μmol m–2s–1 light intensity at 65% relative humidity. Plants were phenotypically scored for NLS formation after 1, 7, and 14 days post treatment. Non-treated (mock) rice plants were cultivated similarly except 2,4-D was not included in the treatment solution to be used as controls for our studies.
GSE92835	GSM2437899	SRR5126162	paired-end	root	7_day_old	auxin(50CM_2,4_D),7_days	Nipponbare	Regulation of gene expression during formation of nodule-like structures (NLS) in rice root	Illumina HiSeq 2500	Seven-day-old whole plants of rice, grown on Fahraeus medium plates under controlled conditions as discussed above were soaked in 50μM of 2,4-D solution for one hour. Ten ml of 2,4-D solution was used per plant for treatment solution. Following this treatment, the plants were transferred to 15-cm petri plates containing low-N Fahraeus medium. All plants were grown in a Percival growth chamber (Model #: CU-22L, Iowa, USA) with a 16-h, 22C day and 8-h, 24C night cycle and 150 to 200 μmol m–2s–1 light intensity at 65% relative humidity. Plants were phenotypically scored for NLS formation after 1, 7, and 14 days post treatment. Non-treated (mock) rice plants were cultivated similarly except 2,4-D was not included in the treatment solution to be used as controls for our studies.
GSE92835	GSM2437900	SRR5126163	paired-end	root	7_day_old	auxin(50CM_2,4_D),7_days	Nipponbare	Regulation of gene expression during formation of nodule-like structures (NLS) in rice root	Illumina HiSeq 2500	Seven-day-old whole plants of rice, grown on Fahraeus medium plates under controlled conditions as discussed above were soaked in 50μM of 2,4-D solution for one hour. Ten ml of 2,4-D solution was used per plant for treatment solution. Following this treatment, the plants were transferred to 15-cm petri plates containing low-N Fahraeus medium. All plants were grown in a Percival growth chamber (Model #: CU-22L, Iowa, USA) with a 16-h, 22C day and 8-h, 24C night cycle and 150 to 200 μmol m–2s–1 light intensity at 65% relative humidity. Plants were phenotypically scored for NLS formation after 1, 7, and 14 days post treatment. Non-treated (mock) rice plants were cultivated similarly except 2,4-D was not included in the treatment solution to be used as controls for our studies.
GSE92835	GSM2437900	SRR5126164	paired-end	root	7_day_old	auxin(50CM_2,4_D),7_days	Nipponbare	Regulation of gene expression during formation of nodule-like structures (NLS) in rice root	Illumina HiSeq 2500	Seven-day-old whole plants of rice, grown on Fahraeus medium plates under controlled conditions as discussed above were soaked in 50μM of 2,4-D solution for one hour. Ten ml of 2,4-D solution was used per plant for treatment solution. Following this treatment, the plants were transferred to 15-cm petri plates containing low-N Fahraeus medium. All plants were grown in a Percival growth chamber (Model #: CU-22L, Iowa, USA) with a 16-h, 22C day and 8-h, 24C night cycle and 150 to 200 μmol m–2s–1 light intensity at 65% relative humidity. Plants were phenotypically scored for NLS formation after 1, 7, and 14 days post treatment. Non-treated (mock) rice plants were cultivated similarly except 2,4-D was not included in the treatment solution to be used as controls for our studies.
GSE92835	GSM2437901	SRR5126165	paired-end	root	7_day_old	mock,14_days	Nipponbare	Regulation of gene expression during formation of nodule-like structures (NLS) in rice root	Illumina HiSeq 2500	Seven-day-old whole plants of rice, grown on Fahraeus medium plates under controlled conditions as discussed above were soaked in 50μM of 2,4-D solution for one hour. Ten ml of 2,4-D solution was used per plant for treatment solution. Following this treatment, the plants were transferred to 15-cm petri plates containing low-N Fahraeus medium. All plants were grown in a Percival growth chamber (Model #: CU-22L, Iowa, USA) with a 16-h, 22C day and 8-h, 24C night cycle and 150 to 200 μmol m–2s–1 light intensity at 65% relative humidity. Plants were phenotypically scored for NLS formation after 1, 7, and 14 days post treatment. Non-treated (mock) rice plants were cultivated similarly except 2,4-D was not included in the treatment solution to be used as controls for our studies.
GSE92835	GSM2437901	SRR5126166	paired-end	root	7_day_old	mock,14_days	Nipponbare	Regulation of gene expression during formation of nodule-like structures (NLS) in rice root	Illumina HiSeq 2500	Seven-day-old whole plants of rice, grown on Fahraeus medium plates under controlled conditions as discussed above were soaked in 50μM of 2,4-D solution for one hour. Ten ml of 2,4-D solution was used per plant for treatment solution. Following this treatment, the plants were transferred to 15-cm petri plates containing low-N Fahraeus medium. All plants were grown in a Percival growth chamber (Model #: CU-22L, Iowa, USA) with a 16-h, 22C day and 8-h, 24C night cycle and 150 to 200 μmol m–2s–1 light intensity at 65% relative humidity. Plants were phenotypically scored for NLS formation after 1, 7, and 14 days post treatment. Non-treated (mock) rice plants were cultivated similarly except 2,4-D was not included in the treatment solution to be used as controls for our studies.
GSE92835	GSM2437902	SRR5126167	paired-end	root	7_day_old	mock,14_days	Nipponbare	Regulation of gene expression during formation of nodule-like structures (NLS) in rice root	Illumina HiSeq 2500	Seven-day-old whole plants of rice, grown on Fahraeus medium plates under controlled conditions as discussed above were soaked in 50μM of 2,4-D solution for one hour. Ten ml of 2,4-D solution was used per plant for treatment solution. Following this treatment, the plants were transferred to 15-cm petri plates containing low-N Fahraeus medium. All plants were grown in a Percival growth chamber (Model #: CU-22L, Iowa, USA) with a 16-h, 22C day and 8-h, 24C night cycle and 150 to 200 μmol m–2s–1 light intensity at 65% relative humidity. Plants were phenotypically scored for NLS formation after 1, 7, and 14 days post treatment. Non-treated (mock) rice plants were cultivated similarly except 2,4-D was not included in the treatment solution to be used as controls for our studies.
GSE92835	GSM2437902	SRR5126168	paired-end	root	7_day_old	mock,14_days	Nipponbare	Regulation of gene expression during formation of nodule-like structures (NLS) in rice root	Illumina HiSeq 2500	Seven-day-old whole plants of rice, grown on Fahraeus medium plates under controlled conditions as discussed above were soaked in 50μM of 2,4-D solution for one hour. Ten ml of 2,4-D solution was used per plant for treatment solution. Following this treatment, the plants were transferred to 15-cm petri plates containing low-N Fahraeus medium. All plants were grown in a Percival growth chamber (Model #: CU-22L, Iowa, USA) with a 16-h, 22C day and 8-h, 24C night cycle and 150 to 200 μmol m–2s–1 light intensity at 65% relative humidity. Plants were phenotypically scored for NLS formation after 1, 7, and 14 days post treatment. Non-treated (mock) rice plants were cultivated similarly except 2,4-D was not included in the treatment solution to be used as controls for our studies.
GSE92835	GSM2437903	SRR5126169	paired-end	root	7_day_old	mock,14_days	Nipponbare	Regulation of gene expression during formation of nodule-like structures (NLS) in rice root	Illumina HiSeq 2500	Seven-day-old whole plants of rice, grown on Fahraeus medium plates under controlled conditions as discussed above were soaked in 50μM of 2,4-D solution for one hour. Ten ml of 2,4-D solution was used per plant for treatment solution. Following this treatment, the plants were transferred to 15-cm petri plates containing low-N Fahraeus medium. All plants were grown in a Percival growth chamber (Model #: CU-22L, Iowa, USA) with a 16-h, 22C day and 8-h, 24C night cycle and 150 to 200 μmol m–2s–1 light intensity at 65% relative humidity. Plants were phenotypically scored for NLS formation after 1, 7, and 14 days post treatment. Non-treated (mock) rice plants were cultivated similarly except 2,4-D was not included in the treatment solution to be used as controls for our studies.
GSE92835	GSM2437903	SRR5126170	paired-end	root	7_day_old	mock,14_days	Nipponbare	Regulation of gene expression during formation of nodule-like structures (NLS) in rice root	Illumina HiSeq 2500	Seven-day-old whole plants of rice, grown on Fahraeus medium plates under controlled conditions as discussed above were soaked in 50μM of 2,4-D solution for one hour. Ten ml of 2,4-D solution was used per plant for treatment solution. Following this treatment, the plants were transferred to 15-cm petri plates containing low-N Fahraeus medium. All plants were grown in a Percival growth chamber (Model #: CU-22L, Iowa, USA) with a 16-h, 22C day and 8-h, 24C night cycle and 150 to 200 μmol m–2s–1 light intensity at 65% relative humidity. Plants were phenotypically scored for NLS formation after 1, 7, and 14 days post treatment. Non-treated (mock) rice plants were cultivated similarly except 2,4-D was not included in the treatment solution to be used as controls for our studies.
GSE92835	GSM2437904	SRR5126171	paired-end	root	7_day_old	auxin(50CM_2,4_D),14_days	Nipponbare	Regulation of gene expression during formation of nodule-like structures (NLS) in rice root	Illumina HiSeq 2500	Seven-day-old whole plants of rice, grown on Fahraeus medium plates under controlled conditions as discussed above were soaked in 50μM of 2,4-D solution for one hour. Ten ml of 2,4-D solution was used per plant for treatment solution. Following this treatment, the plants were transferred to 15-cm petri plates containing low-N Fahraeus medium. All plants were grown in a Percival growth chamber (Model #: CU-22L, Iowa, USA) with a 16-h, 22C day and 8-h, 24C night cycle and 150 to 200 μmol m–2s–1 light intensity at 65% relative humidity. Plants were phenotypically scored for NLS formation after 1, 7, and 14 days post treatment. Non-treated (mock) rice plants were cultivated similarly except 2,4-D was not included in the treatment solution to be used as controls for our studies.
GSE92835	GSM2437904	SRR5126172	paired-end	root	7_day_old	auxin(50CM_2,4_D),14_days	Nipponbare	Regulation of gene expression during formation of nodule-like structures (NLS) in rice root	Illumina HiSeq 2500	Seven-day-old whole plants of rice, grown on Fahraeus medium plates under controlled conditions as discussed above were soaked in 50μM of 2,4-D solution for one hour. Ten ml of 2,4-D solution was used per plant for treatment solution. Following this treatment, the plants were transferred to 15-cm petri plates containing low-N Fahraeus medium. All plants were grown in a Percival growth chamber (Model #: CU-22L, Iowa, USA) with a 16-h, 22C day and 8-h, 24C night cycle and 150 to 200 μmol m–2s–1 light intensity at 65% relative humidity. Plants were phenotypically scored for NLS formation after 1, 7, and 14 days post treatment. Non-treated (mock) rice plants were cultivated similarly except 2,4-D was not included in the treatment solution to be used as controls for our studies.
GSE92835	GSM2437905	SRR5126173	paired-end	root	7_day_old	auxin(50CM_2,4_D),14_days	Nipponbare	Regulation of gene expression during formation of nodule-like structures (NLS) in rice root	Illumina HiSeq 2500	Seven-day-old whole plants of rice, grown on Fahraeus medium plates under controlled conditions as discussed above were soaked in 50μM of 2,4-D solution for one hour. Ten ml of 2,4-D solution was used per plant for treatment solution. Following this treatment, the plants were transferred to 15-cm petri plates containing low-N Fahraeus medium. All plants were grown in a Percival growth chamber (Model #: CU-22L, Iowa, USA) with a 16-h, 22C day and 8-h, 24C night cycle and 150 to 200 μmol m–2s–1 light intensity at 65% relative humidity. Plants were phenotypically scored for NLS formation after 1, 7, and 14 days post treatment. Non-treated (mock) rice plants were cultivated similarly except 2,4-D was not included in the treatment solution to be used as controls for our studies.
GSE92835	GSM2437905	SRR5126174	paired-end	root	7_day_old	auxin(50CM_2,4_D),14_days	Nipponbare	Regulation of gene expression during formation of nodule-like structures (NLS) in rice root	Illumina HiSeq 2500	Seven-day-old whole plants of rice, grown on Fahraeus medium plates under controlled conditions as discussed above were soaked in 50μM of 2,4-D solution for one hour. Ten ml of 2,4-D solution was used per plant for treatment solution. Following this treatment, the plants were transferred to 15-cm petri plates containing low-N Fahraeus medium. All plants were grown in a Percival growth chamber (Model #: CU-22L, Iowa, USA) with a 16-h, 22C day and 8-h, 24C night cycle and 150 to 200 μmol m–2s–1 light intensity at 65% relative humidity. Plants were phenotypically scored for NLS formation after 1, 7, and 14 days post treatment. Non-treated (mock) rice plants were cultivated similarly except 2,4-D was not included in the treatment solution to be used as controls for our studies.
GSE92835	GSM2437906	SRR5126175	paired-end	root	7_day_old	auxin(50CM_2,4_D),14_days	Nipponbare	Regulation of gene expression during formation of nodule-like structures (NLS) in rice root	Illumina HiSeq 2500	Seven-day-old whole plants of rice, grown on Fahraeus medium plates under controlled conditions as discussed above were soaked in 50μM of 2,4-D solution for one hour. Ten ml of 2,4-D solution was used per plant for treatment solution. Following this treatment, the plants were transferred to 15-cm petri plates containing low-N Fahraeus medium. All plants were grown in a Percival growth chamber (Model #: CU-22L, Iowa, USA) with a 16-h, 22C day and 8-h, 24C night cycle and 150 to 200 μmol m–2s–1 light intensity at 65% relative humidity. Plants were phenotypically scored for NLS formation after 1, 7, and 14 days post treatment. Non-treated (mock) rice plants were cultivated similarly except 2,4-D was not included in the treatment solution to be used as controls for our studies.
GSE92835	GSM2437906	SRR5126176	paired-end	root	7_day_old	auxin(50CM_2,4_D),14_days	Nipponbare	Regulation of gene expression during formation of nodule-like structures (NLS) in rice root	Illumina HiSeq 2500	Seven-day-old whole plants of rice, grown on Fahraeus medium plates under controlled conditions as discussed above were soaked in 50μM of 2,4-D solution for one hour. Ten ml of 2,4-D solution was used per plant for treatment solution. Following this treatment, the plants were transferred to 15-cm petri plates containing low-N Fahraeus medium. All plants were grown in a Percival growth chamber (Model #: CU-22L, Iowa, USA) with a 16-h, 22C day and 8-h, 24C night cycle and 150 to 200 μmol m–2s–1 light intensity at 65% relative humidity. Plants were phenotypically scored for NLS formation after 1, 7, and 14 days post treatment. Non-treated (mock) rice plants were cultivated similarly except 2,4-D was not included in the treatment solution to be used as controls for our studies.
GSE121269	GSM3430618	SRR8060835	paired-end	leaves	3_week_old	wild_type	Nipponbare	Insights into Plant N6-Methyladenine DNA Methylation Based on High Contiguity Rice Genomes [RNA-seq]	HiSeq X Ten	3-week-old wild-type and mutant leaves were harvested and total RNA were extracted using the RNeasy Plus Mini kit (QIAGEN) according to the manufacturer＊s instructions.
GSE121269	GSM3430619	SRR8060836	paired-end	leaves	3_week_old	wild_type	Nipponbare	Insights into Plant N6-Methyladenine DNA Methylation Based on High Contiguity Rice Genomes [RNA-seq]	HiSeq X Ten	3-week-old wild-type and mutant leaves were harvested and total RNA were extracted using the RNeasy Plus Mini kit (QIAGEN) according to the manufacturer＊s instructions.
GSE121269	GSM3430620	SRR8060837	paired-end	leaves	3_week_old	wild_type	Nipponbare	Insights into Plant N6-Methyladenine DNA Methylation Based on High Contiguity Rice Genomes [RNA-seq]	HiSeq X Ten	3-week-old wild-type and mutant leaves were harvested and total RNA were extracted using the RNeasy Plus Mini kit (QIAGEN) according to the manufacturer＊s instructions.
GSE108782	GSM2913197	SRR6441554	paired-end	whole_plant	3_week_old	wild_type	Nipponbare	Insights into Plant N6-Methyladenine DNA Methylation Based on Improved Rice Genomes [RNA-Seq Nipponbare]	Illumina HiSeq 2500	Rice plants were grown on Yoshida solution in a growth chamber under short day (SD) condition (10 h light/14 h dark) with a light intensity of 800 Cmol m-2 s-1﹝
GSE108782	GSM2913198	SRR6441555	paired-end	whole_plant	3_week_old	wild_type	Nipponbare	Insights into Plant N6-Methyladenine DNA Methylation Based on Improved Rice Genomes [RNA-Seq Nipponbare]	Illumina HiSeq 2500	Rice plants were grown on Yoshida solution in a growth chamber under short day (SD) condition (10 h light/14 h dark) with a light intensity of 800 Cmol m-2 s-1﹝
GSE122887	GSM3487669	SRR8240824	paired-end	leaves	4_week_old	wild_type	Nipponbare	A stress-responsive bZIP transcription factor OsbZIP62 improves drought and oxidative resistance in rice	Illumina HiSeq 2500	The seedlings were grown with the liquid culture solution in grow chamber with a 16h light (28C)/8h dark(24C) photoperiod.
GSE122887	GSM3487670	SRR8240825	paired-end	leaves	4_week_old	wild_type	Nipponbare	A stress-responsive bZIP transcription factor OsbZIP62 improves drought and oxidative resistance in rice	Illumina HiSeq 2500	The seedlings were grown with the liquid culture solution in grow chamber with a 16h light (28C)/8h dark(24C) photoperiod.
GSE122887	GSM3487671	SRR8240826	paired-end	leaves	4_week_old	wild_type	Nipponbare	A stress-responsive bZIP transcription factor OsbZIP62 improves drought and oxidative resistance in rice	Illumina HiSeq 2500	The seedlings were grown with the liquid culture solution in grow chamber with a 16h light (28C)/8h dark(24C) photoperiod.
GSE81069	GSM2142078	SRR3472897	paired-end	root	2_week_old	nontransgenic_rice_plant	Nipponbare	The regulatory network of OsNAC6 targets drought-related genes orchestrating rice drought tolerance (RNA-Seq)	Illumina HiSeq 2000	Rice was germinated on MS (Murashige and Skoog) media at 28C for 4 days, and transplanted into soil pots (4x4x6 cm; 3 plants per pot) and grown in a greenhouse.
GSE81069	GSM2142081	SRR3472900	paired-end	root	2_week_old	nontransgenic_rice_plant	Nipponbare	The regulatory network of OsNAC6 targets drought-related genes orchestrating rice drought tolerance (RNA-Seq)	Illumina HiSeq 2000	Rice was germinated on MS (Murashige and Skoog) media at 28C for 4 days, and transplanted into soil pots (4x4x6 cm; 3 plants per pot) and grown in a greenhouse.
GSE98924	GSM2627922	SRR5560727	paired-end	caryopsis	post_flowering_day_9	wild_type	Nipponbare	The novel quantitative trait locus qTGW3 encodes a GSK3-like kinase and negatively regulates grain size and weight in rice	Illumina HiSeq 2000	Rice grains were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
GSE98924	GSM2627923	SRR5560728	paired-end	caryopsis	post_flowering_day_9	wild_type	Nipponbare	The novel quantitative trait locus qTGW3 encodes a GSK3-like kinase and negatively regulates grain size and weight in rice	Illumina HiSeq 2000	Rice grains were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
GSE98924	GSM2627924	SRR5560729	paired-end	caryopsis	post_flowering_day_9	wild_type	Nipponbare	The novel quantitative trait locus qTGW3 encodes a GSK3-like kinase and negatively regulates grain size and weight in rice	Illumina HiSeq 2000	Rice grains were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
GSE71925	GSM1847459	SRR2154086	paired-end	seedling	1_week	wt	Nipponbare	Variation in the expression of miRNAs and mRNAs in rice (Oryza sativa)	Illumina Genome Analyzer II	The uniformly germinated seeds were transferred into Yoshida nutrient solution and grown under a 16-hour light (28C) /8-hour dark (25C) photoperiod for 1 week
GSE76798	GSM2038042	SRR3098741	paired-end	seedling	2_week	wt	Nipponbare	Transposable elements (TEs) contribute to stress-related long intergenic noncoding RNAs in Plants (I)	Illumina HiSeq 2500	For growing rice, seeds was grown on the half MS media.  Total RNAs were extracted using Trizol (Sigma), and then were treated with TURBO DNA-free kit (ambion) for removing DNA contamination.
GSE76798	GSM2038042	SRR3098742	paired-end	seedling	2_week	wt	Nipponbare	Transposable elements (TEs) contribute to stress-related long intergenic noncoding RNAs in Plants (I)	Illumina HiSeq 2500	For growing rice, seeds was grown on the half MS media.  Total RNAs were extracted using Trizol (Sigma), and then were treated with TURBO DNA-free kit (ambion) for removing DNA contamination.
GSE76798	GSM2038042	SRR3098743	paired-end	seedling	2_week	wt	Nipponbare	Transposable elements (TEs) contribute to stress-related long intergenic noncoding RNAs in Plants (I)	Illumina HiSeq 2500	For growing rice, seeds was grown on the half MS media.  Total RNAs were extracted using Trizol (Sigma), and then were treated with TURBO DNA-free kit (ambion) for removing DNA contamination.
GSE76051	GSM1973418	SRR3015587	paired-end	coleoptile	2_days_old	wild_type_plus_1hr_shade	Nipponbare	Genome-wide transcriptome of the coleoptile and the first leaves treated by white light or shade in rice seedlings	Illumina HiSeq 2500	The seedlings were either left in white light or transferred to simulated shade (LED light, R: 16 CE?m -2 ?s -1 and Blue: 1.3 CE?m -2 ?s -1 ; FR light: 48 CE?m -2 ?s -1, 28 ⊥) for 1hr before the collections.
GSE76051	GSM1973419	SRR3015588	paired-end	coleoptile	2_days_old	wild_type_plus_1hr_shade	Nipponbare	Genome-wide transcriptome of the coleoptile and the first leaves treated by white light or shade in rice seedlings	Illumina HiSeq 2500	The seedlings were either left in white light or transferred to simulated shade (LED light, R: 16 CE?m -2 ?s -1 and Blue: 1.3 CE?m -2 ?s -1 ; FR light: 48 CE?m -2 ?s -1, 28 ⊥) for 1hr before the collections.
GSE76051	GSM1973420	SRR3015589	paired-end	coleoptile	2_days_old	wild_type_plus_1hr_white_light	Nipponbare	Genome-wide transcriptome of the coleoptile and the first leaves treated by white light or shade in rice seedlings	Illumina HiSeq 2500	The seedlings were either left in white light or transferred to simulated shade (LED light, R: 16 CE?m -2 ?s -1 and Blue: 1.3 CE?m -2 ?s -1 ; FR light: 48 CE?m -2 ?s -1, 28 ⊥) for 1hr before the collections.
GSE76051	GSM1973421	SRR3015591	paired-end	coleoptile	2_days_old	wild_type_plus_1hr_white_light	Nipponbare	Genome-wide transcriptome of the coleoptile and the first leaves treated by white light or shade in rice seedlings	Illumina HiSeq 2500	The seedlings were either left in white light or transferred to simulated shade (LED light, R: 16 CE?m -2 ?s -1 and Blue: 1.3 CE?m -2 ?s -1 ; FR light: 48 CE?m -2 ?s -1, 28 ⊥) for 1hr before the collections.
GSE76051	GSM1973422	SRR3015592	paired-end	leaves	3_days_old	wild_type_plus_1hr_shade	Nipponbare	Genome-wide transcriptome of the coleoptile and the first leaves treated by white light or shade in rice seedlings	Illumina HiSeq 2500	The seedlings were either left in white light or transferred to simulated shade (LED light, R: 16 CE?m -2 ?s -1 and Blue: 1.3 CE?m -2 ?s -1 ; FR light: 48 CE?m -2 ?s -1, 28 ⊥) for 1hr before the collections.
GSE76051	GSM1973423	SRR3015594	paired-end	leaves	3_days_old	wild_type_plus_1hr_shade	Nipponbare	Genome-wide transcriptome of the coleoptile and the first leaves treated by white light or shade in rice seedlings	Illumina HiSeq 2500	The seedlings were either left in white light or transferred to simulated shade (LED light, R: 16 CE?m -2 ?s -1 and Blue: 1.3 CE?m -2 ?s -1 ; FR light: 48 CE?m -2 ?s -1, 28 ⊥) for 1hr before the collections.
GSE76051	GSM1973424	SRR3015595	paired-end	leaves	3_days_old	wild_type_plus_1hr_white_light	Nipponbare	Genome-wide transcriptome of the coleoptile and the first leaves treated by white light or shade in rice seedlings	Illumina HiSeq 2500	The seedlings were either left in white light or transferred to simulated shade (LED light, R: 16 CE?m -2 ?s -1 and Blue: 1.3 CE?m -2 ?s -1 ; FR light: 48 CE?m -2 ?s -1, 28 ⊥) for 1hr before the collections.
GSE76051	GSM1973425	SRR3015597	paired-end	leaves	3_days_old	wild_type_plus_1hr_white_light	Nipponbare	Genome-wide transcriptome of the coleoptile and the first leaves treated by white light or shade in rice seedlings	Illumina HiSeq 2500	The seedlings were either left in white light or transferred to simulated shade (LED light, R: 16 CE?m -2 ?s -1 and Blue: 1.3 CE?m -2 ?s -1 ; FR light: 48 CE?m -2 ?s -1, 28 ⊥) for 1hr before the collections.
GSE74465	GSM1921121	SRR2857719	paired-end	whole_plant	three_leaves_stage	drought_stress_0h	Nipponbare	Genome-wide identification of Drought-responsive Regulatory Coding and Non-coding Transcripts from Oryza sativa L. by deep RNA sequencing	Illumina HiSeq 2000	Rice plants at the three-leaves stage were subjected to drought-stress for 1 and 6 hr by removal of the culture solution. Untreated plants were used as control. After treatment, entire plants were immediately transferred into liquid nitrogen.
GSE74465	GSM1921122	SRR2857720	paired-end	whole_plant	three_leaves_stage	drought_stress_1h	Nipponbare	Genome-wide identification of Drought-responsive Regulatory Coding and Non-coding Transcripts from Oryza sativa L. by deep RNA sequencing	Illumina HiSeq 2000	Rice plants at the three-leaves stage were subjected to drought-stress for 1 and 6 hr by removal of the culture solution. Untreated plants were used as control. After treatment, entire plants were immediately transferred into liquid nitrogen.
GSE74465	GSM1921123	SRR2857721	paired-end	whole_plant	three_leaves_stage	drought_stress_6h	Nipponbare	Genome-wide identification of Drought-responsive Regulatory Coding and Non-coding Transcripts from Oryza sativa L. by deep RNA sequencing	Illumina HiSeq 2000	Rice plants at the three-leaves stage were subjected to drought-stress for 1 and 6 hr by removal of the culture solution. Untreated plants were used as control. After treatment, entire plants were immediately transferred into liquid nitrogen.
GSE75131	GSM1943702	SRR2922622	single-end	leaves	no_collect	Xanthomonas_oryzae_pv._oryzicola_strain_BLS254	Nipponbare	Host transcriptional reprogramming in response to the rice bacterial blight pathogen Xanthomonas oryzae pv. oryzae strain BLS354	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE75131	GSM1943703	SRR2922623	single-end	leaves	no_collect	Xanthomonas_oryzae_pv._oryzicola_strain_BLS254	Nipponbare	Host transcriptional reprogramming in response to the rice bacterial blight pathogen Xanthomonas oryzae pv. oryzae strain BLS354	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE75131	GSM1943704	SRR2922624	single-end	leaves	no_collect	Xanthomonas_oryzae_pv._oryzicola_strain_BLS254	Nipponbare	Host transcriptional reprogramming in response to the rice bacterial blight pathogen Xanthomonas oryzae pv. oryzae strain BLS354	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE67373	GSM1645626	SRR1944582	single-end	seedling	15_day_old	with_chilling_teatment_(4C,33h)	Nipponbare	A global profiling of gene expression in chilling stress in rice	Illumina HiSeq 2000	The aerial part of rice seedlings treated or untreated with chilling (4 C for 33 h) were pooled and used for library construction.
GSE67373	GSM1645627	SRR1944583	single-end	seedling	15_day_old	no_treatment	Nipponbare	A global profiling of gene expression in chilling stress in rice	Illumina HiSeq 2000	The aerial part of rice seedlings treated or untreated with chilling (4 C for 33 h) were pooled and used for library construction.
GSE73220	GSM1888887	SRR2338866	paired-end	endosprem	grain_filling_stage	control	Nipponbare	RNA-Seq of rice endosperm under high temperature	Illumina Genome Analyzer	Five days after pollination rice plants were then transferred to either a 35C /28C or 28C / 22C artificial climate room for high temperature or control treatment
GSE73220	GSM1888888	SRR2338867	paired-end	endosprem	grain_filling_stage	control	Nipponbare	RNA-Seq of rice endosperm under high temperature	Illumina Genome Analyzer	Five days after pollination rice plants were then transferred to either a 35C /28C or 28C / 22C artificial climate room for high temperature or control treatment
GSE73220	GSM1888889	SRR2338868	paired-end	endosprem	grain_filling_stage	high_temperature	Nipponbare	RNA-Seq of rice endosperm under high temperature	Illumina Genome Analyzer	Five days after pollination rice plants were then transferred to either a 35C /28C or 28C / 22C artificial climate room for high temperature or control treatment
GSE73220	GSM1888890	SRR2338869	paired-end	endosprem	grain_filling_stage	high_temperature	Nipponbare	RNA-Seq of rice endosperm under high temperature	Illumina Genome Analyzer	Five days after pollination rice plants were then transferred to either a 35C /28C or 28C / 22C artificial climate room for high temperature or control treatment
GSE57707	GSM1387095	SRR1288363	paired-end	shoot	no_collect	none,3_days_post_infection	Nipponbare	Systemic suppression of the rice shoot metabolism upon roots rot nematode infection	Illumina Genome Analyzer Iix	Hirschmanniella oryzae infected rice root were collected in rice fields in Myanmar and sent to Ghent University by Zin Thu Zar Maung (Plant Protection Division, Yangon, Myanmar). The nematodes were extracted using a Baermann funnel. Five days after transplanting in SAP the plants were inoculated with 400 nematodes per plant or mock-inoculated with tap water. One day after inoculation the plants were transferred to a hydroponic culturing system with Hoagland solution (Reversat et al., 1999) to synchronize the infection process. Systemic shoots were collected 3 and 7 days post inoculation (dpi). At each time point, two independent biological replicates, containing a pool of 6 different plants, were taken for RNA-Sequencing. Similarly, shoot tissue of 2 independent biological replicates of uninfected plants was taken to be used as control.
GSE57707	GSM1387096	SRR1288364	paired-end	shoot	no_collect	none,3_days_post_infection	Nipponbare	Systemic suppression of the rice shoot metabolism upon roots rot nematode infection	Illumina Genome Analyzer Iix	Hirschmanniella oryzae infected rice root were collected in rice fields in Myanmar and sent to Ghent University by Zin Thu Zar Maung (Plant Protection Division, Yangon, Myanmar). The nematodes were extracted using a Baermann funnel. Five days after transplanting in SAP the plants were inoculated with 400 nematodes per plant or mock-inoculated with tap water. One day after inoculation the plants were transferred to a hydroponic culturing system with Hoagland solution (Reversat et al., 1999) to synchronize the infection process. Systemic shoots were collected 3 and 7 days post inoculation (dpi). At each time point, two independent biological replicates, containing a pool of 6 different plants, were taken for RNA-Sequencing. Similarly, shoot tissue of 2 independent biological replicates of uninfected plants was taken to be used as control.
GSE57707	GSM1387097	SRR1288365	paired-end	shoot	no_collect	none,7_days_post_infection	Nipponbare	Systemic suppression of the rice shoot metabolism upon roots rot nematode infection	Illumina Genome Analyzer Iix	Hirschmanniella oryzae infected rice root were collected in rice fields in Myanmar and sent to Ghent University by Zin Thu Zar Maung (Plant Protection Division, Yangon, Myanmar). The nematodes were extracted using a Baermann funnel. Five days after transplanting in SAP the plants were inoculated with 400 nematodes per plant or mock-inoculated with tap water. One day after inoculation the plants were transferred to a hydroponic culturing system with Hoagland solution (Reversat et al., 1999) to synchronize the infection process. Systemic shoots were collected 3 and 7 days post inoculation (dpi). At each time point, two independent biological replicates, containing a pool of 6 different plants, were taken for RNA-Sequencing. Similarly, shoot tissue of 2 independent biological replicates of uninfected plants was taken to be used as control.
GSE57707	GSM1387098	SRR1288366	paired-end	shoot	no_collect	none,7_days_post_infection	Nipponbare	Systemic suppression of the rice shoot metabolism upon roots rot nematode infection	Illumina Genome Analyzer Iix	Hirschmanniella oryzae infected rice root were collected in rice fields in Myanmar and sent to Ghent University by Zin Thu Zar Maung (Plant Protection Division, Yangon, Myanmar). The nematodes were extracted using a Baermann funnel. Five days after transplanting in SAP the plants were inoculated with 400 nematodes per plant or mock-inoculated with tap water. One day after inoculation the plants were transferred to a hydroponic culturing system with Hoagland solution (Reversat et al., 1999) to synchronize the infection process. Systemic shoots were collected 3 and 7 days post inoculation (dpi). At each time point, two independent biological replicates, containing a pool of 6 different plants, were taken for RNA-Sequencing. Similarly, shoot tissue of 2 independent biological replicates of uninfected plants was taken to be used as control.
GSE57707	GSM1387099	SRR1288367	paired-end	shoot	no_collect	roots_rot_nematode_(H._oryzae),3_days_post_infection	Nipponbare	Systemic suppression of the rice shoot metabolism upon roots rot nematode infection	Illumina Genome Analyzer Iix	Hirschmanniella oryzae infected rice root were collected in rice fields in Myanmar and sent to Ghent University by Zin Thu Zar Maung (Plant Protection Division, Yangon, Myanmar). The nematodes were extracted using a Baermann funnel. Five days after transplanting in SAP the plants were inoculated with 400 nematodes per plant or mock-inoculated with tap water. One day after inoculation the plants were transferred to a hydroponic culturing system with Hoagland solution (Reversat et al., 1999) to synchronize the infection process. Systemic shoots were collected 3 and 7 days post inoculation (dpi). At each time point, two independent biological replicates, containing a pool of 6 different plants, were taken for RNA-Sequencing. Similarly, shoot tissue of 2 independent biological replicates of uninfected plants was taken to be used as control.
GSE57707	GSM1387100	SRR1288368	paired-end	shoot	no_collect	roots_rot_nematode_(H._oryzae),3_days_post_infection	Nipponbare	Systemic suppression of the rice shoot metabolism upon roots rot nematode infection	Illumina Genome Analyzer Iix	Hirschmanniella oryzae infected rice root were collected in rice fields in Myanmar and sent to Ghent University by Zin Thu Zar Maung (Plant Protection Division, Yangon, Myanmar). The nematodes were extracted using a Baermann funnel. Five days after transplanting in SAP the plants were inoculated with 400 nematodes per plant or mock-inoculated with tap water. One day after inoculation the plants were transferred to a hydroponic culturing system with Hoagland solution (Reversat et al., 1999) to synchronize the infection process. Systemic shoots were collected 3 and 7 days post inoculation (dpi). At each time point, two independent biological replicates, containing a pool of 6 different plants, were taken for RNA-Sequencing. Similarly, shoot tissue of 2 independent biological replicates of uninfected plants was taken to be used as control.
GSE57707	GSM1387101	SRR1288369	paired-end	shoot	no_collect	roots_rot_nematode_(H._oryzae),7_days_post_infection	Nipponbare	Systemic suppression of the rice shoot metabolism upon roots rot nematode infection	Illumina Genome Analyzer Iix	Hirschmanniella oryzae infected rice root were collected in rice fields in Myanmar and sent to Ghent University by Zin Thu Zar Maung (Plant Protection Division, Yangon, Myanmar). The nematodes were extracted using a Baermann funnel. Five days after transplanting in SAP the plants were inoculated with 400 nematodes per plant or mock-inoculated with tap water. One day after inoculation the plants were transferred to a hydroponic culturing system with Hoagland solution (Reversat et al., 1999) to synchronize the infection process. Systemic shoots were collected 3 and 7 days post inoculation (dpi). At each time point, two independent biological replicates, containing a pool of 6 different plants, were taken for RNA-Sequencing. Similarly, shoot tissue of 2 independent biological replicates of uninfected plants was taken to be used as control.
GSE57707	GSM1387102	SRR1288370	paired-end	shoot	no_collect	roots_rot_nematode_(H._oryzae),7_days_post_infection	Nipponbare	Systemic suppression of the rice shoot metabolism upon roots rot nematode infection	Illumina Genome Analyzer Iix	Hirschmanniella oryzae infected rice root were collected in rice fields in Myanmar and sent to Ghent University by Zin Thu Zar Maung (Plant Protection Division, Yangon, Myanmar). The nematodes were extracted using a Baermann funnel. Five days after transplanting in SAP the plants were inoculated with 400 nematodes per plant or mock-inoculated with tap water. One day after inoculation the plants were transferred to a hydroponic culturing system with Hoagland solution (Reversat et al., 1999) to synchronize the infection process. Systemic shoots were collected 3 and 7 days post inoculation (dpi). At each time point, two independent biological replicates, containing a pool of 6 different plants, were taken for RNA-Sequencing. Similarly, shoot tissue of 2 independent biological replicates of uninfected plants was taken to be used as control.
GSE67588	GSM1650074	SRR1952778	single-end	leaves	2_week_old	48_hrs_after_inoculation_with_BLS256	Nipponbare	Host transcriptional reprogramming across diverse strains of the rice bacterial leaves streak pathogen Xanthomonas oryzae pv.oryzicola	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE67588	GSM1650075	SRR1952779	single-end	leaves	2_week_old	48_hrs_after_inoculation_with_BLS256	Nipponbare	Host transcriptional reprogramming across diverse strains of the rice bacterial leaves streak pathogen Xanthomonas oryzae pv.oryzicola	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE67588	GSM1650076	SRR1952780	single-end	leaves	2_week_old	48_hrs_after_inoculation_with_BLS256	Nipponbare	Host transcriptional reprogramming across diverse strains of the rice bacterial leaves streak pathogen Xanthomonas oryzae pv.oryzicola	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE67588	GSM1650077	SRR1952781	single-end	leaves	2_week_old	48_hrs_after_inoculation_with_BLS279	Nipponbare	Host transcriptional reprogramming across diverse strains of the rice bacterial leaves streak pathogen Xanthomonas oryzae pv.oryzicola	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE67588	GSM1650078	SRR1952782	single-end	leaves	2_week_old	48_hrs_after_inoculation_with_BLS279	Nipponbare	Host transcriptional reprogramming across diverse strains of the rice bacterial leaves streak pathogen Xanthomonas oryzae pv.oryzicola	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE67588	GSM1650079	SRR1952783	single-end	leaves	2_week_old	48_hrs_after_inoculation_with_BLS279	Nipponbare	Host transcriptional reprogramming across diverse strains of the rice bacterial leaves streak pathogen Xanthomonas oryzae pv.oryzicola	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE67588	GSM1650080	SRR1952784	single-end	leaves	2_week_old	48_hrs_after_inoculation_with_CFBP2286	Nipponbare	Host transcriptional reprogramming across diverse strains of the rice bacterial leaves streak pathogen Xanthomonas oryzae pv.oryzicola	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE67588	GSM1650081	SRR1952785	single-end	leaves	2_week_old	48_hrs_after_inoculation_with_CFBP2286	Nipponbare	Host transcriptional reprogramming across diverse strains of the rice bacterial leaves streak pathogen Xanthomonas oryzae pv.oryzicola	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE67588	GSM1650082	SRR1952786	single-end	leaves	2_week_old	48_hrs_after_inoculation_with_CFBP2286	Nipponbare	Host transcriptional reprogramming across diverse strains of the rice bacterial leaves streak pathogen Xanthomonas oryzae pv.oryzicola	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE67588	GSM1650083	SRR1952787	single-end	leaves	2_week_old	48_hrs_after_inoculation_with_B8_12	Nipponbare	Host transcriptional reprogramming across diverse strains of the rice bacterial leaves streak pathogen Xanthomonas oryzae pv.oryzicola	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE67588	GSM1650084	SRR1952788	single-end	leaves	2_week_old	48_hrs_after_inoculation_with_B8_12	Nipponbare	Host transcriptional reprogramming across diverse strains of the rice bacterial leaves streak pathogen Xanthomonas oryzae pv.oryzicola	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE67588	GSM1650085	SRR1952789	single-end	leaves	2_week_old	48_hrs_after_inoculation_with_B8_12	Nipponbare	Host transcriptional reprogramming across diverse strains of the rice bacterial leaves streak pathogen Xanthomonas oryzae pv.oryzicola	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE67588	GSM1650086	SRR1952790	single-end	leaves	2_week_old	48_hrs_after_inoculation_with_L8	Nipponbare	Host transcriptional reprogramming across diverse strains of the rice bacterial leaves streak pathogen Xanthomonas oryzae pv.oryzicola	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE67588	GSM1650087	SRR1952791	single-end	leaves	2_week_old	48_hrs_after_inoculation_with_L8	Nipponbare	Host transcriptional reprogramming across diverse strains of the rice bacterial leaves streak pathogen Xanthomonas oryzae pv.oryzicola	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE67588	GSM1650088	SRR1952792	single-end	leaves	2_week_old	48_hrs_after_inoculation_with_L8	Nipponbare	Host transcriptional reprogramming across diverse strains of the rice bacterial leaves streak pathogen Xanthomonas oryzae pv.oryzicola	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE67588	GSM1650089	SRR1952793	single-end	leaves	2_week_old	48_hrs_after_inoculation_with_RS105	Nipponbare	Host transcriptional reprogramming across diverse strains of the rice bacterial leaves streak pathogen Xanthomonas oryzae pv.oryzicola	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE67588	GSM1650090	SRR1952794	single-end	leaves	2_week_old	48_hrs_after_inoculation_with_RS105	Nipponbare	Host transcriptional reprogramming across diverse strains of the rice bacterial leaves streak pathogen Xanthomonas oryzae pv.oryzicola	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE67588	GSM1650091	SRR1952795	single-end	leaves	2_week_old	48_hrs_after_inoculation_with_RS105	Nipponbare	Host transcriptional reprogramming across diverse strains of the rice bacterial leaves streak pathogen Xanthomonas oryzae pv.oryzicola	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE67588	GSM1650092	SRR1952796	single-end	leaves	2_week_old	48_hrs_after_inoculation_with_BXOR1	Nipponbare	Host transcriptional reprogramming across diverse strains of the rice bacterial leaves streak pathogen Xanthomonas oryzae pv.oryzicola	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE67588	GSM1650093	SRR1952797	single-end	leaves	2_week_old	48_hrs_after_inoculation_with_BXOR1	Nipponbare	Host transcriptional reprogramming across diverse strains of the rice bacterial leaves streak pathogen Xanthomonas oryzae pv.oryzicola	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE67588	GSM1650094	SRR1952798	single-end	leaves	2_week_old	48_hrs_after_inoculation_with_BXOR1	Nipponbare	Host transcriptional reprogramming across diverse strains of the rice bacterial leaves streak pathogen Xanthomonas oryzae pv.oryzicola	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE67588	GSM1650095	SRR1952799	single-end	leaves	2_week_old	48_hrs_after_inoculation_with_CFBP7331	Nipponbare	Host transcriptional reprogramming across diverse strains of the rice bacterial leaves streak pathogen Xanthomonas oryzae pv.oryzicola	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE67588	GSM1650096	SRR1952800	single-end	leaves	2_week_old	48_hrs_after_inoculation_with_CFBP7331	Nipponbare	Host transcriptional reprogramming across diverse strains of the rice bacterial leaves streak pathogen Xanthomonas oryzae pv.oryzicola	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE67588	GSM1650097	SRR1952801	single-end	leaves	2_week_old	48_hrs_after_inoculation_with_CFBP7331	Nipponbare	Host transcriptional reprogramming across diverse strains of the rice bacterial leaves streak pathogen Xanthomonas oryzae pv.oryzicola	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE67588	GSM1650098	SRR1952802	single-end	leaves	2_week_old	48_hrs_after_inoculation_with_CFBP7341	Nipponbare	Host transcriptional reprogramming across diverse strains of the rice bacterial leaves streak pathogen Xanthomonas oryzae pv.oryzicola	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE67588	GSM1650099	SRR1952803	single-end	leaves	2_week_old	48_hrs_after_inoculation_with_CFBP7341	Nipponbare	Host transcriptional reprogramming across diverse strains of the rice bacterial leaves streak pathogen Xanthomonas oryzae pv.oryzicola	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE67588	GSM1650100	SRR1952804	single-end	leaves	2_week_old	48_hrs_after_inoculation_with_CFBP7341	Nipponbare	Host transcriptional reprogramming across diverse strains of the rice bacterial leaves streak pathogen Xanthomonas oryzae pv.oryzicola	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE67588	GSM1650101	SRR1952805	single-end	leaves	2_week_old	48_hrs_after_inoculation_with_CFBP7342	Nipponbare	Host transcriptional reprogramming across diverse strains of the rice bacterial leaves streak pathogen Xanthomonas oryzae pv.oryzicola	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE67588	GSM1650102	SRR1952806	single-end	leaves	2_week_old	48_hrs_after_inoculation_with_CFBP7342	Nipponbare	Host transcriptional reprogramming across diverse strains of the rice bacterial leaves streak pathogen Xanthomonas oryzae pv.oryzicola	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE67588	GSM1650103	SRR1952807	single-end	leaves	2_week_old	48_hrs_after_inoculation_with_CFBP7342	Nipponbare	Host transcriptional reprogramming across diverse strains of the rice bacterial leaves streak pathogen Xanthomonas oryzae pv.oryzicola	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE67588	GSM1650104	SRR1952808	single-end	leaves	2_week_old	48_hrs_after_mock_inoculation	Nipponbare	Host transcriptional reprogramming across diverse strains of the rice bacterial leaves streak pathogen Xanthomonas oryzae pv.oryzicola	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE67588	GSM1650105	SRR1952809	single-end	leaves	2_week_old	48_hrs_after_mock_inoculation	Nipponbare	Host transcriptional reprogramming across diverse strains of the rice bacterial leaves streak pathogen Xanthomonas oryzae pv.oryzicola	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE67588	GSM1650106	SRR1952810	single-end	leaves	2_week_old	48_hrs_after_mock_inoculation	Nipponbare	Host transcriptional reprogramming across diverse strains of the rice bacterial leaves streak pathogen Xanthomonas oryzae pv.oryzicola	Illumina HiSeq 2000	Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaves. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.
GSE65025	GSM1585996	SRR1761788	single-end	leaves	45_day_old	wild_type,drought,2	Nipponbare	Transcriptome analysis of Oshsfa2e mutant plants under controlled drought stress and well-watered conditions at vegetative stage	Illumina Genome Analyzer	Controlled drought stress was applied on 45 day old plants following gravimetric approach. The soil water content was brought down to 40% field capacity over a period of 3-4 days and plants were maintained at that level for 10 days by weighing the pots daily at a fixed time of the day and replenishing the water lost through evapotranspiration. Well-watered plants were maintained at 100% FC.
GSE65025	GSM1585997	SRR1761789	single-end	leaves	45_day_old	wild_type,drought,2	Nipponbare	Transcriptome analysis of Oshsfa2e mutant plants under controlled drought stress and well-watered conditions at vegetative stage	Illumina Genome Analyzer	Controlled drought stress was applied on 45 day old plants following gravimetric approach. The soil water content was brought down to 40% field capacity over a period of 3-4 days and plants were maintained at that level for 10 days by weighing the pots daily at a fixed time of the day and replenishing the water lost through evapotranspiration. Well-watered plants were maintained at 100% FC.
GSE65025	GSM1585998	SRR1761790	single-end	leaves	45_day_old	wild_type,control,2	Nipponbare	Transcriptome analysis of Oshsfa2e mutant plants under controlled drought stress and well-watered conditions at vegetative stage	Illumina Genome Analyzer	Controlled drought stress was applied on 45 day old plants following gravimetric approach. The soil water content was brought down to 40% field capacity over a period of 3-4 days and plants were maintained at that level for 10 days by weighing the pots daily at a fixed time of the day and replenishing the water lost through evapotranspiration. Well-watered plants were maintained at 100% FC.
GSE65025	GSM1585999	SRR1761791	single-end	leaves	45_day_old	wild_type,control,2	Nipponbare	Transcriptome analysis of Oshsfa2e mutant plants under controlled drought stress and well-watered conditions at vegetative stage	Illumina Genome Analyzer	Controlled drought stress was applied on 45 day old plants following gravimetric approach. The soil water content was brought down to 40% field capacity over a period of 3-4 days and plants were maintained at that level for 10 days by weighing the pots daily at a fixed time of the day and replenishing the water lost through evapotranspiration. Well-watered plants were maintained at 100% FC.
GSE65024	GSM1585988	SRR1761780	single-end	leaves	45_day_old	wild_type,drought,1	Nipponbare	Transcriptome analysis of Oshsfa2e mutant plants under controlled drought stress and well-watered conditions at vegetative stage	Illumina Genome Analyzer	Controlled drought stress was applied on 45 day old plants following gravimetric approach. The soil water content was brought down to 40% field capacity over a period of 3-4 days and plants were maintained at that level for 10 days by weighing the pots daily at a fixed time of the day and replenishing the water lost through evapotranspiration. Well-watered plants were maintained at 100% FC.
GSE65024	GSM1585989	SRR1761781	single-end	leaves	45_day_old	wild_type,drought,1	Nipponbare	Transcriptome analysis of Oshsfa2e mutant plants under controlled drought stress and well-watered conditions at vegetative stage	Illumina Genome Analyzer	Controlled drought stress was applied on 45 day old plants following gravimetric approach. The soil water content was brought down to 40% field capacity over a period of 3-4 days and plants were maintained at that level for 10 days by weighing the pots daily at a fixed time of the day and replenishing the water lost through evapotranspiration. Well-watered plants were maintained at 100% FC.
GSE65024	GSM1585990	SRR1761782	single-end	leaves	45_day_old	wild_type,control,1	Nipponbare	Transcriptome analysis of Oshsfa2e mutant plants under controlled drought stress and well-watered conditions at vegetative stage	Illumina Genome Analyzer	Controlled drought stress was applied on 45 day old plants following gravimetric approach. The soil water content was brought down to 40% field capacity over a period of 3-4 days and plants were maintained at that level for 10 days by weighing the pots daily at a fixed time of the day and replenishing the water lost through evapotranspiration. Well-watered plants were maintained at 100% FC.
GSE65024	GSM1585991	SRR1761783	single-end	leaves	45_day_old	wild_type,control,1	Nipponbare	Transcriptome analysis of Oshsfa2e mutant plants under controlled drought stress and well-watered conditions at vegetative stage	Illumina Genome Analyzer	Controlled drought stress was applied on 45 day old plants following gravimetric approach. The soil water content was brought down to 40% field capacity over a period of 3-4 days and plants were maintained at that level for 10 days by weighing the pots daily at a fixed time of the day and replenishing the water lost through evapotranspiration. Well-watered plants were maintained at 100% FC.
GSE65022	GSM1585980	SRR1761528	single-end	leaves	45_day_old	drought	Nipponbare	Genome-wide transcriptome analysis of rice in response to controlled drought stress at vegetative	Illumina Genome Analyzer	Controlled drought stress was applied on 45 day old plants following gravimetric approach. The soil water content was brought down to 40% field capacity over a period of 3-4 days and plants were maintained at that level for 10 days by weighing the pots daily at a fixed time of the day and replenishing the water lost through evapotranspiration. Well-watered plants were maintained at 100% FC.
GSE65022	GSM1585981	SRR1761529	single-end	leaves	45_day_old	drought	Nipponbare	Genome-wide transcriptome analysis of rice in response to controlled drought stress at vegetative	Illumina Genome Analyzer	Controlled drought stress was applied on 45 day old plants following gravimetric approach. The soil water content was brought down to 40% field capacity over a period of 3-4 days and plants were maintained at that level for 10 days by weighing the pots daily at a fixed time of the day and replenishing the water lost through evapotranspiration. Well-watered plants were maintained at 100% FC.
GSE65022	GSM1585982	SRR1761530	single-end	leaves	45_day_old	control	Nipponbare	Genome-wide transcriptome analysis of rice in response to controlled drought stress at vegetative	Illumina Genome Analyzer	Controlled drought stress was applied on 45 day old plants following gravimetric approach. The soil water content was brought down to 40% field capacity over a period of 3-4 days and plants were maintained at that level for 10 days by weighing the pots daily at a fixed time of the day and replenishing the water lost through evapotranspiration. Well-watered plants were maintained at 100% FC.
GSE65022	GSM1585983	SRR1761531	single-end	leaves	45_day_old	control	Nipponbare	Genome-wide transcriptome analysis of rice in response to controlled drought stress at vegetative	Illumina Genome Analyzer	Controlled drought stress was applied on 45 day old plants following gravimetric approach. The soil water content was brought down to 40% field capacity over a period of 3-4 days and plants were maintained at that level for 10 days by weighing the pots daily at a fixed time of the day and replenishing the water lost through evapotranspiration. Well-watered plants were maintained at 100% FC.
GSE50778	GSM1229044	SRR976168	single-end	flag_leaf	no_collect	wild_type	Nipponbare	Control of agricultural traits by hc-siRNA associated MITEs in rice	Illumina Genome Analyzer	These transgenic plants and wild-type (Nipponbare) were grown in the field for phenotypic observation. RNA were extracted from the lamina joints of the flag leaves used for RNA-seq and small RNA-seq analysis.
GSE38480	GSM943197	SRR504365	single-end	leaves	no_collect	wt	Nipponbare	Transcriptome and methylome interactions in rice hybrids	Illumina Genome Analyzer II	Rice plant (NPB) was grown in growth chamber at 26C/20C under a 10h light/14h dark cycle
GSE33265	GSM823081	SRR358791	single-end	seedling	2_week_old	wt	Nipponbare	Transcriptome of rice seedling and callus based on RNA-seq method	Illumina Genome Analyzer II	leaves of two-week old rice cultivar ＆Nipponbare＊ seedlings grown in green house and three-week old calli were collected and ground into fine powder in liquid nitrogen.Total RNA was extracted using a RNeasy Plant Kit (Qiagen Cat. NO. 74904). High-quality (RNA integrity number >8) was used for down-stream DNase I treatment to remove genomic DNA.
GSE33265	GSM823081	SRR358792	single-end	seedling	2_week_old	wt	Nipponbare	Transcriptome of rice seedling and callus based on RNA-seq method	Illumina Genome Analyzer II	leaves of two-week old rice cultivar ＆Nipponbare＊ seedlings grown in green house and three-week old calli were collected and ground into fine powder in liquid nitrogen.Total RNA was extracted using a RNeasy Plant Kit (Qiagen Cat. NO. 74904). High-quality (RNA integrity number >8) was used for down-stream DNase I treatment to remove genomic DNA.
GSE33265	GSM823082	SRR358793	single-end	seedling	2_week_old	wt	Nipponbare	Transcriptome of rice seedling and callus based on RNA-seq method	Illumina Genome Analyzer II	leaves of two-week old rice cultivar ＆Nipponbare＊ seedlings grown in green house and three-week old calli were collected and ground into fine powder in liquid nitrogen.Total RNA was extracted using a RNeasy Plant Kit (Qiagen Cat. NO. 74904). High-quality (RNA integrity number >8) was used for down-stream DNase I treatment to remove genomic DNA.
GSE33265	GSM823082	SRR358794	single-end	seedling	2_week_old	wt	Nipponbare	Transcriptome of rice seedling and callus based on RNA-seq method	Illumina Genome Analyzer II	leaves of two-week old rice cultivar ＆Nipponbare＊ seedlings grown in green house and three-week old calli were collected and ground into fine powder in liquid nitrogen.Total RNA was extracted using a RNeasy Plant Kit (Qiagen Cat. NO. 74904). High-quality (RNA integrity number >8) was used for down-stream DNase I treatment to remove genomic DNA.
GSE33265	GSM823083	SRR358795	single-end	callus	3_week_old	wt	Nipponbare	Transcriptome of rice seedling and callus based on RNA-seq method	Illumina Genome Analyzer II	leaves of two-week old rice cultivar ＆Nipponbare＊ seedlings grown in green house and three-week old calli were collected and ground into fine powder in liquid nitrogen.Total RNA was extracted using a RNeasy Plant Kit (Qiagen Cat. NO. 74904). High-quality (RNA integrity number >8) was used for down-stream DNase I treatment to remove genomic DNA.
GSE33265	GSM823083	SRR358796	single-end	callus	3_week_old	wt	Nipponbare	Transcriptome of rice seedling and callus based on RNA-seq method	Illumina Genome Analyzer II	leaves of two-week old rice cultivar ＆Nipponbare＊ seedlings grown in green house and three-week old calli were collected and ground into fine powder in liquid nitrogen.Total RNA was extracted using a RNeasy Plant Kit (Qiagen Cat. NO. 74904). High-quality (RNA integrity number >8) was used for down-stream DNase I treatment to remove genomic DNA.
GSE33265	GSM823084	SRR358797	single-end	callus	3_week_old	wt	Nipponbare	Transcriptome of rice seedling and callus based on RNA-seq method	Illumina Genome Analyzer II	leaves of two-week old rice cultivar ＆Nipponbare＊ seedlings grown in green house and three-week old calli were collected and ground into fine powder in liquid nitrogen.Total RNA was extracted using a RNeasy Plant Kit (Qiagen Cat. NO. 74904). High-quality (RNA integrity number >8) was used for down-stream DNase I treatment to remove genomic DNA.
GSE33265	GSM823084	SRR358798	single-end	callus	3_week_old	wt	Nipponbare	Transcriptome of rice seedling and callus based on RNA-seq method	Illumina Genome Analyzer II	leaves of two-week old rice cultivar ＆Nipponbare＊ seedlings grown in green house and three-week old calli were collected and ground into fine powder in liquid nitrogen.Total RNA was extracted using a RNeasy Plant Kit (Qiagen Cat. NO. 74904). High-quality (RNA integrity number >8) was used for down-stream DNase I treatment to remove genomic DNA.
GSE90493	GSM2402820	SRR5052708	single-end	shoot_apical_meristems	6_week_old	0_days_after_shift;_1	Nipponbare	PREMATURE INTERNODE ELONGATION 1 coordinates internode elongation in response to florigenic signals at the shoot apex of rice	Illumina HiSeq 2000	6-week-old plants were shifted from chambers with 16 hours light and 8 hours dark to chambers with 10 hours light and 14 hours dark.
GSE90493	GSM2402821	SRR5052709	single-end	shoot_apical_meristems	6_week_old	0_days_after_shift;_3	Nipponbare	PREMATURE INTERNODE ELONGATION 1 coordinates internode elongation in response to florigenic signals at the shoot apex of rice	Illumina HiSeq 2000	6-week-old plants were shifted from chambers with 16 hours light and 8 hours dark to chambers with 10 hours light and 14 hours dark.
GSE90493	GSM2402822	SRR5052710	single-end	shoot_apical_meristems	6_week_old	0_days_after_shift;_5	Nipponbare	PREMATURE INTERNODE ELONGATION 1 coordinates internode elongation in response to florigenic signals at the shoot apex of rice	Illumina HiSeq 2000	6-week-old plants were shifted from chambers with 16 hours light and 8 hours dark to chambers with 10 hours light and 14 hours dark.
GSE90493	GSM2402823	SRR5052711	single-end	shoot_apical_meristems	6_week_old	4_days_after_shift;_7,9	Nipponbare	PREMATURE INTERNODE ELONGATION 1 coordinates internode elongation in response to florigenic signals at the shoot apex of rice	Illumina HiSeq 2000	6-week-old plants were shifted from chambers with 16 hours light and 8 hours dark to chambers with 10 hours light and 14 hours dark.
GSE90493	GSM2402824	SRR5052712	single-end	shoot_apical_meristems	6_week_old	4_days_after_shift;_7,9	Nipponbare	PREMATURE INTERNODE ELONGATION 1 coordinates internode elongation in response to florigenic signals at the shoot apex of rice	Illumina HiSeq 2000	6-week-old plants were shifted from chambers with 16 hours light and 8 hours dark to chambers with 10 hours light and 14 hours dark.
GSE90493	GSM2402825	SRR5052713	single-end	shoot_apical_meristems	6_week_old	4_days_after_shift;_10	Nipponbare	PREMATURE INTERNODE ELONGATION 1 coordinates internode elongation in response to florigenic signals at the shoot apex of rice	Illumina HiSeq 2000	6-week-old plants were shifted from chambers with 16 hours light and 8 hours dark to chambers with 10 hours light and 14 hours dark.
GSE90493	GSM2402826	SRR5052714	single-end	shoot_apical_meristems	6_week_old	4_days_after_shift;_12,14	Nipponbare	PREMATURE INTERNODE ELONGATION 1 coordinates internode elongation in response to florigenic signals at the shoot apex of rice	Illumina HiSeq 2000	6-week-old plants were shifted from chambers with 16 hours light and 8 hours dark to chambers with 10 hours light and 14 hours dark.
GSE90493	GSM2402827	SRR5052715	single-end	shoot_apical_meristems	6_week_old	4_days_after_shift;_12,14	Nipponbare	PREMATURE INTERNODE ELONGATION 1 coordinates internode elongation in response to florigenic signals at the shoot apex of rice	Illumina HiSeq 2000	6-week-old plants were shifted from chambers with 16 hours light and 8 hours dark to chambers with 10 hours light and 14 hours dark.
GSE90493	GSM2402828	SRR5052716	single-end	shoot_apical_meristems	6_week_old	8_days_after_shift;_15,16,17	Nipponbare	PREMATURE INTERNODE ELONGATION 1 coordinates internode elongation in response to florigenic signals at the shoot apex of rice	Illumina HiSeq 2000	6-week-old plants were shifted from chambers with 16 hours light and 8 hours dark to chambers with 10 hours light and 14 hours dark.
GSE90493	GSM2402829	SRR5052717	single-end	shoot_apical_meristems	6_week_old	8_days_after_shift;_15,16,17	Nipponbare	PREMATURE INTERNODE ELONGATION 1 coordinates internode elongation in response to florigenic signals at the shoot apex of rice	Illumina HiSeq 2000	6-week-old plants were shifted from chambers with 16 hours light and 8 hours dark to chambers with 10 hours light and 14 hours dark.
GSE90493	GSM2402830	SRR5052718	single-end	shoot_apical_meristems	6_week_old	8_days_after_shift;_15,16,17	Nipponbare	PREMATURE INTERNODE ELONGATION 1 coordinates internode elongation in response to florigenic signals at the shoot apex of rice	Illumina HiSeq 2000	6-week-old plants were shifted from chambers with 16 hours light and 8 hours dark to chambers with 10 hours light and 14 hours dark.
GSE90493	GSM2402831	SRR5052719	single-end	shoot_apical_meristems	6_week_old	8_days_after_shift;_18	Nipponbare	PREMATURE INTERNODE ELONGATION 1 coordinates internode elongation in response to florigenic signals at the shoot apex of rice	Illumina HiSeq 2000	6-week-old plants were shifted from chambers with 16 hours light and 8 hours dark to chambers with 10 hours light and 14 hours dark.
GSE90493	GSM2402832	SRR5052720	single-end	shoot_apical_meristems	6_week_old	8_days_after_shift;_20	Nipponbare	PREMATURE INTERNODE ELONGATION 1 coordinates internode elongation in response to florigenic signals at the shoot apex of rice	Illumina HiSeq 2000	6-week-old plants were shifted from chambers with 16 hours light and 8 hours dark to chambers with 10 hours light and 14 hours dark.
GSE90493	GSM2402833	SRR5052721	single-end	shoot_apical_meristems	6_week_old	12_days_after_shift;_21	Nipponbare	PREMATURE INTERNODE ELONGATION 1 coordinates internode elongation in response to florigenic signals at the shoot apex of rice	Illumina HiSeq 2000	6-week-old plants were shifted from chambers with 16 hours light and 8 hours dark to chambers with 10 hours light and 14 hours dark.
GSE90493	GSM2402834	SRR5052722	single-end	shoot_apical_meristems	6_week_old	12_days_after_shift;_23	Nipponbare	PREMATURE INTERNODE ELONGATION 1 coordinates internode elongation in response to florigenic signals at the shoot apex of rice	Illumina HiSeq 2000	6-week-old plants were shifted from chambers with 16 hours light and 8 hours dark to chambers with 10 hours light and 14 hours dark.
GSE90493	GSM2402835	SRR5052723	single-end	shoot_apical_meristems	6_week_old	12_days_after_shift;_25	Nipponbare	PREMATURE INTERNODE ELONGATION 1 coordinates internode elongation in response to florigenic signals at the shoot apex of rice	Illumina HiSeq 2000	6-week-old plants were shifted from chambers with 16 hours light and 8 hours dark to chambers with 10 hours light and 14 hours dark.
GSE89449	GSM2372369	SRR4841740	paired-end	shoot	no_collect	shoots_of_Meloidogyne_graminicola_infected_3_dai	Nipponbare	Below ground attack by roots knot nematode Meloidogyne graminicola predisposes rice to blast disease	Illumina Genome Analyzer Iix	The nematodes were extracted using a Baermann funnel from Meloidogyne graminicola infected rice plants cultured under the same conditions. Five days after transplanting in SAP, the plants were inoculated with 250 nematodes per plant. One day after roots-knot nematode inoculation, the plants were transferred to a hydroponic culturing system with Hoagland solution to synchronize the infection process.
GSE89449	GSM2372370	SRR4841741	paired-end	shoot	no_collect	shoots_of_Meloidogyne_graminicola_infected_3_dai	Nipponbare	Below ground attack by roots knot nematode Meloidogyne graminicola predisposes rice to blast disease	Illumina Genome Analyzer Iix	The nematodes were extracted using a Baermann funnel from Meloidogyne graminicola infected rice plants cultured under the same conditions. Five days after transplanting in SAP, the plants were inoculated with 250 nematodes per plant. One day after roots-knot nematode inoculation, the plants were transferred to a hydroponic culturing system with Hoagland solution to synchronize the infection process.
GSE89449	GSM2372371	SRR4841742	paired-end	shoot	no_collect	shoots_of_Meloidogyne_graminicola_infected_7_dai	Nipponbare	Below ground attack by roots knot nematode Meloidogyne graminicola predisposes rice to blast disease	Illumina Genome Analyzer Iix	The nematodes were extracted using a Baermann funnel from Meloidogyne graminicola infected rice plants cultured under the same conditions. Five days after transplanting in SAP, the plants were inoculated with 250 nematodes per plant. One day after roots-knot nematode inoculation, the plants were transferred to a hydroponic culturing system with Hoagland solution to synchronize the infection process.
GSE89449	GSM2372372	SRR4841743	paired-end	shoot	no_collect	shoots_of_Meloidogyne_graminicola_infected_7_dai	Nipponbare	Below ground attack by roots knot nematode Meloidogyne graminicola predisposes rice to blast disease	Illumina Genome Analyzer Iix	The nematodes were extracted using a Baermann funnel from Meloidogyne graminicola infected rice plants cultured under the same conditions. Five days after transplanting in SAP, the plants were inoculated with 250 nematodes per plant. One day after roots-knot nematode inoculation, the plants were transferred to a hydroponic culturing system with Hoagland solution to synchronize the infection process.
GSE108504	GSM2902389	SRR6417964	paired-end	leaves	no_collect	Xanthomonas_oryzae_pv._Oryzae_MAI1_inoculated_24hpi	Nipponbare	Rice (Nipponbare) transcriptome upon inoculation with Malian Xanthomonas oryzae pv. oryzae strain MAI1	Illumina HiSeq 2000	leaves of 3-week-old rice plants were infiltrated with water or Xo strains using an OD600 of 0.5. In each experiment, at least three leaves from three individuals were inoculated with a syringe. 3 independent experiments were made for each treatment.
GSE108504	GSM2902390	SRR6417965	paired-end	leaves	3_weeks	Xanthomonas_oryzae_pv._Oryzae_MAI1_inoculated_24hpi	Nipponbare	Rice (Nipponbare) transcriptome upon inoculation with Malian Xanthomonas oryzae pv. oryzae strain MAI1	Illumina HiSeq 2000	leaves of 3-week-old rice plants were infiltrated with water or Xo strains using an OD600 of 0.5. In each experiment, at least three leaves from three individuals were inoculated with a syringe. 3 independent experiments were made for each treatment.
GSE108504	GSM2902391	SRR6417966	paired-end	leaves	3_weeks	Xanthomonas_oryzae_pv._Oryzae_MAI1_inoculated_24hpi	Nipponbare	Rice (Nipponbare) transcriptome upon inoculation with Malian Xanthomonas oryzae pv. oryzae strain MAI1	Illumina HiSeq 2000	leaves of 3-week-old rice plants were infiltrated with water or Xo strains using an OD600 of 0.5. In each experiment, at least three leaves from three individuals were inoculated with a syringe. 3 independent experiments were made for each treatment.
GSE108504	GSM2902392	SRR6417967	paired-end	leaves	3_weeks	H2O_control	Nipponbare	Rice (Nipponbare) transcriptome upon inoculation with Malian Xanthomonas oryzae pv. oryzae strain MAI1	Illumina HiSeq 2000	leaves of 3-week-old rice plants were infiltrated with water or Xo strains using an OD600 of 0.5. In each experiment, at least three leaves from three individuals were inoculated with a syringe. 3 independent experiments were made for each treatment.
GSE108504	GSM2902393	SRR6417968	paired-end	leaves	3_weeks	H2O_control	Nipponbare	Rice (Nipponbare) transcriptome upon inoculation with Malian Xanthomonas oryzae pv. oryzae strain MAI1	Illumina HiSeq 2000	leaves of 3-week-old rice plants were infiltrated with water or Xo strains using an OD600 of 0.5. In each experiment, at least three leaves from three individuals were inoculated with a syringe. 3 independent experiments were made for each treatment.
GSE108504	GSM2902394	SRR6417969	paired-end	leaves	3_weeks	H2O_control	Nipponbare	Rice (Nipponbare) transcriptome upon inoculation with Malian Xanthomonas oryzae pv. oryzae strain MAI1	Illumina HiSeq 2000	leaves of 3-week-old rice plants were infiltrated with water or Xo strains using an OD600 of 0.5. In each experiment, at least three leaves from three individuals were inoculated with a syringe. 3 independent experiments were made for each treatment.
GSE86272	GSM2299260	SRR4104639	paired-end	crown	no_collect	Zn_deficiency,8_days_of_treatment	Nipponbare	Transcriptomic study of rice crowns from genotypes differing in tolerance to Zn deficiency	Illumina HiSeq 2500	Plants were grown in full strength Yoshida nutrient solution containing 0.1% agar, 1 mM KHCO3 and 0 or 1.5 CM ZnSO4 for 8 days.
GSE86272	GSM2299266	SRR4104645	paired-end	crown	no_collect	Zn_Efficient,8_days_of_treatment	Nipponbare	Transcriptomic study of rice crowns from genotypes differing in tolerance to Zn deficiency	Illumina HiSeq 2500	Plants were grown in full strength Yoshida nutrient solution containing 0.1% agar, 1 mM KHCO3 and 0 or 1.5 CM ZnSO4 for 8 days.
GSE84800	GSM2251588	SRR3950244	single-end	shoot	21_day_old	Drought_during_3_days;Fr13_inoculated	Nipponbare	Molecular basis of drought-induced susceptibility to the rice blast fungus Magnaporthe oryzae	Illumina HiSeq 2000	Plants were inoculated either with Magnaporthe oryzae isolate Fr13 spore suspensions at 150000 spore/ml or with a mock solution corresponding to the solution into which spores are re-suspended (ie 0,5% gelatin solution).
GSE84800	GSM2251589	SRR3950245	single-end	shoot	21_day_old	Drought_during_3_days;Fr13_inoculated	Nipponbare	Molecular basis of drought-induced susceptibility to the rice blast fungus Magnaporthe oryzae	Illumina HiSeq 2000	Plants were inoculated either with Magnaporthe oryzae isolate Fr13 spore suspensions at 150000 spore/ml or with a mock solution corresponding to the solution into which spores are re-suspended (ie 0,5% gelatin solution).
GSE84800	GSM2251590	SRR3950246	single-end	shoot	21_day_old	Drought_during_3_days;Fr13_inoculated	Nipponbare	Molecular basis of drought-induced susceptibility to the rice blast fungus Magnaporthe oryzae	Illumina HiSeq 2000	Plants were inoculated either with Magnaporthe oryzae isolate Fr13 spore suspensions at 150000 spore/ml or with a mock solution corresponding to the solution into which spores are re-suspended (ie 0,5% gelatin solution).
GSE84800	GSM2251591	SRR3950247	single-end	shoot	21_day_old	No_DIS;Fr13_inoculated	Nipponbare	Molecular basis of drought-induced susceptibility to the rice blast fungus Magnaporthe oryzae	Illumina HiSeq 2000	Plants were inoculated either with Magnaporthe oryzae isolate Fr13 spore suspensions at 150000 spore/ml or with a mock solution corresponding to the solution into which spores are re-suspended (ie 0,5% gelatin solution).
GSE84800	GSM2251592	SRR3950248	single-end	shoot	21_day_old	No_DIS;Fr13_inoculated	Nipponbare	Molecular basis of drought-induced susceptibility to the rice blast fungus Magnaporthe oryzae	Illumina HiSeq 2000	Plants were inoculated either with Magnaporthe oryzae isolate Fr13 spore suspensions at 150000 spore/ml or with a mock solution corresponding to the solution into which spores are re-suspended (ie 0,5% gelatin solution).
GSE84800	GSM2251593	SRR3950249	single-end	shoot	21_day_old	No_DIS;Fr13_inoculated	Nipponbare	Molecular basis of drought-induced susceptibility to the rice blast fungus Magnaporthe oryzae	Illumina HiSeq 2000	Plants were inoculated either with Magnaporthe oryzae isolate Fr13 spore suspensions at 150000 spore/ml or with a mock solution corresponding to the solution into which spores are re-suspended (ie 0,5% gelatin solution).
GSE84800	GSM2251594	SRR3950250	single-end	shoot	21_day_old	Drought_during_3_days;_mock_inoculated	Nipponbare	Molecular basis of drought-induced susceptibility to the rice blast fungus Magnaporthe oryzae	Illumina HiSeq 2000	Plants were inoculated either with Magnaporthe oryzae isolate Fr13 spore suspensions at 150000 spore/ml or with a mock solution corresponding to the solution into which spores are re-suspended (ie 0,5% gelatin solution).
GSE84800	GSM2251595	SRR3950251	single-end	shoot	21_day_old	Drought_during_3_days;_mock_inoculated	Nipponbare	Molecular basis of drought-induced susceptibility to the rice blast fungus Magnaporthe oryzae	Illumina HiSeq 2000	Plants were inoculated either with Magnaporthe oryzae isolate Fr13 spore suspensions at 150000 spore/ml or with a mock solution corresponding to the solution into which spores are re-suspended (ie 0,5% gelatin solution).
GSE84800	GSM2251596	SRR3950252	single-end	shoot	21_day_old	Drought_during_3_days;_mock_inoculated	Nipponbare	Molecular basis of drought-induced susceptibility to the rice blast fungus Magnaporthe oryzae	Illumina HiSeq 2000	Plants were inoculated either with Magnaporthe oryzae isolate Fr13 spore suspensions at 150000 spore/ml or with a mock solution corresponding to the solution into which spores are re-suspended (ie 0,5% gelatin solution).
GSE84800	GSM2251597	SRR3950253	single-end	shoot	21_day_old	No_DIS;_mock_inoculated	Nipponbare	Molecular basis of drought-induced susceptibility to the rice blast fungus Magnaporthe oryzae	Illumina HiSeq 2000	Plants were inoculated either with Magnaporthe oryzae isolate Fr13 spore suspensions at 150000 spore/ml or with a mock solution corresponding to the solution into which spores are re-suspended (ie 0,5% gelatin solution).
GSE84800	GSM2251598	SRR3950254	single-end	shoot	21_day_old	No_DIS;_mock_inoculated	Nipponbare	Molecular basis of drought-induced susceptibility to the rice blast fungus Magnaporthe oryzae	Illumina HiSeq 2000	Plants were inoculated either with Magnaporthe oryzae isolate Fr13 spore suspensions at 150000 spore/ml or with a mock solution corresponding to the solution into which spores are re-suspended (ie 0,5% gelatin solution).
GSE84800	GSM2251599	SRR3950255	single-end	shoot	21_day_old	No_DIS;_mock_inoculated	Nipponbare	Molecular basis of drought-induced susceptibility to the rice blast fungus Magnaporthe oryzae	Illumina HiSeq 2000	Plants were inoculated either with Magnaporthe oryzae isolate Fr13 spore suspensions at 150000 spore/ml or with a mock solution corresponding to the solution into which spores are re-suspended (ie 0,5% gelatin solution).
GSE62554	GSM1528766	SRR1617549	single-end	shoot_apical_meristems	no_collect	no collect	Nipponbare	Rare Allele of A Novel Histone H4 Acetyltransferase Enhances Grain Weight, Yield and Plant Biomass Presumably Through the Regulation of Transcription	Illumina Genome Analyzer Iix	Total RNA was isolated by using the RNeasy Plant Mini Kit (Qiagene) and then digested by recombinant DNase I (RNase-free, Takara) to remove possible genomic DNA contamination, following the manufacturer＊s instructions.
GSE62554	GSM1528767	SRR1617550	single-end	shoot_apical_meristems	no_collect	no collect	Nipponbare	Rare Allele of A Novel Histone H4 Acetyltransferase Enhances Grain Weight, Yield and Plant Biomass Presumably Through the Regulation of Transcription	Illumina Genome Analyzer Iix	Total RNA was isolated by using the RNeasy Plant Mini Kit (Qiagene) and then digested by recombinant DNase I (RNase-free, Takara) to remove possible genomic DNA contamination, following the manufacturer＊s instructions.
GSE62554	GSM1528767	SRR1617551	single-end	shoot_apical_meristems	no_collect	no collect	Nipponbare	Rare Allele of A Novel Histone H4 Acetyltransferase Enhances Grain Weight, Yield and Plant Biomass Presumably Through the Regulation of Transcription	Illumina Genome Analyzer Iix	Total RNA was isolated by using the RNeasy Plant Mini Kit (Qiagene) and then digested by recombinant DNase I (RNase-free, Takara) to remove possible genomic DNA contamination, following the manufacturer＊s instructions.
GSE62554	GSM1528767	SRR1617552	single-end	shoot_apical_meristems	no_collect	no collect	Nipponbare	Rare Allele of A Novel Histone H4 Acetyltransferase Enhances Grain Weight, Yield and Plant Biomass Presumably Through the Regulation of Transcription	Illumina Genome Analyzer Iix	Total RNA was isolated by using the RNeasy Plant Mini Kit (Qiagene) and then digested by recombinant DNase I (RNase-free, Takara) to remove possible genomic DNA contamination, following the manufacturer＊s instructions.
GSE78972	GSM2082857	SRR3209769	single-end	leaves	4_week_old	Watered;Long_Day	Nipponbare	Hd3a, RFT1 and Ehd1 integrate photoperiodic and drought stress signals to delay the floral transition in rice	Illumina HiSeq 2000	One hundred seeds of NB were planted on soil in 10L square boxes and plants were grown for 4 weeks under LD conditions and a normal water regime. After 4 weeks, half of the pots were moved to SD. Under each photoperiod, half of the pots were watered normally (control), while the remaining half was subjected to drought stress. Soil water content was monitored every hour using moisture sensors.
GSE78972	GSM2082858	SRR3209770	single-end	leaves	4_week_old	Watered;Long_Day	Nipponbare	Hd3a, RFT1 and Ehd1 integrate photoperiodic and drought stress signals to delay the floral transition in rice	Illumina HiSeq 2000	One hundred seeds of NB were planted on soil in 10L square boxes and plants were grown for 4 weeks under LD conditions and a normal water regime. After 4 weeks, half of the pots were moved to SD. Under each photoperiod, half of the pots were watered normally (control), while the remaining half was subjected to drought stress. Soil water content was monitored every hour using moisture sensors.
GSE78972	GSM2082859	SRR3209771	single-end	leaves	4_week_old	Drought;Long_Day	Nipponbare	Hd3a, RFT1 and Ehd1 integrate photoperiodic and drought stress signals to delay the floral transition in rice	Illumina HiSeq 2000	One hundred seeds of NB were planted on soil in 10L square boxes and plants were grown for 4 weeks under LD conditions and a normal water regime. After 4 weeks, half of the pots were moved to SD. Under each photoperiod, half of the pots were watered normally (control), while the remaining half was subjected to drought stress. Soil water content was monitored every hour using moisture sensors.
GSE78972	GSM2082860	SRR3209772	single-end	leaves	4_week_old	Drought;Long_Day	Nipponbare	Hd3a, RFT1 and Ehd1 integrate photoperiodic and drought stress signals to delay the floral transition in rice	Illumina HiSeq 2000	One hundred seeds of NB were planted on soil in 10L square boxes and plants were grown for 4 weeks under LD conditions and a normal water regime. After 4 weeks, half of the pots were moved to SD. Under each photoperiod, half of the pots were watered normally (control), while the remaining half was subjected to drought stress. Soil water content was monitored every hour using moisture sensors.
GSE78972	GSM2082861	SRR3209773	single-end	leaves	4_week_old	Watered;Short_Day	Nipponbare	Hd3a, RFT1 and Ehd1 integrate photoperiodic and drought stress signals to delay the floral transition in rice	Illumina HiSeq 2000	One hundred seeds of NB were planted on soil in 10L square boxes and plants were grown for 4 weeks under LD conditions and a normal water regime. After 4 weeks, half of the pots were moved to SD. Under each photoperiod, half of the pots were watered normally (control), while the remaining half was subjected to drought stress. Soil water content was monitored every hour using moisture sensors.
GSE78972	GSM2082862	SRR3209774	single-end	leaves	4_week_old	Watered;Short_Day	Nipponbare	Hd3a, RFT1 and Ehd1 integrate photoperiodic and drought stress signals to delay the floral transition in rice	Illumina HiSeq 2000	One hundred seeds of NB were planted on soil in 10L square boxes and plants were grown for 4 weeks under LD conditions and a normal water regime. After 4 weeks, half of the pots were moved to SD. Under each photoperiod, half of the pots were watered normally (control), while the remaining half was subjected to drought stress. Soil water content was monitored every hour using moisture sensors.
GSE78972	GSM2082863	SRR3209775	single-end	leaves	4_week_old	Drought;Short_Day	Nipponbare	Hd3a, RFT1 and Ehd1 integrate photoperiodic and drought stress signals to delay the floral transition in rice	Illumina HiSeq 2000	One hundred seeds of NB were planted on soil in 10L square boxes and plants were grown for 4 weeks under LD conditions and a normal water regime. After 4 weeks, half of the pots were moved to SD. Under each photoperiod, half of the pots were watered normally (control), while the remaining half was subjected to drought stress. Soil water content was monitored every hour using moisture sensors.
GSE78972	GSM2082864	SRR3209776	single-end	leaves	4_week_old	Drought;Short_Day	Nipponbare	Hd3a, RFT1 and Ehd1 integrate photoperiodic and drought stress signals to delay the floral transition in rice	Illumina HiSeq 2000	One hundred seeds of NB were planted on soil in 10L square boxes and plants were grown for 4 weeks under LD conditions and a normal water regime. After 4 weeks, half of the pots were moved to SD. Under each photoperiod, half of the pots were watered normally (control), while the remaining half was subjected to drought stress. Soil water content was monitored every hour using moisture sensors.
GSE78972	GSM2082865	SRR3209777	single-end	leaves	4_week_old	Watered;Long_Day	Nipponbare	Hd3a, RFT1 and Ehd1 integrate photoperiodic and drought stress signals to delay the floral transition in rice	Illumina HiSeq 2000	One hundred seeds of NB were planted on soil in 10L square boxes and plants were grown for 4 weeks under LD conditions and a normal water regime. After 4 weeks, half of the pots were moved to SD. Under each photoperiod, half of the pots were watered normally (control), while the remaining half was subjected to drought stress. Soil water content was monitored every hour using moisture sensors.
GSE78972	GSM2082866	SRR3209778	single-end	leaves	4_week_old	Drought;Long_Day	Nipponbare	Hd3a, RFT1 and Ehd1 integrate photoperiodic and drought stress signals to delay the floral transition in rice	Illumina HiSeq 2000	One hundred seeds of NB were planted on soil in 10L square boxes and plants were grown for 4 weeks under LD conditions and a normal water regime. After 4 weeks, half of the pots were moved to SD. Under each photoperiod, half of the pots were watered normally (control), while the remaining half was subjected to drought stress. Soil water content was monitored every hour using moisture sensors.
GSE78972	GSM2082867	SRR3209779	single-end	leaves	4_week_old	Watered;Short_Day	Nipponbare	Hd3a, RFT1 and Ehd1 integrate photoperiodic and drought stress signals to delay the floral transition in rice	Illumina HiSeq 2000	One hundred seeds of NB were planted on soil in 10L square boxes and plants were grown for 4 weeks under LD conditions and a normal water regime. After 4 weeks, half of the pots were moved to SD. Under each photoperiod, half of the pots were watered normally (control), while the remaining half was subjected to drought stress. Soil water content was monitored every hour using moisture sensors.
GSE78972	GSM2082868	SRR3209780	single-end	leaves	4_week_old	Drought;Short_Day	Nipponbare	Hd3a, RFT1 and Ehd1 integrate photoperiodic and drought stress signals to delay the floral transition in rice	Illumina HiSeq 2000	One hundred seeds of NB were planted on soil in 10L square boxes and plants were grown for 4 weeks under LD conditions and a normal water regime. After 4 weeks, half of the pots were moved to SD. Under each photoperiod, half of the pots were watered normally (control), while the remaining half was subjected to drought stress. Soil water content was monitored every hour using moisture sensors.
GSE126650	GSM3610456	SRR8582888	single-end	panicle	no_collect	AM	Nipponbare	Analysis of differential gene expression and alternative splicing is significantly influenced by choice of mapping genome	Illumina HiSeq 2500	AM samples were harvest 30min prior to light coming on. PM samples were harvest 30min prior to lights going off.   Rice plants were grown on Chu's media in climate controlled chambers. 12hrs Light and 12hrs Dark at 28C.
GSE126650	GSM3610457	SRR8582889	single-end	panicle	no_collect	AM	Nipponbare	Analysis of differential gene expression and alternative splicing is significantly influenced by choice of mapping genome	Illumina HiSeq 2500	AM samples were harvest 30min prior to light coming on. PM samples were harvest 30min prior to lights going off.   Rice plants were grown on Chu's media in climate controlled chambers. 12hrs Light and 12hrs Dark at 28C.
GSE126650	GSM3610458	SRR8582890	single-end	panicle	no_collect	AM	Nipponbare	Analysis of differential gene expression and alternative splicing is significantly influenced by choice of mapping genome	Illumina HiSeq 2500	AM samples were harvest 30min prior to light coming on. PM samples were harvest 30min prior to lights going off.   Rice plants were grown on Chu's media in climate controlled chambers. 12hrs Light and 12hrs Dark at 28C.
GSE126650	GSM3610459	SRR8582891	single-end	panicle	no_collect	PM	Nipponbare	Analysis of differential gene expression and alternative splicing is significantly influenced by choice of mapping genome	Illumina HiSeq 2500	AM samples were harvest 30min prior to light coming on. PM samples were harvest 30min prior to lights going off.   Rice plants were grown on Chu's media in climate controlled chambers. 12hrs Light and 12hrs Dark at 28C.
GSE126650	GSM3610460	SRR8582892	single-end	panicle	no_collect	PM	Nipponbare	Analysis of differential gene expression and alternative splicing is significantly influenced by choice of mapping genome	Illumina HiSeq 2500	AM samples were harvest 30min prior to light coming on. PM samples were harvest 30min prior to lights going off.   Rice plants were grown on Chu's media in climate controlled chambers. 12hrs Light and 12hrs Dark at 28C.
GSE126650	GSM3610461	SRR8582893	single-end	panicle	no_collect	PM	Nipponbare	Analysis of differential gene expression and alternative splicing is significantly influenced by choice of mapping genome	Illumina HiSeq 2500	AM samples were harvest 30min prior to light coming on. PM samples were harvest 30min prior to lights going off.   Rice plants were grown on Chu's media in climate controlled chambers. 12hrs Light and 12hrs Dark at 28C.
GSE126961	GSM3618871	SRR8611900	paired-end	leaves	3_week_old	Non-inoculated	Nipponbare	Bayogenin 3-O-Cellobioside is a novel anti-blast metabolite produced in rice in response to Pyricularia oryzae infection	Illumina HiSeq 2000	Susceptible (CO39 and NPB) and resistant (Pi_gm) rice cultivars were spray inoculated with P. oryzae spore and incubated for 12-hours.
GSE126961	GSM3618872	SRR8611901	paired-end	leaves	3_week_old	Non-inoculated	Nipponbare	Bayogenin 3-O-Cellobioside is a novel anti-blast metabolite produced in rice in response to Pyricularia oryzae infection	Illumina HiSeq 2000	Susceptible (CO39 and NPB) and resistant (Pi_gm) rice cultivars were spray inoculated with P. oryzae spore and incubated for 12-hours.
GSE126961	GSM3618873	SRR8611902	paired-end	leaves	3_week_old	Non-inoculated	Nipponbare	Bayogenin 3-O-Cellobioside is a novel anti-blast metabolite produced in rice in response to Pyricularia oryzae infection	Illumina HiSeq 2000	Susceptible (CO39 and NPB) and resistant (Pi_gm) rice cultivars were spray inoculated with P. oryzae spore and incubated for 12-hours.
GSE126961	GSM3618880	SRR8611909	paired-end	leaves	3_week_old	Inoculated with Pyricularia oryzae	Nipponbare	Bayogenin 3-O-Cellobioside is a novel anti-blast metabolite produced in rice in response to Pyricularia oryzae infection	Illumina HiSeq 2000	Susceptible (CO39 and NPB) and resistant (Pi_gm) rice cultivars were spray inoculated with P. oryzae spore and incubated for 12-hours.
GSE126961	GSM3618881	SRR8611910	paired-end	leaves	3_week_old	Inoculated with Pyricularia oryzae	Nipponbare	Bayogenin 3-O-Cellobioside is a novel anti-blast metabolite produced in rice in response to Pyricularia oryzae infection	Illumina HiSeq 2000	Susceptible (CO39 and NPB) and resistant (Pi_gm) rice cultivars were spray inoculated with P. oryzae spore and incubated for 12-hours.
GSE126961	GSM3618882	SRR8611911	paired-end	leaves	3_week_old	Inoculated with Pyricularia oryzae	Nipponbare	Bayogenin 3-O-Cellobioside is a novel anti-blast metabolite produced in rice in response to Pyricularia oryzae infection	Illumina HiSeq 2000	Susceptible (CO39 and NPB) and resistant (Pi_gm) rice cultivars were spray inoculated with P. oryzae spore and incubated for 12-hours.
GSE100715	GSM2691952	SRR5796940	single-end	shoot	2_week_old	Control,22C for 10 min	Nipponbare	Genome-wide analysis of heat effect on rice transcriptome and RNA secondary structurome	Illumina HiSeq 2500	Two week old rice plants in pots were inverted and the shoots were immersed in a water bath at 22C or 42C for 10 min treatment, and the plants were then transferred to a growth chamber set at the same temperature as in the greenhouse (30C) for ease of sampling during the recovery period. Three rice shoots comprised one biological replicate, and two biological replicates were obtained for each treatment and time-point.
GSE100715	GSM2691953	SRR5796941	single-end	shoot	2_week_old	Control,22C for 10 min	Nipponbare	Genome-wide analysis of heat effect on rice transcriptome and RNA secondary structurome	Illumina HiSeq 2500	Two week old rice plants in pots were inverted and the shoots were immersed in a water bath at 22C or 42C for 10 min treatment, and the plants were then transferred to a growth chamber set at the same temperature as in the greenhouse (30C) for ease of sampling during the recovery period. Three rice shoots comprised one biological replicate, and two biological replicates were obtained for each treatment and time-point.
GSE100715	GSM2691954	SRR5796942	single-end	shoot	2_week_old	Control,22C for 10 min, then 30C for 10 min	Nipponbare	Genome-wide analysis of heat effect on rice transcriptome and RNA secondary structurome	Illumina HiSeq 2500	Two week old rice plants in pots were inverted and the shoots were immersed in a water bath at 22C or 42C for 10 min treatment, and the plants were then transferred to a growth chamber set at the same temperature as in the greenhouse (30C) for ease of sampling during the recovery period. Three rice shoots comprised one biological replicate, and two biological replicates were obtained for each treatment and time-point.
GSE100715	GSM2691955	SRR5796943	single-end	shoot	2_week_old	Control,22C for 10 min, then 30C for 10 min	Nipponbare	Genome-wide analysis of heat effect on rice transcriptome and RNA secondary structurome	Illumina HiSeq 2500	Two week old rice plants in pots were inverted and the shoots were immersed in a water bath at 22C or 42C for 10 min treatment, and the plants were then transferred to a growth chamber set at the same temperature as in the greenhouse (30C) for ease of sampling during the recovery period. Three rice shoots comprised one biological replicate, and two biological replicates were obtained for each treatment and time-point.
GSE100715	GSM2691956	SRR5796944	single-end	shoot	2_week_old	Control, 22C for 10 min, then 30C for 50 min	Nipponbare	Genome-wide analysis of heat effect on rice transcriptome and RNA secondary structurome	Illumina HiSeq 2500	Two week old rice plants in pots were inverted and the shoots were immersed in a water bath at 22C or 42C for 10 min treatment, and the plants were then transferred to a growth chamber set at the same temperature as in the greenhouse (30C) for ease of sampling during the recovery period. Three rice shoots comprised one biological replicate, and two biological replicates were obtained for each treatment and time-point.
GSE100715	GSM2691957	SRR5796945	single-end	shoot	2_week_old	Control, 22C for 10 min, then 30C for 50 min	Nipponbare	Genome-wide analysis of heat effect on rice transcriptome and RNA secondary structurome	Illumina HiSeq 2500	Two week old rice plants in pots were inverted and the shoots were immersed in a water bath at 22C or 42C for 10 min treatment, and the plants were then transferred to a growth chamber set at the same temperature as in the greenhouse (30C) for ease of sampling during the recovery period. Three rice shoots comprised one biological replicate, and two biological replicates were obtained for each treatment and time-point.
GSE100715	GSM2691958	SRR5796946	single-end	shoot	2_week_old	Control,22C for 10 min, then 30C for 1h50 min	Nipponbare	Genome-wide analysis of heat effect on rice transcriptome and RNA secondary structurome	Illumina HiSeq 2500	Two week old rice plants in pots were inverted and the shoots were immersed in a water bath at 22C or 42C for 10 min treatment, and the plants were then transferred to a growth chamber set at the same temperature as in the greenhouse (30C) for ease of sampling during the recovery period. Three rice shoots comprised one biological replicate, and two biological replicates were obtained for each treatment and time-point.
GSE100715	GSM2691959	SRR5796947	single-end	shoot	2_week_old	Control,22C for 10 min, then 30C for 1h50 min	Nipponbare	Genome-wide analysis of heat effect on rice transcriptome and RNA secondary structurome	Illumina HiSeq 2500	Two week old rice plants in pots were inverted and the shoots were immersed in a water bath at 22C or 42C for 10 min treatment, and the plants were then transferred to a growth chamber set at the same temperature as in the greenhouse (30C) for ease of sampling during the recovery period. Three rice shoots comprised one biological replicate, and two biological replicates were obtained for each treatment and time-point.
GSE100715	GSM2691960	SRR5796948	single-end	shoot	2_week_old	Control,22C for 10 min, then 30C for 9h50 min	Nipponbare	Genome-wide analysis of heat effect on rice transcriptome and RNA secondary structurome	Illumina HiSeq 2500	Two week old rice plants in pots were inverted and the shoots were immersed in a water bath at 22C or 42C for 10 min treatment, and the plants were then transferred to a growth chamber set at the same temperature as in the greenhouse (30C) for ease of sampling during the recovery period. Three rice shoots comprised one biological replicate, and two biological replicates were obtained for each treatment and time-point.
GSE100715	GSM2691961	SRR5796949	single-end	shoot	2_week_old	Control,22C for 10 min, then 30C for 9h50 min	Nipponbare	Genome-wide analysis of heat effect on rice transcriptome and RNA secondary structurome	Illumina HiSeq 2500	Two week old rice plants in pots were inverted and the shoots were immersed in a water bath at 22C or 42C for 10 min treatment, and the plants were then transferred to a growth chamber set at the same temperature as in the greenhouse (30C) for ease of sampling during the recovery period. Three rice shoots comprised one biological replicate, and two biological replicates were obtained for each treatment and time-point.
GSE100715	GSM2691962	SRR5796950	single-end	shoot	2_week_old	Heat,42C for 10 min	Nipponbare	Genome-wide analysis of heat effect on rice transcriptome and RNA secondary structurome	Illumina HiSeq 2500	Two week old rice plants in pots were inverted and the shoots were immersed in a water bath at 22C or 42C for 10 min treatment, and the plants were then transferred to a growth chamber set at the same temperature as in the greenhouse (30C) for ease of sampling during the recovery period. Three rice shoots comprised one biological replicate, and two biological replicates were obtained for each treatment and time-point.
GSE100715	GSM2691963	SRR5796951	single-end	shoot	2_week_old	Heat,42C for 10 min	Nipponbare	Genome-wide analysis of heat effect on rice transcriptome and RNA secondary structurome	Illumina HiSeq 2500	Two week old rice plants in pots were inverted and the shoots were immersed in a water bath at 22C or 42C for 10 min treatment, and the plants were then transferred to a growth chamber set at the same temperature as in the greenhouse (30C) for ease of sampling during the recovery period. Three rice shoots comprised one biological replicate, and two biological replicates were obtained for each treatment and time-point.
GSE100715	GSM2691964	SRR5796952	single-end	shoot	2_week_old	Heat,42C for 10 min, then 30C for 10 min	Nipponbare	Genome-wide analysis of heat effect on rice transcriptome and RNA secondary structurome	Illumina HiSeq 2500	Two week old rice plants in pots were inverted and the shoots were immersed in a water bath at 22C or 42C for 10 min treatment, and the plants were then transferred to a growth chamber set at the same temperature as in the greenhouse (30C) for ease of sampling during the recovery period. Three rice shoots comprised one biological replicate, and two biological replicates were obtained for each treatment and time-point.
GSE100715	GSM2691965	SRR5796953	single-end	shoot	2_week_old	Heat,42C for 10 min, then 30C for 10 min	Nipponbare	Genome-wide analysis of heat effect on rice transcriptome and RNA secondary structurome	Illumina HiSeq 2500	Two week old rice plants in pots were inverted and the shoots were immersed in a water bath at 22C or 42C for 10 min treatment, and the plants were then transferred to a growth chamber set at the same temperature as in the greenhouse (30C) for ease of sampling during the recovery period. Three rice shoots comprised one biological replicate, and two biological replicates were obtained for each treatment and time-point.
GSE100715	GSM2691966	SRR5796954	single-end	shoot	2_week_old	Heat, 42C for 10 min, then 30C for 50 min	Nipponbare	Genome-wide analysis of heat effect on rice transcriptome and RNA secondary structurome	Illumina HiSeq 2500	Two week old rice plants in pots were inverted and the shoots were immersed in a water bath at 22C or 42C for 10 min treatment, and the plants were then transferred to a growth chamber set at the same temperature as in the greenhouse (30C) for ease of sampling during the recovery period. Three rice shoots comprised one biological replicate, and two biological replicates were obtained for each treatment and time-point.
GSE100715	GSM2691967	SRR5796955	single-end	shoot	2_week_old	Heat, 42C for 10 min, then 30C for 50 min	Nipponbare	Genome-wide analysis of heat effect on rice transcriptome and RNA secondary structurome	Illumina HiSeq 2500	Two week old rice plants in pots were inverted and the shoots were immersed in a water bath at 22C or 42C for 10 min treatment, and the plants were then transferred to a growth chamber set at the same temperature as in the greenhouse (30C) for ease of sampling during the recovery period. Three rice shoots comprised one biological replicate, and two biological replicates were obtained for each treatment and time-point.
GSE100715	GSM2691968	SRR5796956	single-end	shoot	2_week_old	Heat,42C for 10 min, then 30C for 1h50 min	Nipponbare	Genome-wide analysis of heat effect on rice transcriptome and RNA secondary structurome	Illumina HiSeq 2500	Two week old rice plants in pots were inverted and the shoots were immersed in a water bath at 22C or 42C for 10 min treatment, and the plants were then transferred to a growth chamber set at the same temperature as in the greenhouse (30C) for ease of sampling during the recovery period. Three rice shoots comprised one biological replicate, and two biological replicates were obtained for each treatment and time-point.
GSE100715	GSM2691969	SRR5796957	single-end	shoot	2_week_old	Heat,42C for 10 min, then 30C for 1h50 min	Nipponbare	Genome-wide analysis of heat effect on rice transcriptome and RNA secondary structurome	Illumina HiSeq 2500	Two week old rice plants in pots were inverted and the shoots were immersed in a water bath at 22C or 42C for 10 min treatment, and the plants were then transferred to a growth chamber set at the same temperature as in the greenhouse (30C) for ease of sampling during the recovery period. Three rice shoots comprised one biological replicate, and two biological replicates were obtained for each treatment and time-point.
GSE100715	GSM2691970	SRR5796958	single-end	shoot	2_week_old	Heat,42C for 10 min, then 30C for 9h50 min	Nipponbare	Genome-wide analysis of heat effect on rice transcriptome and RNA secondary structurome	Illumina HiSeq 2500	Two week old rice plants in pots were inverted and the shoots were immersed in a water bath at 22C or 42C for 10 min treatment, and the plants were then transferred to a growth chamber set at the same temperature as in the greenhouse (30C) for ease of sampling during the recovery period. Three rice shoots comprised one biological replicate, and two biological replicates were obtained for each treatment and time-point.
GSE100715	GSM2691971	SRR5796959	single-end	shoot	2_week_old	Heat,42C for 10 min, then 30C for 9h50 min	Nipponbare	Genome-wide analysis of heat effect on rice transcriptome and RNA secondary structurome	Illumina HiSeq 2500	Two week old rice plants in pots were inverted and the shoots were immersed in a water bath at 22C or 42C for 10 min treatment, and the plants were then transferred to a growth chamber set at the same temperature as in the greenhouse (30C) for ease of sampling during the recovery period. Three rice shoots comprised one biological replicate, and two biological replicates were obtained for each treatment and time-point.
GSE106150	GSM2830514	SRR6216698	paired-end	leaves	3_week_old	nontransgenic rice plant	Nipponbare	Overexpression of OsNAC14 improves drought tolerance in rice	Illumina HiSeq 2500	Rice was germinated on MS (Murashige and Skoog) media at 28C for 4 days, and transplanted into soil pots (4x4x6 cm; 3 plants per pot) and grown in a greenhouse.
GSE106150	GSM2830515	SRR6216699	paired-end	leaves	3_week_old	nontransgenic rice plant	Nipponbare	Overexpression of OsNAC14 improves drought tolerance in rice	Illumina HiSeq 2500	Rice was germinated on MS (Murashige and Skoog) media at 28C for 4 days, and transplanted into soil pots (4x4x6 cm; 3 plants per pot) and grown in a greenhouse.
GSE64665	GSM1576590	SRR1740428	single-end	root_meristematic_zone	4_days_after_plating	wt	Japonica	Conserved Molecular Program for Root Development in Diverse Plants	Illumina HiSeq 2000	Seeds were sterilized and germinated on agarose-solidified MS media under constant light at 21C.  The growing tips of the seedling primary roots were dissected along the longitudinal axis into 3 development zones. RNA was extracted by Qiagen RNeasy Plant Mini Kit.RNA libraries were constructed by Illumina TrueSeq kit according to manufacturer procedures.
GSE64665	GSM1576591	SRR1740429	single-end	root_meristematic_zone	4_days_after_plating	wt	Japonica	Conserved Molecular Program for Root Development in Diverse Plants	Illumina HiSeq 2000	Seeds were sterilized and germinated on agarose-solidified MS media under constant light at 21C.  The growing tips of the seedling primary roots were dissected along the longitudinal axis into 3 development zones. RNA was extracted by Qiagen RNeasy Plant Mini Kit.RNA libraries were constructed by Illumina TrueSeq kit according to manufacturer procedures.
GSE64665	GSM1576592	SRR1740430	single-end	root_meristematic_zone	4_days_after_plating	wt	Japonica	Conserved Molecular Program for Root Development in Diverse Plants	Illumina HiSeq 2000	Seeds were sterilized and germinated on agarose-solidified MS media under constant light at 21C.  The growing tips of the seedling primary roots were dissected along the longitudinal axis into 3 development zones. RNA was extracted by Qiagen RNeasy Plant Mini Kit.RNA libraries were constructed by Illumina TrueSeq kit according to manufacturer procedures.
GSE64665	GSM1576593	SRR1740431	single-end	root_elongation_zone	4_days_after_plating	wt	Japonica	Conserved Molecular Program for Root Development in Diverse Plants	Illumina HiSeq 2000	Seeds were sterilized and germinated on agarose-solidified MS media under constant light at 21C.  The growing tips of the seedling primary roots were dissected along the longitudinal axis into 3 development zones. RNA was extracted by Qiagen RNeasy Plant Mini Kit.RNA libraries were constructed by Illumina TrueSeq kit according to manufacturer procedures.
GSE64665	GSM1576594	SRR1740432	single-end	root_elongation_zone	4_days_after_plating	wt	Japonica	Conserved Molecular Program for Root Development in Diverse Plants	Illumina HiSeq 2000	Seeds were sterilized and germinated on agarose-solidified MS media under constant light at 21C.  The growing tips of the seedling primary roots were dissected along the longitudinal axis into 3 development zones. RNA was extracted by Qiagen RNeasy Plant Mini Kit.RNA libraries were constructed by Illumina TrueSeq kit according to manufacturer procedures.
GSE64665	GSM1576595	SRR1740433	single-end	root_elongation_zone	4_days_after_plating	wt	Japonica	Conserved Molecular Program for Root Development in Diverse Plants	Illumina HiSeq 2000	Seeds were sterilized and germinated on agarose-solidified MS media under constant light at 21C.  The growing tips of the seedling primary roots were dissected along the longitudinal axis into 3 development zones. RNA was extracted by Qiagen RNeasy Plant Mini Kit.RNA libraries were constructed by Illumina TrueSeq kit according to manufacturer procedures.
GSE64665	GSM1576596	SRR1740434	single-end	root_differentiation_zone	4_days_after_plating	wt	Japonica	Conserved Molecular Program for Root Development in Diverse Plants	Illumina HiSeq 2000	Seeds were sterilized and germinated on agarose-solidified MS media under constant light at 21C.  The growing tips of the seedling primary roots were dissected along the longitudinal axis into 3 development zones. RNA was extracted by Qiagen RNeasy Plant Mini Kit.RNA libraries were constructed by Illumina TrueSeq kit according to manufacturer procedures.
GSE64665	GSM1576597	SRR1740435	single-end	root_differentiation_zone	4_days_after_plating	wt	Japonica	Conserved Molecular Program for Root Development in Diverse Plants	Illumina HiSeq 2000	Seeds were sterilized and germinated on agarose-solidified MS media under constant light at 21C.  The growing tips of the seedling primary roots were dissected along the longitudinal axis into 3 development zones. RNA was extracted by Qiagen RNeasy Plant Mini Kit.RNA libraries were constructed by Illumina TrueSeq kit according to manufacturer procedures.
GSE64665	GSM1576598	SRR1740436	single-end	root_differentiation_zone	4_days_after_plating	wt	Japonica	Conserved Molecular Program for Root Development in Diverse Plants	Illumina HiSeq 2000	Seeds were sterilized and germinated on agarose-solidified MS media under constant light at 21C.  The growing tips of the seedling primary roots were dissected along the longitudinal axis into 3 development zones. RNA was extracted by Qiagen RNeasy Plant Mini Kit.RNA libraries were constructed by Illumina TrueSeq kit according to manufacturer procedures.
GSE95200	GSM2498562	SRR5278374	paired-end	pistil	before_meiosis	Balilla,S1	Balilla	RNA-seq analysis of genes regulated by S5 at different development stages	Illumina HiSeq 2000	All the rice plants were grown in the fields of experimental station of Huazhong Agricultural University, Wuhan, China.  RNA was extracted using TRIzol reagent (Invitrogen) according to the manual. RNA yields and quality were measured using Nanodrop 2000 (Thermo Scientific), and further quantified using Qubit2.0 Fluorometer (Invitrogen). RNA integrity was evaluated using Experion RNA Analysis Kits (Bio-rad) and Experion Automated Electrophoresis Station (Bio-rad). Each library was constructed using 3 Cg total RNA using the TruSeq RNA Library Preparation Kit v2 (Illumina).
GSE95200	GSM2498563	SRR5278375	paired-end	pistil	before_meiosis	Balilla,S1	Balilla	RNA-seq analysis of genes regulated by S5 at different development stages	Illumina HiSeq 2000	All the rice plants were grown in the fields of experimental station of Huazhong Agricultural University, Wuhan, China.  RNA was extracted using TRIzol reagent (Invitrogen) according to the manual. RNA yields and quality were measured using Nanodrop 2000 (Thermo Scientific), and further quantified using Qubit2.0 Fluorometer (Invitrogen). RNA integrity was evaluated using Experion RNA Analysis Kits (Bio-rad) and Experion Automated Electrophoresis Station (Bio-rad). Each library was constructed using 3 Cg total RNA using the TruSeq RNA Library Preparation Kit v2 (Illumina).
GSE95200	GSM2498564	SRR5278376	paired-end	pistil	during_meiosis	Balilla,S2	Balilla	RNA-seq analysis of genes regulated by S5 at different development stages	Illumina HiSeq 2000	All the rice plants were grown in the fields of experimental station of Huazhong Agricultural University, Wuhan, China.  RNA was extracted using TRIzol reagent (Invitrogen) according to the manual. RNA yields and quality were measured using Nanodrop 2000 (Thermo Scientific), and further quantified using Qubit2.0 Fluorometer (Invitrogen). RNA integrity was evaluated using Experion RNA Analysis Kits (Bio-rad) and Experion Automated Electrophoresis Station (Bio-rad). Each library was constructed using 3 Cg total RNA using the TruSeq RNA Library Preparation Kit v2 (Illumina).
GSE95200	GSM2498565	SRR5278377	paired-end	pistil	during_meiosis	Balilla,S2	Balilla	RNA-seq analysis of genes regulated by S5 at different development stages	Illumina HiSeq 2000	All the rice plants were grown in the fields of experimental station of Huazhong Agricultural University, Wuhan, China.  RNA was extracted using TRIzol reagent (Invitrogen) according to the manual. RNA yields and quality were measured using Nanodrop 2000 (Thermo Scientific), and further quantified using Qubit2.0 Fluorometer (Invitrogen). RNA integrity was evaluated using Experion RNA Analysis Kits (Bio-rad) and Experion Automated Electrophoresis Station (Bio-rad). Each library was constructed using 3 Cg total RNA using the TruSeq RNA Library Preparation Kit v2 (Illumina).
GSE95200	GSM2498566	SRR5278378	paired-end	pistil	after_meiosis	Balilla,S3	Balilla	RNA-seq analysis of genes regulated by S5 at different development stages	Illumina HiSeq 2000	All the rice plants were grown in the fields of experimental station of Huazhong Agricultural University, Wuhan, China.  RNA was extracted using TRIzol reagent (Invitrogen) according to the manual. RNA yields and quality were measured using Nanodrop 2000 (Thermo Scientific), and further quantified using Qubit2.0 Fluorometer (Invitrogen). RNA integrity was evaluated using Experion RNA Analysis Kits (Bio-rad) and Experion Automated Electrophoresis Station (Bio-rad). Each library was constructed using 3 Cg total RNA using the TruSeq RNA Library Preparation Kit v2 (Illumina).
GSE95200	GSM2498567	SRR5278379	paired-end	pistil	after_meiosis	Balilla,S3	Balilla	RNA-seq analysis of genes regulated by S5 at different development stages	Illumina HiSeq 2000	All the rice plants were grown in the fields of experimental station of Huazhong Agricultural University, Wuhan, China.  RNA was extracted using TRIzol reagent (Invitrogen) according to the manual. RNA yields and quality were measured using Nanodrop 2000 (Thermo Scientific), and further quantified using Qubit2.0 Fluorometer (Invitrogen). RNA integrity was evaluated using Experion RNA Analysis Kits (Bio-rad) and Experion Automated Electrophoresis Station (Bio-rad). Each library was constructed using 3 Cg total RNA using the TruSeq RNA Library Preparation Kit v2 (Illumina).
GSE89233	GSM2362452	SRR4457231	paired-end	flag_leaf	after_heading	DAH4	Dongjin	Fundamental molecular bases for differential transcriptional programs of top leaves during grain-filling in rice	Illumina HiSeq 2500	mRNA expression profiles of the flag leaf and 2nd leaf of Oryza Sativa during grain filling (Day After Heading, DAH, 4-44) were examined by Illumina Hi-seq 2500.
GSE89233	GSM2362453	SRR4457232	paired-end	flag_leaf	after_heading	DAH4	Dongjin	Fundamental molecular bases for differential transcriptional programs of top leaves during grain-filling in rice	Illumina HiSeq 2500	mRNA expression profiles of the flag leaf and 2nd leaf of Oryza Sativa during grain filling (Day After Heading, DAH, 4-44) were examined by Illumina Hi-seq 2500.
GSE89233	GSM2362454	SRR4457233	paired-end	flag_leaf	after_heading	DAH4	Dongjin	Fundamental molecular bases for differential transcriptional programs of top leaves during grain-filling in rice	Illumina HiSeq 2500	mRNA expression profiles of the flag leaf and 2nd leaf of Oryza Sativa during grain filling (Day After Heading, DAH, 4-44) were examined by Illumina Hi-seq 2500.
GSE89233	GSM2362455	SRR4457234	paired-end	flag_leaf	after_heading	DAH12	Dongjin	Fundamental molecular bases for differential transcriptional programs of top leaves during grain-filling in rice	Illumina HiSeq 2500	mRNA expression profiles of the flag leaf and 2nd leaf of Oryza Sativa during grain filling (Day After Heading, DAH, 4-44) were examined by Illumina Hi-seq 2500.
GSE89233	GSM2362456	SRR4457235	paired-end	flag_leaf	after_heading	DAH12	Dongjin	Fundamental molecular bases for differential transcriptional programs of top leaves during grain-filling in rice	Illumina HiSeq 2500	mRNA expression profiles of the flag leaf and 2nd leaf of Oryza Sativa during grain filling (Day After Heading, DAH, 4-44) were examined by Illumina Hi-seq 2500.
GSE89233	GSM2362457	SRR4457236	paired-end	flag_leaf	after_heading	DAH12	Dongjin	Fundamental molecular bases for differential transcriptional programs of top leaves during grain-filling in rice	Illumina HiSeq 2500	mRNA expression profiles of the flag leaf and 2nd leaf of Oryza Sativa during grain filling (Day After Heading, DAH, 4-44) were examined by Illumina Hi-seq 2500.
GSE89233	GSM2362458	SRR4457237	paired-end	flag_leaf	after_heading	DAH20	Dongjin	Fundamental molecular bases for differential transcriptional programs of top leaves during grain-filling in rice	Illumina HiSeq 2500	mRNA expression profiles of the flag leaf and 2nd leaf of Oryza Sativa during grain filling (Day After Heading, DAH, 4-44) were examined by Illumina Hi-seq 2500.
GSE89233	GSM2362459	SRR4457238	paired-end	flag_leaf	after_heading	DAH20	Dongjin	Fundamental molecular bases for differential transcriptional programs of top leaves during grain-filling in rice	Illumina HiSeq 2500	mRNA expression profiles of the flag leaf and 2nd leaf of Oryza Sativa during grain filling (Day After Heading, DAH, 4-44) were examined by Illumina Hi-seq 2500.
GSE89233	GSM2362460	SRR4457239	paired-end	flag_leaf	after_heading	DAH20	Dongjin	Fundamental molecular bases for differential transcriptional programs of top leaves during grain-filling in rice	Illumina HiSeq 2500	mRNA expression profiles of the flag leaf and 2nd leaf of Oryza Sativa during grain filling (Day After Heading, DAH, 4-44) were examined by Illumina Hi-seq 2500.
GSE89233	GSM2362461	SRR4457240	paired-end	flag_leaf	after_heading	DAH28	Dongjin	Fundamental molecular bases for differential transcriptional programs of top leaves during grain-filling in rice	Illumina HiSeq 2500	mRNA expression profiles of the flag leaf and 2nd leaf of Oryza Sativa during grain filling (Day After Heading, DAH, 4-44) were examined by Illumina Hi-seq 2500.
GSE89233	GSM2362462	SRR4457241	paired-end	flag_leaf	after_heading	DAH28	Dongjin	Fundamental molecular bases for differential transcriptional programs of top leaves during grain-filling in rice	Illumina HiSeq 2500	mRNA expression profiles of the flag leaf and 2nd leaf of Oryza Sativa during grain filling (Day After Heading, DAH, 4-44) were examined by Illumina Hi-seq 2500.
GSE89233	GSM2362463	SRR4457242	paired-end	flag_leaf	after_heading	DAH28	Dongjin	Fundamental molecular bases for differential transcriptional programs of top leaves during grain-filling in rice	Illumina HiSeq 2500	mRNA expression profiles of the flag leaf and 2nd leaf of Oryza Sativa during grain filling (Day After Heading, DAH, 4-44) were examined by Illumina Hi-seq 2500.
GSE89233	GSM2362464	SRR4457243	paired-end	flag_leaf	after_heading	DAH36	Dongjin	Fundamental molecular bases for differential transcriptional programs of top leaves during grain-filling in rice	Illumina HiSeq 2500	mRNA expression profiles of the flag leaf and 2nd leaf of Oryza Sativa during grain filling (Day After Heading, DAH, 4-44) were examined by Illumina Hi-seq 2500.
GSE89233	GSM2362465	SRR4457244	paired-end	flag_leaf	after_heading	DAH36	Dongjin	Fundamental molecular bases for differential transcriptional programs of top leaves during grain-filling in rice	Illumina HiSeq 2500	mRNA expression profiles of the flag leaf and 2nd leaf of Oryza Sativa during grain filling (Day After Heading, DAH, 4-44) were examined by Illumina Hi-seq 2500.
GSE89233	GSM2362466	SRR4457245	paired-end	flag_leaf	after_heading	DAH36	Dongjin	Fundamental molecular bases for differential transcriptional programs of top leaves during grain-filling in rice	Illumina HiSeq 2500	mRNA expression profiles of the flag leaf and 2nd leaf of Oryza Sativa during grain filling (Day After Heading, DAH, 4-44) were examined by Illumina Hi-seq 2500.
GSE89233	GSM2362467	SRR4457246	paired-end	flag_leaf	after_heading	DAH44	Dongjin	Fundamental molecular bases for differential transcriptional programs of top leaves during grain-filling in rice	Illumina HiSeq 2500	mRNA expression profiles of the flag leaf and 2nd leaf of Oryza Sativa during grain filling (Day After Heading, DAH, 4-44) were examined by Illumina Hi-seq 2500.
GSE89233	GSM2362468	SRR4457247	paired-end	flag_leaf	after_heading	DAH44	Dongjin	Fundamental molecular bases for differential transcriptional programs of top leaves during grain-filling in rice	Illumina HiSeq 2500	mRNA expression profiles of the flag leaf and 2nd leaf of Oryza Sativa during grain filling (Day After Heading, DAH, 4-44) were examined by Illumina Hi-seq 2500.
GSE89233	GSM2362469	SRR4457248	paired-end	flag_leaf	after_heading	DAH44	Dongjin	Fundamental molecular bases for differential transcriptional programs of top leaves during grain-filling in rice	Illumina HiSeq 2500	mRNA expression profiles of the flag leaf and 2nd leaf of Oryza Sativa during grain filling (Day After Heading, DAH, 4-44) were examined by Illumina Hi-seq 2500.
GSE77300	GSM2048352	SRR3129121	paired-end	spikelet	anther_development_stage_3	Wild_type_9522_S3	9522	A Widespread Impact on Small RNAs and Gene Networks in Rice msp1/ostdl1a Mutants, Partners with Key Roles in Anther Development	Illumina HiSeq 2000	In this study, we analyzed small RNA and mRNA changes in different stages of spikelet from wildtype rice, and from msp1 and ostdl1a mutants. Analysis across different stages of rice spikelet of the small RNA data identified miRNAs demonstrating differential abundances.Materials were collected and flash frozen in liquid nitrogen. Total RNA was extracted by TRIzol (Invitrogen) according to manufacturer's protocol. Small RNA libraries were constructed from 1 microgram of total RNA using Illumina Truseq small RNA sample preparation kit (RS-200-0012). RNA-seq libraries were constructed using the Illumina TruSeq RNA sample preparation kit (RS-122-2001).
GSE77300	GSM2048353	SRR3129122	paired-end	spikelet	anther_development_stage_3	Wild_type_9522_S3	9522	A Widespread Impact on Small RNAs and Gene Networks in Rice msp1/ostdl1a Mutants, Partners with Key Roles in Anther Development	Illumina HiSeq 2000	In this study, we analyzed small RNA and mRNA changes in different stages of spikelet from wildtype rice, and from msp1 and ostdl1a mutants. Analysis across different stages of rice spikelet of the small RNA data identified miRNAs demonstrating differential abundances.Materials were collected and flash frozen in liquid nitrogen. Total RNA was extracted by TRIzol (Invitrogen) according to manufacturer's protocol. Small RNA libraries were constructed from 1 microgram of total RNA using Illumina Truseq small RNA sample preparation kit (RS-200-0012). RNA-seq libraries were constructed using the Illumina TruSeq RNA sample preparation kit (RS-122-2001).
GSE77300	GSM2048354	SRR3129123	paired-end	spikelet	anther_development_stage_3	Wild_type_9522_S3	9522	A Widespread Impact on Small RNAs and Gene Networks in Rice msp1/ostdl1a Mutants, Partners with Key Roles in Anther Development	Illumina HiSeq 2000	In this study, we analyzed small RNA and mRNA changes in different stages of spikelet from wildtype rice, and from msp1 and ostdl1a mutants. Analysis across different stages of rice spikelet of the small RNA data identified miRNAs demonstrating differential abundances.Materials were collected and flash frozen in liquid nitrogen. Total RNA was extracted by TRIzol (Invitrogen) according to manufacturer's protocol. Small RNA libraries were constructed from 1 microgram of total RNA using Illumina Truseq small RNA sample preparation kit (RS-200-0012). RNA-seq libraries were constructed using the Illumina TruSeq RNA sample preparation kit (RS-122-2001).
GSE77300	GSM2048355	SRR3129124	paired-end	spikelet	anther_development_stage_5	Wild_type_9522_S5	9522	A Widespread Impact on Small RNAs and Gene Networks in Rice msp1/ostdl1a Mutants, Partners with Key Roles in Anther Development	Illumina HiSeq 2000	In this study, we analyzed small RNA and mRNA changes in different stages of spikelet from wildtype rice, and from msp1 and ostdl1a mutants. Analysis across different stages of rice spikelet of the small RNA data identified miRNAs demonstrating differential abundances.Materials were collected and flash frozen in liquid nitrogen. Total RNA was extracted by TRIzol (Invitrogen) according to manufacturer's protocol. Small RNA libraries were constructed from 1 microgram of total RNA using Illumina Truseq small RNA sample preparation kit (RS-200-0012). RNA-seq libraries were constructed using the Illumina TruSeq RNA sample preparation kit (RS-122-2001).
GSE77300	GSM2048356	SRR3129125	paired-end	spikelet	anther_development_stage_5	Wild_type_9522_S5	9522	A Widespread Impact on Small RNAs and Gene Networks in Rice msp1/ostdl1a Mutants, Partners with Key Roles in Anther Development	Illumina HiSeq 2000	In this study, we analyzed small RNA and mRNA changes in different stages of spikelet from wildtype rice, and from msp1 and ostdl1a mutants. Analysis across different stages of rice spikelet of the small RNA data identified miRNAs demonstrating differential abundances.Materials were collected and flash frozen in liquid nitrogen. Total RNA was extracted by TRIzol (Invitrogen) according to manufacturer's protocol. Small RNA libraries were constructed from 1 microgram of total RNA using Illumina Truseq small RNA sample preparation kit (RS-200-0012). RNA-seq libraries were constructed using the Illumina TruSeq RNA sample preparation kit (RS-122-2001).
GSE77300	GSM2048357	SRR3129126	paired-end	spikelet	anther_development_stage_5	Wild_type_9522_S5	9522	A Widespread Impact on Small RNAs and Gene Networks in Rice msp1/ostdl1a Mutants, Partners with Key Roles in Anther Development	Illumina HiSeq 2000	In this study, we analyzed small RNA and mRNA changes in different stages of spikelet from wildtype rice, and from msp1 and ostdl1a mutants. Analysis across different stages of rice spikelet of the small RNA data identified miRNAs demonstrating differential abundances.Materials were collected and flash frozen in liquid nitrogen. Total RNA was extracted by TRIzol (Invitrogen) according to manufacturer's protocol. Small RNA libraries were constructed from 1 microgram of total RNA using Illumina Truseq small RNA sample preparation kit (RS-200-0012). RNA-seq libraries were constructed using the Illumina TruSeq RNA sample preparation kit (RS-122-2001).
GSE77300	GSM2048358	SRR3129127	paired-end	spikelet	anther_development_stage_7	Wild_type_9522_S7	9522	A Widespread Impact on Small RNAs and Gene Networks in Rice msp1/ostdl1a Mutants, Partners with Key Roles in Anther Development	Illumina HiSeq 2000	In this study, we analyzed small RNA and mRNA changes in different stages of spikelet from wildtype rice, and from msp1 and ostdl1a mutants. Analysis across different stages of rice spikelet of the small RNA data identified miRNAs demonstrating differential abundances.Materials were collected and flash frozen in liquid nitrogen. Total RNA was extracted by TRIzol (Invitrogen) according to manufacturer's protocol. Small RNA libraries were constructed from 1 microgram of total RNA using Illumina Truseq small RNA sample preparation kit (RS-200-0012). RNA-seq libraries were constructed using the Illumina TruSeq RNA sample preparation kit (RS-122-2001).
GSE77300	GSM2048359	SRR3129128	paired-end	spikelet	anther_development_stage_7	Wild_type_9522_S7	9522	A Widespread Impact on Small RNAs and Gene Networks in Rice msp1/ostdl1a Mutants, Partners with Key Roles in Anther Development	Illumina HiSeq 2000	In this study, we analyzed small RNA and mRNA changes in different stages of spikelet from wildtype rice, and from msp1 and ostdl1a mutants. Analysis across different stages of rice spikelet of the small RNA data identified miRNAs demonstrating differential abundances.Materials were collected and flash frozen in liquid nitrogen. Total RNA was extracted by TRIzol (Invitrogen) according to manufacturer's protocol. Small RNA libraries were constructed from 1 microgram of total RNA using Illumina Truseq small RNA sample preparation kit (RS-200-0012). RNA-seq libraries were constructed using the Illumina TruSeq RNA sample preparation kit (RS-122-2001).
GSE77300	GSM2048360	SRR3129129	paired-end	spikelet	anther_development_stage_7	Wild_type_9522_S7	9522	A Widespread Impact on Small RNAs and Gene Networks in Rice msp1/ostdl1a Mutants, Partners with Key Roles in Anther Development	Illumina HiSeq 2000	In this study, we analyzed small RNA and mRNA changes in different stages of spikelet from wildtype rice, and from msp1 and ostdl1a mutants. Analysis across different stages of rice spikelet of the small RNA data identified miRNAs demonstrating differential abundances.Materials were collected and flash frozen in liquid nitrogen. Total RNA was extracted by TRIzol (Invitrogen) according to manufacturer's protocol. Small RNA libraries were constructed from 1 microgram of total RNA using Illumina Truseq small RNA sample preparation kit (RS-200-0012). RNA-seq libraries were constructed using the Illumina TruSeq RNA sample preparation kit (RS-122-2001).
GSE92302	GSM2425416	SRR5110429	single-end	panicle	50%_flowering	Dawn	IR64	Temporal anaylsis of mRNA from pannicle tissue from field grown rice	Illumina HiSeq 2500	Plants were grown in a field setting. This group of samples is untreated.An IR64 land variety was grown on a on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.
GSE92302	GSM2425417	SRR5110430	single-end	panicle	50%_flowering	Dawn	IR64	Temporal anaylsis of mRNA from pannicle tissue from field grown rice	Illumina HiSeq 2500	Plants were grown in a field setting. This group of samples is untreated.An IR64 land variety was grown on a on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.
GSE92302	GSM2425418	SRR5110431	single-end	panicle	50%_flowering	Dawn	IR64	Temporal anaylsis of mRNA from pannicle tissue from field grown rice	Illumina HiSeq 2500	Plants were grown in a field setting. This group of samples is untreated.An IR64 land variety was grown on a on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.
GSE92302	GSM2425419	SRR5110432	single-end	panicle	50%_flowering	Dawn	IR64	Temporal anaylsis of mRNA from pannicle tissue from field grown rice	Illumina HiSeq 2500	Plants were grown in a field setting. This group of samples is untreated.An IR64 land variety was grown on a on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.
GSE92302	GSM2425420	SRR5110433	single-end	panicle	50%_flowering	Dawn + 3.5h	IR64	Temporal anaylsis of mRNA from pannicle tissue from field grown rice	Illumina HiSeq 2500	Plants were grown in a field setting. This group of samples is untreated.An IR64 land variety was grown on a on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.
GSE92302	GSM2425421	SRR5110434	single-end	panicle	50%_flowering	Dawn + 3.5h	IR64	Temporal anaylsis of mRNA from pannicle tissue from field grown rice	Illumina HiSeq 2500	Plants were grown in a field setting. This group of samples is untreated.An IR64 land variety was grown on a on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.
GSE92302	GSM2425422	SRR5110435	single-end	panicle	50%_flowering	Dawn + 3.5h	IR64	Temporal anaylsis of mRNA from pannicle tissue from field grown rice	Illumina HiSeq 2500	Plants were grown in a field setting. This group of samples is untreated.An IR64 land variety was grown on a on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.
GSE92302	GSM2425423	SRR5110436	single-end	panicle	50%_flowering	Dawn + 3.5h	IR64	Temporal anaylsis of mRNA from pannicle tissue from field grown rice	Illumina HiSeq 2500	Plants were grown in a field setting. This group of samples is untreated.An IR64 land variety was grown on a on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.
GSE92302	GSM2425424	SRR5110437	single-end	panicle	50%_flowering	Dawn + 7h	IR64	Temporal anaylsis of mRNA from pannicle tissue from field grown rice	Illumina HiSeq 2500	Plants were grown in a field setting. This group of samples is untreated.An IR64 land variety was grown on a on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.
GSE92302	GSM2425425	SRR5110438	single-end	panicle	50%_flowering	Dawn + 7h	IR64	Temporal anaylsis of mRNA from pannicle tissue from field grown rice	Illumina HiSeq 2500	Plants were grown in a field setting. This group of samples is untreated.An IR64 land variety was grown on a on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.
GSE92302	GSM2425426	SRR5110439	single-end	panicle	50%_flowering	Dawn + 7h	IR64	Temporal anaylsis of mRNA from pannicle tissue from field grown rice	Illumina HiSeq 2500	Plants were grown in a field setting. This group of samples is untreated.An IR64 land variety was grown on a on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.
GSE92302	GSM2425427	SRR5110440	single-end	panicle	50%_flowering	Dawn + 7h	IR64	Temporal anaylsis of mRNA from pannicle tissue from field grown rice	Illumina HiSeq 2500	Plants were grown in a field setting. This group of samples is untreated.An IR64 land variety was grown on a on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.
GSE92302	GSM2425428	SRR5110441	single-end	panicle	50%_flowering	Dawn + 10.5h	IR64	Temporal anaylsis of mRNA from pannicle tissue from field grown rice	Illumina HiSeq 2500	Plants were grown in a field setting. This group of samples is untreated.An IR64 land variety was grown on a on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.
GSE92302	GSM2425429	SRR5110442	single-end	panicle	50%_flowering	Dawn + 10.5h	IR64	Temporal anaylsis of mRNA from pannicle tissue from field grown rice	Illumina HiSeq 2500	Plants were grown in a field setting. This group of samples is untreated.An IR64 land variety was grown on a on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.
GSE92302	GSM2425430	SRR5110443	single-end	panicle	50%_flowering	Dawn + 10.5h	IR64	Temporal anaylsis of mRNA from pannicle tissue from field grown rice	Illumina HiSeq 2500	Plants were grown in a field setting. This group of samples is untreated.An IR64 land variety was grown on a on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.
GSE92302	GSM2425431	SRR5110444	single-end	panicle	50%_flowering	Dawn + 10.5h	IR64	Temporal anaylsis of mRNA from pannicle tissue from field grown rice	Illumina HiSeq 2500	Plants were grown in a field setting. This group of samples is untreated.An IR64 land variety was grown on a on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.
GSE92302	GSM2425432	SRR5110445	single-end	panicle	50%_flowering	Dusk	IR64	Temporal anaylsis of mRNA from pannicle tissue from field grown rice	Illumina HiSeq 2500	Plants were grown in a field setting. This group of samples is untreated.An IR64 land variety was grown on a on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.
GSE92302	GSM2425433	SRR5110446	single-end	panicle	50%_flowering	Dusk	IR64	Temporal anaylsis of mRNA from pannicle tissue from field grown rice	Illumina HiSeq 2500	Plants were grown in a field setting. This group of samples is untreated.An IR64 land variety was grown on a on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.
GSE92302	GSM2425434	SRR5110447	single-end	panicle	50%_flowering	Dusk	IR64	Temporal anaylsis of mRNA from pannicle tissue from field grown rice	Illumina HiSeq 2500	Plants were grown in a field setting. This group of samples is untreated.An IR64 land variety was grown on a on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.
GSE92302	GSM2425435	SRR5110448	single-end	panicle	50%_flowering	Dusk	IR64	Temporal anaylsis of mRNA from pannicle tissue from field grown rice	Illumina HiSeq 2500	Plants were grown in a field setting. This group of samples is untreated.An IR64 land variety was grown on a on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.
GSE92302	GSM2425436	SRR5110449	single-end	panicle	50%_flowering	Dawn + 14h	IR64	Temporal anaylsis of mRNA from pannicle tissue from field grown rice	Illumina HiSeq 2500	Plants were grown in a field setting. This group of samples is untreated.An IR64 land variety was grown on a on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.
GSE92302	GSM2425437	SRR5110450	single-end	panicle	50%_flowering	Dawn + 14h	IR64	Temporal anaylsis of mRNA from pannicle tissue from field grown rice	Illumina HiSeq 2500	Plants were grown in a field setting. This group of samples is untreated.An IR64 land variety was grown on a on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.
GSE92302	GSM2425438	SRR5110451	single-end	panicle	50%_flowering	Dawn + 14h	IR64	Temporal anaylsis of mRNA from pannicle tissue from field grown rice	Illumina HiSeq 2500	Plants were grown in a field setting. This group of samples is untreated.An IR64 land variety was grown on a on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.
GSE92302	GSM2425439	SRR5110452	single-end	panicle	50%_flowering	Dawn + 14h	IR64	Temporal anaylsis of mRNA from pannicle tissue from field grown rice	Illumina HiSeq 2500	Plants were grown in a field setting. This group of samples is untreated.An IR64 land variety was grown on a on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.
GSE92302	GSM2425440	SRR5110453	single-end	panicle	50%_flowering	Dawn + 17.5h	IR64	Temporal anaylsis of mRNA from pannicle tissue from field grown rice	Illumina HiSeq 2500	Plants were grown in a field setting. This group of samples is untreated.An IR64 land variety was grown on a on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.
GSE92302	GSM2425441	SRR5110454	single-end	panicle	50%_flowering	Dawn + 17.5h	IR64	Temporal anaylsis of mRNA from pannicle tissue from field grown rice	Illumina HiSeq 2500	Plants were grown in a field setting. This group of samples is untreated.An IR64 land variety was grown on a on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.
GSE92302	GSM2425442	SRR5110455	single-end	panicle	50%_flowering	Dawn + 17.5h	IR64	Temporal anaylsis of mRNA from pannicle tissue from field grown rice	Illumina HiSeq 2500	Plants were grown in a field setting. This group of samples is untreated.An IR64 land variety was grown on a on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.
GSE92302	GSM2425443	SRR5110456	single-end	panicle	50%_flowering	Dawn + 17.5h	IR64	Temporal anaylsis of mRNA from pannicle tissue from field grown rice	Illumina HiSeq 2500	Plants were grown in a field setting. This group of samples is untreated.An IR64 land variety was grown on a on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.
GSE92302	GSM2425444	SRR5110457	single-end	panicle	50%_flowering	Dawn + 21h	IR64	Temporal anaylsis of mRNA from pannicle tissue from field grown rice	Illumina HiSeq 2500	Plants were grown in a field setting. This group of samples is untreated.An IR64 land variety was grown on a on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.
GSE92302	GSM2425445	SRR5110458	single-end	panicle	50%_flowering	Dawn + 21h	IR64	Temporal anaylsis of mRNA from pannicle tissue from field grown rice	Illumina HiSeq 2500	Plants were grown in a field setting. This group of samples is untreated.An IR64 land variety was grown on a on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.
GSE92302	GSM2425446	SRR5110459	single-end	panicle	50%_flowering	Dawn + 21h	IR64	Temporal anaylsis of mRNA from pannicle tissue from field grown rice	Illumina HiSeq 2500	Plants were grown in a field setting. This group of samples is untreated.An IR64 land variety was grown on a on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.
GSE92302	GSM2425447	SRR5110460	single-end	panicle	50%_flowering	Dawn + 21h	IR64	Temporal anaylsis of mRNA from pannicle tissue from field grown rice	Illumina HiSeq 2500	Plants were grown in a field setting. This group of samples is untreated.An IR64 land variety was grown on a on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.
GSE56463	GSM1361891	SRR1213690	single-end	flower	no_collect	wt(flower buds)	Japonica	Transcriptome profiling of various organs at different developmental stages in rice (single-end)	Illumina HiSeq 2500	Seeds from the cultivated rice subspecies Oryza sativa L. ssp. Japonica were grown in a greenhouse in Singapore . Flower buds were collected before flowering and flowers were collected at the flowering day. Flag leaves and roots were collected at the before- and after-flowering stage. The before-flowering sample was defined as a mixture of different stages in a period from panicle initiation to 1 day before flowering. The after-flowering sample was defined as a mixture of different stages after the flowering day. Milk grains and mature seeds were also collected.
GSE56463	GSM1361892	SRR1213691	single-end	flower	no_collect	wt	Japonica	Transcriptome profiling of various organs at different developmental stages in rice (single-end)	Illumina HiSeq 2500	Seeds from the cultivated rice subspecies Oryza sativa L. ssp. Japonica were grown in a greenhouse in Singapore . Flower buds were collected before flowering and flowers were collected at the flowering day. Flag leaves and roots were collected at the before- and after-flowering stage. The before-flowering sample was defined as a mixture of different stages in a period from panicle initiation to 1 day before flowering. The after-flowering sample was defined as a mixture of different stages after the flowering day. Milk grains and mature seeds were also collected.
GSE56463	GSM1361893	SRR1213692	single-end	leaves	leaves_sampled_before_flowering	wt	Japonica	Transcriptome profiling of various organs at different developmental stages in rice (single-end)	Illumina HiSeq 2500	Seeds from the cultivated rice subspecies Oryza sativa L. ssp. Japonica were grown in a greenhouse in Singapore . Flower buds were collected before flowering and flowers were collected at the flowering day. Flag leaves and roots were collected at the before- and after-flowering stage. The before-flowering sample was defined as a mixture of different stages in a period from panicle initiation to 1 day before flowering. The after-flowering sample was defined as a mixture of different stages after the flowering day. Milk grains and mature seeds were also collected.
GSE56463	GSM1361894	SRR1213693	single-end	leaves	leaves_sampled_after_flowering	wt	Japonica	Transcriptome profiling of various organs at different developmental stages in rice (single-end)	Illumina HiSeq 2500	Seeds from the cultivated rice subspecies Oryza sativa L. ssp. Japonica were grown in a greenhouse in Singapore . Flower buds were collected before flowering and flowers were collected at the flowering day. Flag leaves and roots were collected at the before- and after-flowering stage. The before-flowering sample was defined as a mixture of different stages in a period from panicle initiation to 1 day before flowering. The after-flowering sample was defined as a mixture of different stages after the flowering day. Milk grains and mature seeds were also collected.
GSE56463	GSM1361895	SRR1213694	single-end	root	roots_sampled_before_flowering	wt	Japonica	Transcriptome profiling of various organs at different developmental stages in rice (single-end)	Illumina HiSeq 2500	Seeds from the cultivated rice subspecies Oryza sativa L. ssp. Japonica were grown in a greenhouse in Singapore . Flower buds were collected before flowering and flowers were collected at the flowering day. Flag leaves and roots were collected at the before- and after-flowering stage. The before-flowering sample was defined as a mixture of different stages in a period from panicle initiation to 1 day before flowering. The after-flowering sample was defined as a mixture of different stages after the flowering day. Milk grains and mature seeds were also collected.
GSE56463	GSM1361896	SRR1213695	single-end	root	roots_sampled_after_flowering	wt	Japonica	Transcriptome profiling of various organs at different developmental stages in rice (single-end)	Illumina HiSeq 2500	Seeds from the cultivated rice subspecies Oryza sativa L. ssp. Japonica were grown in a greenhouse in Singapore . Flower buds were collected before flowering and flowers were collected at the flowering day. Flag leaves and roots were collected at the before- and after-flowering stage. The before-flowering sample was defined as a mixture of different stages in a period from panicle initiation to 1 day before flowering. The after-flowering sample was defined as a mixture of different stages after the flowering day. Milk grains and mature seeds were also collected.
GSE56463	GSM1361897	SRR1213696	single-end	panicle	no_collect	wt(milk grains)	Japonica	Transcriptome profiling of various organs at different developmental stages in rice (single-end)	Illumina HiSeq 2500	Seeds from the cultivated rice subspecies Oryza sativa L. ssp. Japonica were grown in a greenhouse in Singapore . Flower buds were collected before flowering and flowers were collected at the flowering day. Flag leaves and roots were collected at the before- and after-flowering stage. The before-flowering sample was defined as a mixture of different stages in a period from panicle initiation to 1 day before flowering. The after-flowering sample was defined as a mixture of different stages after the flowering day. Milk grains and mature seeds were also collected.
GSE56463	GSM1361898	SRR1213697	single-end	panicle	no_collect	wt(mature seeds)	Japonica	Transcriptome profiling of various organs at different developmental stages in rice (single-end)	Illumina HiSeq 2500	Seeds from the cultivated rice subspecies Oryza sativa L. ssp. Japonica were grown in a greenhouse in Singapore . Flower buds were collected before flowering and flowers were collected at the flowering day. Flag leaves and roots were collected at the before- and after-flowering stage. The before-flowering sample was defined as a mixture of different stages in a period from panicle initiation to 1 day before flowering. The after-flowering sample was defined as a mixture of different stages after the flowering day. Milk grains and mature seeds were also collected.
GSE115371	GSM3176761	SRR7265373	single-end	embryos	no_collect	wt	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176762	SRR7265374	single-end	embryos	no_collect	wt	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176763	SRR7265375	single-end	embryos	no_collect	wt	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176764	SRR7265376	single-end	embryos	no_collect	air (aerobic-A) at 30 C in the dark for 1 h.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176765	SRR7265377	single-end	embryos	no_collect	air (aerobic-A) at 30 C in the dark for 1 h.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176766	SRR7265378	single-end	embryos	no_collect	air (aerobic-A) at 30 C in the dark for 1 h.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176767	SRR7265379	single-end	embryos	no_collect	nitrogen gas (anaerobic-N) at 30 C in the dark for 1 h.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176768	SRR7265380	single-end	embryos	no_collect	nitrogen gas (anaerobic-N) at 30 C in the dark for 1 h.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176769	SRR7265381	single-end	embryos	no_collect	nitrogen gas (anaerobic-N) at 30 C in the dark for 1 h.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176770	SRR7265382	single-end	embryos	no_collect	air (aerobic-A) at 30 C in the dark for 3 h.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176771	SRR7265383	single-end	embryos	no_collect	air (aerobic-A) at 30 C in the dark for 3 h.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176772	SRR7265384	single-end	embryos	no_collect	air (aerobic-A) at 30 C in the dark for 3 h.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176773	SRR7265385	single-end	embryos	no_collect	nitrogen gas (anaerobic-N) at 30 C in the dark for 3 h.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176774	SRR7265386	single-end	embryos	no_collect	nitrogen gas (anaerobic-N) at 30 C in the dark for 3 h.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176775	SRR7265387	single-end	embryos	no_collect	nitrogen gas (anaerobic-N) at 30 C in the dark for 3 h.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176776	SRR7265388	single-end	embryos	no_collect	air (aerobic-A) at 30 C in the dark for 12 h.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176777	SRR7265389	single-end	embryos	no_collect	air (aerobic-A) at 30 C in the dark for 12 h.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176778	SRR7265390	single-end	embryos	no_collect	air (aerobic-A) at 30 C in the dark for 12 h.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176779	SRR7265391	single-end	embryos	no_collect	nitrogen gas (anaerobic-N) at 30 C in the dark for 12 h.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176780	SRR7265392	single-end	embryos	no_collect	nitrogen gas (anaerobic-N) at 30 C in the dark for 12 h.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176781	SRR7265393	single-end	embryos	no_collect	nitrogen gas (anaerobic-N) at 30 C in the dark for 12 h.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176782	SRR7265394	single-end	embryos	no_collect	air (aerobic-A) at 30 C in the dark for 24 h.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176783	SRR7265395	single-end	embryos	no_collect	air (aerobic-A) at 30 C in the dark for 24 h.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176784	SRR7265396	single-end	embryos	no_collect	air (aerobic-A) at 30 C in the dark for 24 h.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176785	SRR7265397	single-end	embryos	no_collect	nitrogen gas (anaerobic-N) at 30 C in the dark for 24 h.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176786	SRR7265398	single-end	embryos	no_collect	nitrogen gas (anaerobic-N) at 30 C in the dark for 24 h.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176787	SRR7265399	single-end	embryos	no_collect	nitrogen gas (anaerobic-N) at 30 C in the dark for 24 h.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176788	SRR7265400	single-end	coleoptile	no_collect	air (aerobic-A) at 30 C in the dark for 2 d.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176789	SRR7265401	single-end	coleoptile	no_collect	air (aerobic-A) at 30 C in the dark for 2 d.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176790	SRR7265402	single-end	coleoptile	no_collect	air (aerobic-A) at 30 C in the dark for 2 d.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176791	SRR7265403	single-end	coleoptile	no_collect	nitrogen gas (anaerobic-N) at 30 C in the dark for 2 d.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176792	SRR7265404	single-end	coleoptile	no_collect	nitrogen gas (anaerobic-N) at 30 C in the dark for 2 d.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176793	SRR7265405	single-end	coleoptile	no_collect	nitrogen gas (anaerobic-N) at 30 C in the dark for 2 d.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176794	SRR7265406	single-end	coleoptile	no_collect	air (aerobic-A) at 30 C in the dark for 3 d.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176795	SRR7265407	single-end	coleoptile	no_collect	air (aerobic-A) at 30 C in the dark for 3 d.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176796	SRR7265408	single-end	coleoptile	no_collect	air (aerobic-A) at 30 C in the dark for 3 d.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176797	SRR7265409	single-end	coleoptile	no_collect	nitrogen gas (anaerobic-N) at 30 C in the dark for 3 d.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176798	SRR7265410	single-end	coleoptile	no_collect	nitrogen gas (anaerobic-N) at 30 C in the dark for 3 d.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176799	SRR7265411	single-end	coleoptile	no_collect	nitrogen gas (anaerobic-N) at 30 C in the dark for 3 d.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176800	SRR7265412	single-end	coleoptile	no_collect	air (aerobic-A) at 30 C in the dark for 4 d.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176801	SRR7265413	single-end	coleoptile	no_collect	air (aerobic-A) at 30 C in the dark for 4 d.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176802	SRR7265414	single-end	coleoptile	no_collect	air (aerobic-A) at 30 C in the dark for 4 d.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176803	SRR7265415	single-end	coleoptile	no_collect	nitrogen gas (anaerobic-N) at 30 C in the dark for 4 d.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176804	SRR7265416	single-end	coleoptile	no_collect	nitrogen gas (anaerobic-N) at 30 C in the dark for 4 d.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176805	SRR7265417	single-end	coleoptile	no_collect	nitrogen gas (anaerobic-N) at 30 C in the dark for 4 d.	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176806	SRR7265418	single-end	coleoptile	no_collect	nitrogen gas (anaerobic-N) at 30 C in the dark for 3 d,(3dN1dA).	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176807	SRR7265419	single-end	coleoptile	no_collect	nitrogen gas (anaerobic-N) at 30 C in the dark for 3 d,(3dN1dA).	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE115371	GSM3176808	SRR7265420	single-end	coleoptile	no_collect	nitrogen gas (anaerobic-N) at 30 C in the dark for 3 d,(3dN1dA).	Amaroo	RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)	Illumina HiSeq 1500	For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
GSE119109	GSM3358179	SRR7760291	single-end	spikelet	anthesis_stage	control condition (29C) for 7 hrs	IRGA_428	Transcriptome analysis of flooded rice spikelet in response to high temperature at flowering	Illumina HiSeq 2500	Two rice cultivars (BR-IRGA 409 and IRGA 428) were submitted to daytime c (9 am to 16 pm) during a period of three days at anthesis stage. spikelet of the middle third of the panicle of plants were sampled in each cultivar at the end of the thermal treatment.
GSE119109	GSM3358180	SRR7760292	single-end	spikelet	anthesis_stage	control condition (29C) for 7 hrs	IRGA_428	Transcriptome analysis of flooded rice spikelet in response to high temperature at flowering	Illumina HiSeq 2500	Two rice cultivars (BR-IRGA 409 and IRGA 428) were submitted to daytime c (9 am to 16 pm) during a period of three days at anthesis stage. spikelet of the middle third of the panicle of plants were sampled in each cultivar at the end of the thermal treatment.
GSE119109	GSM3358181	SRR7760293	single-end	spikelet	anthesis_stage	control condition (29C) for 7 hrs	IRGA_428	Transcriptome analysis of flooded rice spikelet in response to high temperature at flowering	Illumina HiSeq 2500	Two rice cultivars (BR-IRGA 409 and IRGA 428) were submitted to daytime c (9 am to 16 pm) during a period of three days at anthesis stage. spikelet of the middle third of the panicle of plants were sampled in each cultivar at the end of the thermal treatment.
GSE119109	GSM3358182	SRR7760294	single-end	spikelet	anthesis_stage	high temperature treatment (38C) for 7 hrs	IRGA_428	Transcriptome analysis of flooded rice spikelet in response to high temperature at flowering	Illumina HiSeq 2500	Two rice cultivars (BR-IRGA 409 and IRGA 428) were submitted to daytime c (9 am to 16 pm) during a period of three days at anthesis stage. spikelet of the middle third of the panicle of plants were sampled in each cultivar at the end of the thermal treatment.
GSE119109	GSM3358183	SRR7760295	single-end	spikelet	anthesis_stage	high temperature treatment (38C) for 7 hrs	IRGA_428	Transcriptome analysis of flooded rice spikelet in response to high temperature at flowering	Illumina HiSeq 2500	Two rice cultivars (BR-IRGA 409 and IRGA 428) were submitted to daytime c (9 am to 16 pm) during a period of three days at anthesis stage. spikelet of the middle third of the panicle of plants were sampled in each cultivar at the end of the thermal treatment.
GSE119109	GSM3358184	SRR7760296	single-end	spikelet	anthesis_stage	high temperature treatment (38C) for 7 hrs	IRGA_428	Transcriptome analysis of flooded rice spikelet in response to high temperature at flowering	Illumina HiSeq 2500	Two rice cultivars (BR-IRGA 409 and IRGA 428) were submitted to daytime c (9 am to 16 pm) during a period of three days at anthesis stage. spikelet of the middle third of the panicle of plants were sampled in each cultivar at the end of the thermal treatment.
GSE119109	GSM3358185	SRR7760297	single-end	spikelet	anthesis_stage	control condition (29C) for 7 hrs	BR-IRGA_409	Transcriptome analysis of flooded rice spikelet in response to high temperature at flowering	Illumina HiSeq 2500	Two rice cultivars (BR-IRGA 409 and IRGA 428) were submitted to daytime c (9 am to 16 pm) during a period of three days at anthesis stage. spikelet of the middle third of the panicle of plants were sampled in each cultivar at the end of the thermal treatment.
GSE119109	GSM3358186	SRR7760298	single-end	spikelet	anthesis_stage	control condition (29C) for 7 hrs	BR-IRGA_409	Transcriptome analysis of flooded rice spikelet in response to high temperature at flowering	Illumina HiSeq 2500	Two rice cultivars (BR-IRGA 409 and IRGA 428) were submitted to daytime c (9 am to 16 pm) during a period of three days at anthesis stage. spikelet of the middle third of the panicle of plants were sampled in each cultivar at the end of the thermal treatment.
GSE119109	GSM3358187	SRR7760299	single-end	spikelet	anthesis_stage	control condition (29C) for 7 hrs	BR-IRGA_409	Transcriptome analysis of flooded rice spikelet in response to high temperature at flowering	Illumina HiSeq 2500	Two rice cultivars (BR-IRGA 409 and IRGA 428) were submitted to daytime c (9 am to 16 pm) during a period of three days at anthesis stage. spikelet of the middle third of the panicle of plants were sampled in each cultivar at the end of the thermal treatment.
GSE119109	GSM3358188	SRR7760300	single-end	spikelet	anthesis_stage	high temperature treatment (38C) for 7 hrs	BR-IRGA_409	Transcriptome analysis of flooded rice spikelet in response to high temperature at flowering	Illumina HiSeq 2500	Two rice cultivars (BR-IRGA 409 and IRGA 428) were submitted to daytime c (9 am to 16 pm) during a period of three days at anthesis stage. spikelet of the middle third of the panicle of plants were sampled in each cultivar at the end of the thermal treatment.
GSE119109	GSM3358189	SRR7760301	single-end	spikelet	anthesis_stage	high temperature treatment (38C) for 7 hrs	BR-IRGA_409	Transcriptome analysis of flooded rice spikelet in response to high temperature at flowering	Illumina HiSeq 2500	Two rice cultivars (BR-IRGA 409 and IRGA 428) were submitted to daytime c (9 am to 16 pm) during a period of three days at anthesis stage. spikelet of the middle third of the panicle of plants were sampled in each cultivar at the end of the thermal treatment.
GSE119109	GSM3358190	SRR7760302	single-end	spikelet	anthesis_stage	high temperature treatment (38C) for 7 hrs	BR-IRGA_409	Transcriptome analysis of flooded rice spikelet in response to high temperature at flowering	Illumina HiSeq 2500	Two rice cultivars (BR-IRGA 409 and IRGA 428) were submitted to daytime c (9 am to 16 pm) during a period of three days at anthesis stage. spikelet of the middle third of the panicle of plants were sampled in each cultivar at the end of the thermal treatment.
GSE84077	GSM2226844	SRR3745125	single-end	anther	anthesis_stage	wt	no_collect	Genome-wide identification of genes involved in phytochrome (phy)-mediated anther development in rice	Illumina HiSeq 2500	Seeds were surface sterilized in 70% (v/v) ethanol for 30 s, then they were transferred into 5% NaClO (v/v) for 20 min. After six times rinsed in sterile double-distilled water, seeds were incubated in the dark at 28C for 3 days to induce germination. During July to August, seedlings were transferred to the soil in the farm of Shandong Academy of Agricultrual Sciences in Jinan, Shandong, China (latitude 3640＊N; longitude 11700＊E). Anthers from the four plant materials were collected before anthesis, they were stored firstly in liquid nitrogen, and then transferred to -80C refrigerator until RNA extraction.
GSE84077	GSM2226845	SRR3745126	single-end	anther	anthesis_stage	wt	no_collect	Genome-wide identification of genes involved in phytochrome (phy)-mediated anther development in rice	Illumina HiSeq 2500	Seeds were surface sterilized in 70% (v/v) ethanol for 30 s, then they were transferred into 5% NaClO (v/v) for 20 min. After six times rinsed in sterile double-distilled water, seeds were incubated in the dark at 28C for 3 days to induce germination. During July to August, seedlings were transferred to the soil in the farm of Shandong Academy of Agricultrual Sciences in Jinan, Shandong, China (latitude 3640＊N; longitude 11700＊E). Anthers from the four plant materials were collected before anthesis, they were stored firstly in liquid nitrogen, and then transferred to -80C refrigerator until RNA extraction.
GSE84077	GSM2226846	SRR3745127	single-end	anther	anthesis_stage	wt	no_collect	Genome-wide identification of genes involved in phytochrome (phy)-mediated anther development in rice	Illumina HiSeq 2500	Seeds were surface sterilized in 70% (v/v) ethanol for 30 s, then they were transferred into 5% NaClO (v/v) for 20 min. After six times rinsed in sterile double-distilled water, seeds were incubated in the dark at 28C for 3 days to induce germination. During July to August, seedlings were transferred to the soil in the farm of Shandong Academy of Agricultrual Sciences in Jinan, Shandong, China (latitude 3640＊N; longitude 11700＊E). Anthers from the four plant materials were collected before anthesis, they were stored firstly in liquid nitrogen, and then transferred to -80C refrigerator until RNA extraction.
GSE49633	GSM1203190	SRR1633182	single-end	panicle	Inflorescence_7_stage	WT	Dongjin	The Polycomb Group Gene EMF2B is required for meristem determinacy and organ specification in rice flowers.	Illumina Genome Analyzer Ilx	All rice plants were grown in greenhouse conditions of 30oC daytime and 25oC nighttime temperatures. Light regimes were dictated by natural light conditions.
GSE49633	GSM1203190	SRR1633183	single-end	panicle	Inflorescence_7_stage	WT	Dongjin	The Polycomb Group Gene EMF2B is required for meristem determinacy and organ specification in rice flowers.	Illumina Genome Analyzer Ilx	All rice plants were grown in greenhouse conditions of 30oC daytime and 25oC nighttime temperatures. Light regimes were dictated by natural light conditions.
GSE49633	GSM1203190	SRR1633184	single-end	panicle	Inflorescence_7_stage	WT	Dongjin	The Polycomb Group Gene EMF2B is required for meristem determinacy and organ specification in rice flowers.	Illumina Genome Analyzer Ilx	All rice plants were grown in greenhouse conditions of 30oC daytime and 25oC nighttime temperatures. Light regimes were dictated by natural light conditions.
GSE49633	GSM1203191	SRR1633185	single-end	panicle	Inflorescence_7_stage	WT	Dongjin	The Polycomb Group Gene EMF2B is required for meristem determinacy and organ specification in rice flowers.	Illumina Genome Analyzer Ilx	All rice plants were grown in greenhouse conditions of 30oC daytime and 25oC nighttime temperatures. Light regimes were dictated by natural light conditions.
GSE49633	GSM1203191	SRR1633186	single-end	panicle	Inflorescence_7_stage	WT	Dongjin	The Polycomb Group Gene EMF2B is required for meristem determinacy and organ specification in rice flowers.	Illumina Genome Analyzer Ilx	All rice plants were grown in greenhouse conditions of 30oC daytime and 25oC nighttime temperatures. Light regimes were dictated by natural light conditions.
GSE49633	GSM1203191	SRR1633187	single-end	panicle	Inflorescence_7_stage	WT	Dongjin	The Polycomb Group Gene EMF2B is required for meristem determinacy and organ specification in rice flowers.	Illumina Genome Analyzer Ilx	All rice plants were grown in greenhouse conditions of 30oC daytime and 25oC nighttime temperatures. Light regimes were dictated by natural light conditions.
GSE116581	GSM3243307	SRR6320473	paired-end	carpel	no_collect	wt	Fengsizhan	fruitENCODE: An encyclopedia of DNA elements for fruit ripening	HiSeq X Ten	Standard non-stranded illumina RNA-Seq libraries protocol mRNA was extracted from tissue using standard protocol
GSE116581	GSM3243308	SRR6320498	paired-end	carpel	no_collect	wt	Fengsizhan	fruitENCODE: An encyclopedia of DNA elements for fruit ripening	HiSeq X Ten	Standard non-stranded illumina RNA-Seq libraries protocol mRNA was extracted from tissue using standard protocol
GSE89494	GSM2373864	SRR4947478	single-end	root	no_collect	control	IR64	Whole genome transcriptional responses to aluminum stress in rice roots	Illumina HiSeq 2000	40 uniform seedlings per genotype were grown under control condition for five days, subsequently 20 seedlings per genotype were transferred into a hydroponic solution with 80 CM of Al3+ activity for 4 hours before total root tissue was harvested for RNA extraction. Four independent biological replicates were performed.
GSE89494	GSM2373865	SRR4947479	single-end	root	no_collect	control	IR64NIL	Whole genome transcriptional responses to aluminum stress in rice roots	Illumina HiSeq 2000	40 uniform seedlings per genotype were grown under control condition for five days, subsequently 20 seedlings per genotype were transferred into a hydroponic solution with 80 CM of Al3+ activity for 4 hours before total root tissue was harvested for RNA extraction. Four independent biological replicates were performed.
GSE89494	GSM2373866	SRR4947480	single-end	root	no_collect	control	Azucena	Whole genome transcriptional responses to aluminum stress in rice roots	Illumina HiSeq 2000	40 uniform seedlings per genotype were grown under control condition for five days, subsequently 20 seedlings per genotype were transferred into a hydroponic solution with 80 CM of Al3+ activity for 4 hours before total root tissue was harvested for RNA extraction. Four independent biological replicates were performed.
GSE89494	GSM2373867	SRR4947481	single-end	root	no_collect	control	AzuNIL	Whole genome transcriptional responses to aluminum stress in rice roots	Illumina HiSeq 2000	40 uniform seedlings per genotype were grown under control condition for five days, subsequently 20 seedlings per genotype were transferred into a hydroponic solution with 80 CM of Al3+ activity for 4 hours before total root tissue was harvested for RNA extraction. Four independent biological replicates were performed.
GSE89494	GSM2373868	SRR4947482	single-end	root	no_collect	Al	IR64	Whole genome transcriptional responses to aluminum stress in rice roots	Illumina HiSeq 2000	40 uniform seedlings per genotype were grown under control condition for five days, subsequently 20 seedlings per genotype were transferred into a hydroponic solution with 80 CM of Al3+ activity for 4 hours before total root tissue was harvested for RNA extraction. Four independent biological replicates were performed.
GSE89494	GSM2373869	SRR4947483	single-end	root	no_collect	Al	IR64NIL	Whole genome transcriptional responses to aluminum stress in rice roots	Illumina HiSeq 2000	40 uniform seedlings per genotype were grown under control condition for five days, subsequently 20 seedlings per genotype were transferred into a hydroponic solution with 80 CM of Al3+ activity for 4 hours before total root tissue was harvested for RNA extraction. Four independent biological replicates were performed.
GSE89494	GSM2373870	SRR4947484	single-end	root	no_collect	Al	Azucena	Whole genome transcriptional responses to aluminum stress in rice roots	Illumina HiSeq 2000	40 uniform seedlings per genotype were grown under control condition for five days, subsequently 20 seedlings per genotype were transferred into a hydroponic solution with 80 CM of Al3+ activity for 4 hours before total root tissue was harvested for RNA extraction. Four independent biological replicates were performed.
GSE89494	GSM2373871	SRR4947485	single-end	root	no_collect	Al	AzuNIL	Whole genome transcriptional responses to aluminum stress in rice roots	Illumina HiSeq 2000	40 uniform seedlings per genotype were grown under control condition for five days, subsequently 20 seedlings per genotype were transferred into a hydroponic solution with 80 CM of Al3+ activity for 4 hours before total root tissue was harvested for RNA extraction. Four independent biological replicates were performed.
GSE89494	GSM2373872	SRR4947486	single-end	root	no_collect	control	IR64	Whole genome transcriptional responses to aluminum stress in rice roots	Illumina HiSeq 2000	40 uniform seedlings per genotype were grown under control condition for five days, subsequently 20 seedlings per genotype were transferred into a hydroponic solution with 80 CM of Al3+ activity for 4 hours before total root tissue was harvested for RNA extraction. Four independent biological replicates were performed.
GSE89494	GSM2373873	SRR4947487	single-end	root	no_collect	control	IR64NIL	Whole genome transcriptional responses to aluminum stress in rice roots	Illumina HiSeq 2000	40 uniform seedlings per genotype were grown under control condition for five days, subsequently 20 seedlings per genotype were transferred into a hydroponic solution with 80 CM of Al3+ activity for 4 hours before total root tissue was harvested for RNA extraction. Four independent biological replicates were performed.
GSE89494	GSM2373874	SRR4947488	single-end	root	no_collect	control	Azucena	Whole genome transcriptional responses to aluminum stress in rice roots	Illumina HiSeq 2000	40 uniform seedlings per genotype were grown under control condition for five days, subsequently 20 seedlings per genotype were transferred into a hydroponic solution with 80 CM of Al3+ activity for 4 hours before total root tissue was harvested for RNA extraction. Four independent biological replicates were performed.
GSE89494	GSM2373875	SRR4947489	single-end	root	no_collect	control	AzuNIL	Whole genome transcriptional responses to aluminum stress in rice roots	Illumina HiSeq 2000	40 uniform seedlings per genotype were grown under control condition for five days, subsequently 20 seedlings per genotype were transferred into a hydroponic solution with 80 CM of Al3+ activity for 4 hours before total root tissue was harvested for RNA extraction. Four independent biological replicates were performed.
GSE89494	GSM2373876	SRR4947490	single-end	root	no_collect	Al	IR64	Whole genome transcriptional responses to aluminum stress in rice roots	Illumina HiSeq 2000	40 uniform seedlings per genotype were grown under control condition for five days, subsequently 20 seedlings per genotype were transferred into a hydroponic solution with 80 CM of Al3+ activity for 4 hours before total root tissue was harvested for RNA extraction. Four independent biological replicates were performed.
GSE89494	GSM2373877	SRR4947491	single-end	root	no_collect	Al	IR64NIL	Whole genome transcriptional responses to aluminum stress in rice roots	Illumina HiSeq 2000	40 uniform seedlings per genotype were grown under control condition for five days, subsequently 20 seedlings per genotype were transferred into a hydroponic solution with 80 CM of Al3+ activity for 4 hours before total root tissue was harvested for RNA extraction. Four independent biological replicates were performed.
GSE89494	GSM2373878	SRR4947492	single-end	root	no_collect	Al	Azucena	Whole genome transcriptional responses to aluminum stress in rice roots	Illumina HiSeq 2000	40 uniform seedlings per genotype were grown under control condition for five days, subsequently 20 seedlings per genotype were transferred into a hydroponic solution with 80 CM of Al3+ activity for 4 hours before total root tissue was harvested for RNA extraction. Four independent biological replicates were performed.
GSE89494	GSM2373879	SRR4947493	single-end	root	no_collect	Al	AzuNIL	Whole genome transcriptional responses to aluminum stress in rice roots	Illumina HiSeq 2000	40 uniform seedlings per genotype were grown under control condition for five days, subsequently 20 seedlings per genotype were transferred into a hydroponic solution with 80 CM of Al3+ activity for 4 hours before total root tissue was harvested for RNA extraction. Four independent biological replicates were performed.
GSE89494	GSM2373880	SRR4947494	single-end	root	no_collect	control	IR64	Whole genome transcriptional responses to aluminum stress in rice roots	Illumina HiSeq 2000	40 uniform seedlings per genotype were grown under control condition for five days, subsequently 20 seedlings per genotype were transferred into a hydroponic solution with 80 CM of Al3+ activity for 4 hours before total root tissue was harvested for RNA extraction. Four independent biological replicates were performed.
GSE89494	GSM2373881	SRR4947495	single-end	root	no_collect	control	IR64NIL	Whole genome transcriptional responses to aluminum stress in rice roots	Illumina HiSeq 2000	40 uniform seedlings per genotype were grown under control condition for five days, subsequently 20 seedlings per genotype were transferred into a hydroponic solution with 80 CM of Al3+ activity for 4 hours before total root tissue was harvested for RNA extraction. Four independent biological replicates were performed.
GSE89494	GSM2373882	SRR4947496	single-end	root	no_collect	control	Azucena	Whole genome transcriptional responses to aluminum stress in rice roots	Illumina HiSeq 2000	40 uniform seedlings per genotype were grown under control condition for five days, subsequently 20 seedlings per genotype were transferred into a hydroponic solution with 80 CM of Al3+ activity for 4 hours before total root tissue was harvested for RNA extraction. Four independent biological replicates were performed.
GSE89494	GSM2373883	SRR4947497	single-end	root	no_collect	control	AzuNIL	Whole genome transcriptional responses to aluminum stress in rice roots	Illumina HiSeq 2000	40 uniform seedlings per genotype were grown under control condition for five days, subsequently 20 seedlings per genotype were transferred into a hydroponic solution with 80 CM of Al3+ activity for 4 hours before total root tissue was harvested for RNA extraction. Four independent biological replicates were performed.
GSE89494	GSM2373884	SRR4947498	single-end	root	no_collect	Al	IR64	Whole genome transcriptional responses to aluminum stress in rice roots	Illumina HiSeq 2000	40 uniform seedlings per genotype were grown under control condition for five days, subsequently 20 seedlings per genotype were transferred into a hydroponic solution with 80 CM of Al3+ activity for 4 hours before total root tissue was harvested for RNA extraction. Four independent biological replicates were performed.
GSE89494	GSM2373885	SRR4947499	single-end	root	no_collect	Al	IR64NIL	Whole genome transcriptional responses to aluminum stress in rice roots	Illumina HiSeq 2000	40 uniform seedlings per genotype were grown under control condition for five days, subsequently 20 seedlings per genotype were transferred into a hydroponic solution with 80 CM of Al3+ activity for 4 hours before total root tissue was harvested for RNA extraction. Four independent biological replicates were performed.
GSE89494	GSM2373886	SRR4947500	single-end	root	no_collect	Al	Azucena	Whole genome transcriptional responses to aluminum stress in rice roots	Illumina HiSeq 2000	40 uniform seedlings per genotype were grown under control condition for five days, subsequently 20 seedlings per genotype were transferred into a hydroponic solution with 80 CM of Al3+ activity for 4 hours before total root tissue was harvested for RNA extraction. Four independent biological replicates were performed.
GSE89494	GSM2373887	SRR4947501	single-end	root	no_collect	Al	AzuNIL	Whole genome transcriptional responses to aluminum stress in rice roots	Illumina HiSeq 2000	40 uniform seedlings per genotype were grown under control condition for five days, subsequently 20 seedlings per genotype were transferred into a hydroponic solution with 80 CM of Al3+ activity for 4 hours before total root tissue was harvested for RNA extraction. Four independent biological replicates were performed.
GSE89494	GSM2373888	SRR4947502	single-end	root	no_collect	control	IR64	Whole genome transcriptional responses to aluminum stress in rice roots	Illumina HiSeq 2000	40 uniform seedlings per genotype were grown under control condition for five days, subsequently 20 seedlings per genotype were transferred into a hydroponic solution with 80 CM of Al3+ activity for 4 hours before total root tissue was harvested for RNA extraction. Four independent biological replicates were performed.
GSE89494	GSM2373889	SRR4947503	single-end	root	no_collect	control	IR64NIL	Whole genome transcriptional responses to aluminum stress in rice roots	Illumina HiSeq 2000	40 uniform seedlings per genotype were grown under control condition for five days, subsequently 20 seedlings per genotype were transferred into a hydroponic solution with 80 CM of Al3+ activity for 4 hours before total root tissue was harvested for RNA extraction. Four independent biological replicates were performed.
GSE89494	GSM2373890	SRR4947504	single-end	root	no_collect	control	Azucena	Whole genome transcriptional responses to aluminum stress in rice roots	Illumina HiSeq 2000	40 uniform seedlings per genotype were grown under control condition for five days, subsequently 20 seedlings per genotype were transferred into a hydroponic solution with 80 CM of Al3+ activity for 4 hours before total root tissue was harvested for RNA extraction. Four independent biological replicates were performed.
GSE89494	GSM2373891	SRR4947505	single-end	root	no_collect	control	AzuNIL	Whole genome transcriptional responses to aluminum stress in rice roots	Illumina HiSeq 2000	40 uniform seedlings per genotype were grown under control condition for five days, subsequently 20 seedlings per genotype were transferred into a hydroponic solution with 80 CM of Al3+ activity for 4 hours before total root tissue was harvested for RNA extraction. Four independent biological replicates were performed.
GSE89494	GSM2373892	SRR4947506	single-end	root	no_collect	Al	IR64	Whole genome transcriptional responses to aluminum stress in rice roots	Illumina HiSeq 2000	40 uniform seedlings per genotype were grown under control condition for five days, subsequently 20 seedlings per genotype were transferred into a hydroponic solution with 80 CM of Al3+ activity for 4 hours before total root tissue was harvested for RNA extraction. Four independent biological replicates were performed.
GSE89494	GSM2373893	SRR4947507	single-end	root	no_collect	Al	IR64NIL	Whole genome transcriptional responses to aluminum stress in rice roots	Illumina HiSeq 2000	40 uniform seedlings per genotype were grown under control condition for five days, subsequently 20 seedlings per genotype were transferred into a hydroponic solution with 80 CM of Al3+ activity for 4 hours before total root tissue was harvested for RNA extraction. Four independent biological replicates were performed.
GSE89494	GSM2373894	SRR4947508	single-end	root	no_collect	Al	Azucena	Whole genome transcriptional responses to aluminum stress in rice roots	Illumina HiSeq 2000	40 uniform seedlings per genotype were grown under control condition for five days, subsequently 20 seedlings per genotype were transferred into a hydroponic solution with 80 CM of Al3+ activity for 4 hours before total root tissue was harvested for RNA extraction. Four independent biological replicates were performed.
GSE89494	GSM2373895	SRR4947509	single-end	root	no_collect	Al	AzuNIL	Whole genome transcriptional responses to aluminum stress in rice roots	Illumina HiSeq 2000	40 uniform seedlings per genotype were grown under control condition for five days, subsequently 20 seedlings per genotype were transferred into a hydroponic solution with 80 CM of Al3+ activity for 4 hours before total root tissue was harvested for RNA extraction. Four independent biological replicates were performed.
GSE109341	GSM2940029	SRR6502085	single-end	leaves	no_collect	100 mM NaCl	Vialone_Nano	Adaptation Versus Senescence In Rice: Early Signalling Events Play A Role In Inducing Specificity And Tolerance To Salinity	Illumina HiSeq 2000	Seedlings at the V2 stage were grown with or without the saline solution (NaCl:MgSO4:CaCl2:NaNO2 = 10:2:1:1). Leaves (blade + sheath), stems and roots (thoroughly washed) were collected. Samples (leaves and roots) were frozen in liquid nitrogen. To minimize the effect of individual polymorphisms, each biological replicate was a mix of 6 plants. Three biological replicates were used in each experiment.
GSE109341	GSM2940030	SRR6502086	single-end	leaves	no_collect	100 mM NaCl	Vialone_Nano	Adaptation Versus Senescence In Rice: Early Signalling Events Play A Role In Inducing Specificity And Tolerance To Salinity	Illumina HiSeq 2000	Seedlings at the V2 stage were grown with or without the saline solution (NaCl:MgSO4:CaCl2:NaNO2 = 10:2:1:1). Leaves (blade + sheath), stems and roots (thoroughly washed) were collected. Samples (leaves and roots) were frozen in liquid nitrogen. To minimize the effect of individual polymorphisms, each biological replicate was a mix of 6 plants. Three biological replicates were used in each experiment.
GSE109341	GSM2940031	SRR6502087	single-end	leaves	no_collect	100 mM NaCl	Vialone_Nano	Adaptation Versus Senescence In Rice: Early Signalling Events Play A Role In Inducing Specificity And Tolerance To Salinity	Illumina HiSeq 2000	Seedlings at the V2 stage were grown with or without the saline solution (NaCl:MgSO4:CaCl2:NaNO2 = 10:2:1:1). Leaves (blade + sheath), stems and roots (thoroughly washed) were collected. Samples (leaves and roots) were frozen in liquid nitrogen. To minimize the effect of individual polymorphisms, each biological replicate was a mix of 6 plants. Three biological replicates were used in each experiment.
GSE109341	GSM2940032	SRR6502088	single-end	leaves	no_collect	control	Vialone_Nano	Adaptation Versus Senescence In Rice: Early Signalling Events Play A Role In Inducing Specificity And Tolerance To Salinity	Illumina HiSeq 2000	Seedlings at the V2 stage were grown with or without the saline solution (NaCl:MgSO4:CaCl2:NaNO2 = 10:2:1:1). Leaves (blade + sheath), stems and roots (thoroughly washed) were collected. Samples (leaves and roots) were frozen in liquid nitrogen. To minimize the effect of individual polymorphisms, each biological replicate was a mix of 6 plants. Three biological replicates were used in each experiment.
GSE109341	GSM2940033	SRR6502089	single-end	leaves	no_collect	control	Vialone_Nano	Adaptation Versus Senescence In Rice: Early Signalling Events Play A Role In Inducing Specificity And Tolerance To Salinity	Illumina HiSeq 2000	Seedlings at the V2 stage were grown with or without the saline solution (NaCl:MgSO4:CaCl2:NaNO2 = 10:2:1:1). Leaves (blade + sheath), stems and roots (thoroughly washed) were collected. Samples (leaves and roots) were frozen in liquid nitrogen. To minimize the effect of individual polymorphisms, each biological replicate was a mix of 6 plants. Three biological replicates were used in each experiment.
GSE109341	GSM2940034	SRR6502090	single-end	leaves	no_collect	control	Vialone_Nano	Adaptation Versus Senescence In Rice: Early Signalling Events Play A Role In Inducing Specificity And Tolerance To Salinity	Illumina HiSeq 2000	Seedlings at the V2 stage were grown with or without the saline solution (NaCl:MgSO4:CaCl2:NaNO2 = 10:2:1:1). Leaves (blade + sheath), stems and roots (thoroughly washed) were collected. Samples (leaves and roots) were frozen in liquid nitrogen. To minimize the effect of individual polymorphisms, each biological replicate was a mix of 6 plants. Three biological replicates were used in each experiment.
GSE109341	GSM2940035	SRR6502091	single-end	root	no_collect	100 mM NaCl	Vialone_Nano	Adaptation Versus Senescence In Rice: Early Signalling Events Play A Role In Inducing Specificity And Tolerance To Salinity	Illumina HiSeq 2000	Seedlings at the V2 stage were grown with or without the saline solution (NaCl:MgSO4:CaCl2:NaNO2 = 10:2:1:1). Leaves (blade + sheath), stems and roots (thoroughly washed) were collected. Samples (leaves and roots) were frozen in liquid nitrogen. To minimize the effect of individual polymorphisms, each biological replicate was a mix of 6 plants. Three biological replicates were used in each experiment.
GSE109341	GSM2940036	SRR6502092	single-end	root	no_collect	100 mM NaCl	Vialone_Nano	Adaptation Versus Senescence In Rice: Early Signalling Events Play A Role In Inducing Specificity And Tolerance To Salinity	Illumina HiSeq 2000	Seedlings at the V2 stage were grown with or without the saline solution (NaCl:MgSO4:CaCl2:NaNO2 = 10:2:1:1). Leaves (blade + sheath), stems and roots (thoroughly washed) were collected. Samples (leaves and roots) were frozen in liquid nitrogen. To minimize the effect of individual polymorphisms, each biological replicate was a mix of 6 plants. Three biological replicates were used in each experiment.
GSE109341	GSM2940037	SRR6502093	single-end	root	no_collect	100 mM NaCl	Vialone_Nano	Adaptation Versus Senescence In Rice: Early Signalling Events Play A Role In Inducing Specificity And Tolerance To Salinity	Illumina HiSeq 2000	Seedlings at the V2 stage were grown with or without the saline solution (NaCl:MgSO4:CaCl2:NaNO2 = 10:2:1:1). Leaves (blade + sheath), stems and roots (thoroughly washed) were collected. Samples (leaves and roots) were frozen in liquid nitrogen. To minimize the effect of individual polymorphisms, each biological replicate was a mix of 6 plants. Three biological replicates were used in each experiment.
GSE109341	GSM2940038	SRR6502094	single-end	root	no_collect	control	Vialone_Nano	Adaptation Versus Senescence In Rice: Early Signalling Events Play A Role In Inducing Specificity And Tolerance To Salinity	Illumina HiSeq 2000	Seedlings at the V2 stage were grown with or without the saline solution (NaCl:MgSO4:CaCl2:NaNO2 = 10:2:1:1). Leaves (blade + sheath), stems and roots (thoroughly washed) were collected. Samples (leaves and roots) were frozen in liquid nitrogen. To minimize the effect of individual polymorphisms, each biological replicate was a mix of 6 plants. Three biological replicates were used in each experiment.
GSE109341	GSM2940039	SRR6502095	single-end	root	no_collect	control	Vialone_Nano	Adaptation Versus Senescence In Rice: Early Signalling Events Play A Role In Inducing Specificity And Tolerance To Salinity	Illumina HiSeq 2000	Seedlings at the V2 stage were grown with or without the saline solution (NaCl:MgSO4:CaCl2:NaNO2 = 10:2:1:1). Leaves (blade + sheath), stems and roots (thoroughly washed) were collected. Samples (leaves and roots) were frozen in liquid nitrogen. To minimize the effect of individual polymorphisms, each biological replicate was a mix of 6 plants. Three biological replicates were used in each experiment.
GSE109341	GSM2940040	SRR6502096	single-end	root	no_collect	control	Vialone_Nano	Adaptation Versus Senescence In Rice: Early Signalling Events Play A Role In Inducing Specificity And Tolerance To Salinity	Illumina HiSeq 2000	Seedlings at the V2 stage were grown with or without the saline solution (NaCl:MgSO4:CaCl2:NaNO2 = 10:2:1:1). Leaves (blade + sheath), stems and roots (thoroughly washed) were collected. Samples (leaves and roots) were frozen in liquid nitrogen. To minimize the effect of individual polymorphisms, each biological replicate was a mix of 6 plants. Three biological replicates were used in each experiment.
GSE109341	GSM2940041	SRR6502097	single-end	leaves	no_collect	100 mM NaCl	Baldo	Adaptation Versus Senescence In Rice: Early Signalling Events Play A Role In Inducing Specificity And Tolerance To Salinity	Illumina HiSeq 2000	Seedlings at the V2 stage were grown with or without the saline solution (NaCl:MgSO4:CaCl2:NaNO2 = 10:2:1:1). Leaves (blade + sheath), stems and roots (thoroughly washed) were collected. Samples (leaves and roots) were frozen in liquid nitrogen. To minimize the effect of individual polymorphisms, each biological replicate was a mix of 6 plants. Three biological replicates were used in each experiment.
GSE109341	GSM2940042	SRR6502098	single-end	leaves	no_collect	100 mM NaCl	Baldo	Adaptation Versus Senescence In Rice: Early Signalling Events Play A Role In Inducing Specificity And Tolerance To Salinity	Illumina HiSeq 2000	Seedlings at the V2 stage were grown with or without the saline solution (NaCl:MgSO4:CaCl2:NaNO2 = 10:2:1:1). Leaves (blade + sheath), stems and roots (thoroughly washed) were collected. Samples (leaves and roots) were frozen in liquid nitrogen. To minimize the effect of individual polymorphisms, each biological replicate was a mix of 6 plants. Three biological replicates were used in each experiment.
GSE109341	GSM2940043	SRR6502099	single-end	leaves	no_collect	100 mM NaCl	Baldo	Adaptation Versus Senescence In Rice: Early Signalling Events Play A Role In Inducing Specificity And Tolerance To Salinity	Illumina HiSeq 2000	Seedlings at the V2 stage were grown with or without the saline solution (NaCl:MgSO4:CaCl2:NaNO2 = 10:2:1:1). Leaves (blade + sheath), stems and roots (thoroughly washed) were collected. Samples (leaves and roots) were frozen in liquid nitrogen. To minimize the effect of individual polymorphisms, each biological replicate was a mix of 6 plants. Three biological replicates were used in each experiment.
GSE109341	GSM2940044	SRR6502100	single-end	leaves	no_collect	control	Baldo	Adaptation Versus Senescence In Rice: Early Signalling Events Play A Role In Inducing Specificity And Tolerance To Salinity	Illumina HiSeq 2000	Seedlings at the V2 stage were grown with or without the saline solution (NaCl:MgSO4:CaCl2:NaNO2 = 10:2:1:1). Leaves (blade + sheath), stems and roots (thoroughly washed) were collected. Samples (leaves and roots) were frozen in liquid nitrogen. To minimize the effect of individual polymorphisms, each biological replicate was a mix of 6 plants. Three biological replicates were used in each experiment.
GSE109341	GSM2940045	SRR6502101	single-end	leaves	no_collect	control	Baldo	Adaptation Versus Senescence In Rice: Early Signalling Events Play A Role In Inducing Specificity And Tolerance To Salinity	Illumina HiSeq 2000	Seedlings at the V2 stage were grown with or without the saline solution (NaCl:MgSO4:CaCl2:NaNO2 = 10:2:1:1). Leaves (blade + sheath), stems and roots (thoroughly washed) were collected. Samples (leaves and roots) were frozen in liquid nitrogen. To minimize the effect of individual polymorphisms, each biological replicate was a mix of 6 plants. Three biological replicates were used in each experiment.
GSE109341	GSM2940046	SRR6502102	single-end	leaves	no_collect	control	Baldo	Adaptation Versus Senescence In Rice: Early Signalling Events Play A Role In Inducing Specificity And Tolerance To Salinity	Illumina HiSeq 2000	Seedlings at the V2 stage were grown with or without the saline solution (NaCl:MgSO4:CaCl2:NaNO2 = 10:2:1:1). Leaves (blade + sheath), stems and roots (thoroughly washed) were collected. Samples (leaves and roots) were frozen in liquid nitrogen. To minimize the effect of individual polymorphisms, each biological replicate was a mix of 6 plants. Three biological replicates were used in each experiment.
GSE109341	GSM2940047	SRR6502103	single-end	root	no_collect	100 mM NaCl	Baldo	Adaptation Versus Senescence In Rice: Early Signalling Events Play A Role In Inducing Specificity And Tolerance To Salinity	Illumina HiSeq 2000	Seedlings at the V2 stage were grown with or without the saline solution (NaCl:MgSO4:CaCl2:NaNO2 = 10:2:1:1). Leaves (blade + sheath), stems and roots (thoroughly washed) were collected. Samples (leaves and roots) were frozen in liquid nitrogen. To minimize the effect of individual polymorphisms, each biological replicate was a mix of 6 plants. Three biological replicates were used in each experiment.
GSE109341	GSM2940048	SRR6502104	single-end	root	no_collect	100 mM NaCl	Baldo	Adaptation Versus Senescence In Rice: Early Signalling Events Play A Role In Inducing Specificity And Tolerance To Salinity	Illumina HiSeq 2000	Seedlings at the V2 stage were grown with or without the saline solution (NaCl:MgSO4:CaCl2:NaNO2 = 10:2:1:1). Leaves (blade + sheath), stems and roots (thoroughly washed) were collected. Samples (leaves and roots) were frozen in liquid nitrogen. To minimize the effect of individual polymorphisms, each biological replicate was a mix of 6 plants. Three biological replicates were used in each experiment.
GSE109341	GSM2940049	SRR6502105	single-end	root	no_collect	100 mM NaCl	Baldo	Adaptation Versus Senescence In Rice: Early Signalling Events Play A Role In Inducing Specificity And Tolerance To Salinity	Illumina HiSeq 2000	Seedlings at the V2 stage were grown with or without the saline solution (NaCl:MgSO4:CaCl2:NaNO2 = 10:2:1:1). Leaves (blade + sheath), stems and roots (thoroughly washed) were collected. Samples (leaves and roots) were frozen in liquid nitrogen. To minimize the effect of individual polymorphisms, each biological replicate was a mix of 6 plants. Three biological replicates were used in each experiment.
GSE109341	GSM2940050	SRR6502106	single-end	root	no_collect	control	Baldo	Adaptation Versus Senescence In Rice: Early Signalling Events Play A Role In Inducing Specificity And Tolerance To Salinity	Illumina HiSeq 2000	Seedlings at the V2 stage were grown with or without the saline solution (NaCl:MgSO4:CaCl2:NaNO2 = 10:2:1:1). Leaves (blade + sheath), stems and roots (thoroughly washed) were collected. Samples (leaves and roots) were frozen in liquid nitrogen. To minimize the effect of individual polymorphisms, each biological replicate was a mix of 6 plants. Three biological replicates were used in each experiment.
GSE109341	GSM2940051	SRR6502107	single-end	root	no_collect	control	Baldo	Adaptation Versus Senescence In Rice: Early Signalling Events Play A Role In Inducing Specificity And Tolerance To Salinity	Illumina HiSeq 2000	Seedlings at the V2 stage were grown with or without the saline solution (NaCl:MgSO4:CaCl2:NaNO2 = 10:2:1:1). Leaves (blade + sheath), stems and roots (thoroughly washed) were collected. Samples (leaves and roots) were frozen in liquid nitrogen. To minimize the effect of individual polymorphisms, each biological replicate was a mix of 6 plants. Three biological replicates were used in each experiment.
GSE109341	GSM2940052	SRR6502108	single-end	root	no_collect	control	Baldo	Adaptation Versus Senescence In Rice: Early Signalling Events Play A Role In Inducing Specificity And Tolerance To Salinity	Illumina HiSeq 2000	Seedlings at the V2 stage were grown with or without the saline solution (NaCl:MgSO4:CaCl2:NaNO2 = 10:2:1:1). Leaves (blade + sheath), stems and roots (thoroughly washed) were collected. Samples (leaves and roots) were frozen in liquid nitrogen. To minimize the effect of individual polymorphisms, each biological replicate was a mix of 6 plants. Three biological replicates were used in each experiment.
GSE101734	GSM2714232	SRR5856927	paired-end	leaves	two_half_leaf	control	9311	RNA-seq data of two half-leaf seedlings under salt treatment and control condition	Illumina HiSeq 2500	Two-half leaf seedlings were transferred to full-strength Yoshida＊s solution containing 125 mM NaCl and treated for 1h, the control grown to be collected for RNA extraction in full-strength Yoshida＊s solution.
GSE101734	GSM2714233	SRR5856928	paired-end	leaves	two_half_leaf	control	9311	RNA-seq data of two half-leaf seedlings under salt treatment and control condition	Illumina HiSeq 2500	Two-half leaf seedlings were transferred to full-strength Yoshida＊s solution containing 125 mM NaCl and treated for 1h, the control grown to be collected for RNA extraction in full-strength Yoshida＊s solution.
GSE101734	GSM2714234	SRR5856929	paired-end	leaves	two_half_leaf	control	9311	RNA-seq data of two half-leaf seedlings under salt treatment and control condition	Illumina HiSeq 2500	Two-half leaf seedlings were transferred to full-strength Yoshida＊s solution containing 125 mM NaCl and treated for 1h, the control grown to be collected for RNA extraction in full-strength Yoshida＊s solution.
GSE101734	GSM2714235	SRR5856930	paired-end	leaves	two_half_leaf	salt	9311	RNA-seq data of two half-leaf seedlings under salt treatment and control condition	Illumina HiSeq 2500	Two-half leaf seedlings were transferred to full-strength Yoshida＊s solution containing 125 mM NaCl and treated for 1h, the control grown to be collected for RNA extraction in full-strength Yoshida＊s solution.
GSE101734	GSM2714236	SRR5856931	paired-end	leaves	two_half_leaf	salt	9311	RNA-seq data of two half-leaf seedlings under salt treatment and control condition	Illumina HiSeq 2500	Two-half leaf seedlings were transferred to full-strength Yoshida＊s solution containing 125 mM NaCl and treated for 1h, the control grown to be collected for RNA extraction in full-strength Yoshida＊s solution.
GSE101734	GSM2714237	SRR5856932	paired-end	leaves	two_half_leaf	salt	9311	RNA-seq data of two half-leaf seedlings under salt treatment and control condition	Illumina HiSeq 2500	Two-half leaf seedlings were transferred to full-strength Yoshida＊s solution containing 125 mM NaCl and treated for 1h, the control grown to be collected for RNA extraction in full-strength Yoshida＊s solution.
GSE101734	GSM2714238	SRR5856933	paired-end	leaves	two_half_leaf	control	9L136	RNA-seq data of two half-leaf seedlings under salt treatment and control condition	Illumina HiSeq 2500	Two-half leaf seedlings were transferred to full-strength Yoshida＊s solution containing 125 mM NaCl and treated for 1h, the control grown to be collected for RNA extraction in full-strength Yoshida＊s solution.
GSE101734	GSM2714239	SRR5856934	paired-end	leaves	two_half_leaf	control	9L136	RNA-seq data of two half-leaf seedlings under salt treatment and control condition	Illumina HiSeq 2500	Two-half leaf seedlings were transferred to full-strength Yoshida＊s solution containing 125 mM NaCl and treated for 1h, the control grown to be collected for RNA extraction in full-strength Yoshida＊s solution.
GSE101734	GSM2714240	SRR5856935	paired-end	leaves	two_half_leaf	control	9L136	RNA-seq data of two half-leaf seedlings under salt treatment and control condition	Illumina HiSeq 2500	Two-half leaf seedlings were transferred to full-strength Yoshida＊s solution containing 125 mM NaCl and treated for 1h, the control grown to be collected for RNA extraction in full-strength Yoshida＊s solution.
GSE101734	GSM2714241	SRR5856936	paired-end	leaves	two_half_leaf	salt	9L136	RNA-seq data of two half-leaf seedlings under salt treatment and control condition	Illumina HiSeq 2500	Two-half leaf seedlings were transferred to full-strength Yoshida＊s solution containing 125 mM NaCl and treated for 1h, the control grown to be collected for RNA extraction in full-strength Yoshida＊s solution.
GSE101734	GSM2714242	SRR5856937	paired-end	leaves	two_half_leaf	salt	9L136	RNA-seq data of two half-leaf seedlings under salt treatment and control condition	Illumina HiSeq 2500	Two-half leaf seedlings were transferred to full-strength Yoshida＊s solution containing 125 mM NaCl and treated for 1h, the control grown to be collected for RNA extraction in full-strength Yoshida＊s solution.
GSE101734	GSM2714243	SRR5856938	paired-end	leaves	two_half_leaf	salt	9L136	RNA-seq data of two half-leaf seedlings under salt treatment and control condition	Illumina HiSeq 2500	Two-half leaf seedlings were transferred to full-strength Yoshida＊s solution containing 125 mM NaCl and treated for 1h, the control grown to be collected for RNA extraction in full-strength Yoshida＊s solution.
GSE104035	GSM2788025	SRR6053392	paired-end	leaves	no_collect	ethanol solvent (untreated control)	IR64	Transcriptomic analysis of gibberellic acid and paclobutrazol treated rice seedlings under submergence	Illumina HiSeq 2000	PB and GA stock solutions were made by pre-dissolving 300 mg and 150 mg powders in 2 mL 95% ethanol and then diluted to 200 mg.L-1 and 100 mg.L-1 by water, respectively. Twenty DAG seedlings were sprayed with 25ml of 200 mg.L-1 PB, 100 mg.L-1 GA, or ethanol solvent (0.1% final concentration) as control at two days prior to the submergence. Plants were completely submerged and water depth was maintained at 100 cm for 0, 4, 8, 12, and 16 days in concrete tanks (180 cm in length, 120 cm in width and 100 cm in height), respectively.
GSE104035	GSM2788026	SRR6053393	paired-end	leaves	no_collect	ethanol solvent (untreated control)	IR64	Transcriptomic analysis of gibberellic acid and paclobutrazol treated rice seedlings under submergence	Illumina HiSeq 2000	PB and GA stock solutions were made by pre-dissolving 300 mg and 150 mg powders in 2 mL 95% ethanol and then diluted to 200 mg.L-1 and 100 mg.L-1 by water, respectively. Twenty DAG seedlings were sprayed with 25ml of 200 mg.L-1 PB, 100 mg.L-1 GA, or ethanol solvent (0.1% final concentration) as control at two days prior to the submergence. Plants were completely submerged and water depth was maintained at 100 cm for 0, 4, 8, 12, and 16 days in concrete tanks (180 cm in length, 120 cm in width and 100 cm in height), respectively.
GSE104035	GSM2788027	SRR6053394	paired-end	leaves	no_collect	ethanol solvent (untreated control)	IR64	Transcriptomic analysis of gibberellic acid and paclobutrazol treated rice seedlings under submergence	Illumina HiSeq 2000	PB and GA stock solutions were made by pre-dissolving 300 mg and 150 mg powders in 2 mL 95% ethanol and then diluted to 200 mg.L-1 and 100 mg.L-1 by water, respectively. Twenty DAG seedlings were sprayed with 25ml of 200 mg.L-1 PB, 100 mg.L-1 GA, or ethanol solvent (0.1% final concentration) as control at two days prior to the submergence. Plants were completely submerged and water depth was maintained at 100 cm for 0, 4, 8, 12, and 16 days in concrete tanks (180 cm in length, 120 cm in width and 100 cm in height), respectively.
GSE104035	GSM2788028	SRR6053395	paired-end	leaves	no_collect	gibberellic acid (GA)	IR64	Transcriptomic analysis of gibberellic acid and paclobutrazol treated rice seedlings under submergence	Illumina HiSeq 2000	PB and GA stock solutions were made by pre-dissolving 300 mg and 150 mg powders in 2 mL 95% ethanol and then diluted to 200 mg.L-1 and 100 mg.L-1 by water, respectively. Twenty DAG seedlings were sprayed with 25ml of 200 mg.L-1 PB, 100 mg.L-1 GA, or ethanol solvent (0.1% final concentration) as control at two days prior to the submergence. Plants were completely submerged and water depth was maintained at 100 cm for 0, 4, 8, 12, and 16 days in concrete tanks (180 cm in length, 120 cm in width and 100 cm in height), respectively.
GSE104035	GSM2788029	SRR6053396	paired-end	leaves	no_collect	gibberellic acid (GA)	IR64	Transcriptomic analysis of gibberellic acid and paclobutrazol treated rice seedlings under submergence	Illumina HiSeq 2000	PB and GA stock solutions were made by pre-dissolving 300 mg and 150 mg powders in 2 mL 95% ethanol and then diluted to 200 mg.L-1 and 100 mg.L-1 by water, respectively. Twenty DAG seedlings were sprayed with 25ml of 200 mg.L-1 PB, 100 mg.L-1 GA, or ethanol solvent (0.1% final concentration) as control at two days prior to the submergence. Plants were completely submerged and water depth was maintained at 100 cm for 0, 4, 8, 12, and 16 days in concrete tanks (180 cm in length, 120 cm in width and 100 cm in height), respectively.
GSE104035	GSM2788030	SRR6053397	paired-end	leaves	no_collect	gibberellic acid (GA)	IR64	Transcriptomic analysis of gibberellic acid and paclobutrazol treated rice seedlings under submergence	Illumina HiSeq 2000	PB and GA stock solutions were made by pre-dissolving 300 mg and 150 mg powders in 2 mL 95% ethanol and then diluted to 200 mg.L-1 and 100 mg.L-1 by water, respectively. Twenty DAG seedlings were sprayed with 25ml of 200 mg.L-1 PB, 100 mg.L-1 GA, or ethanol solvent (0.1% final concentration) as control at two days prior to the submergence. Plants were completely submerged and water depth was maintained at 100 cm for 0, 4, 8, 12, and 16 days in concrete tanks (180 cm in length, 120 cm in width and 100 cm in height), respectively.
GSE104035	GSM2788031	SRR6053398	paired-end	leaves	no_collect	Paclobutrazol (PB)	IR64	Transcriptomic analysis of gibberellic acid and paclobutrazol treated rice seedlings under submergence	Illumina HiSeq 2000	PB and GA stock solutions were made by pre-dissolving 300 mg and 150 mg powders in 2 mL 95% ethanol and then diluted to 200 mg.L-1 and 100 mg.L-1 by water, respectively. Twenty DAG seedlings were sprayed with 25ml of 200 mg.L-1 PB, 100 mg.L-1 GA, or ethanol solvent (0.1% final concentration) as control at two days prior to the submergence. Plants were completely submerged and water depth was maintained at 100 cm for 0, 4, 8, 12, and 16 days in concrete tanks (180 cm in length, 120 cm in width and 100 cm in height), respectively.
GSE104035	GSM2788032	SRR6053399	paired-end	leaves	no_collect	Paclobutrazol (PB)	IR64	Transcriptomic analysis of gibberellic acid and paclobutrazol treated rice seedlings under submergence	Illumina HiSeq 2000	PB and GA stock solutions were made by pre-dissolving 300 mg and 150 mg powders in 2 mL 95% ethanol and then diluted to 200 mg.L-1 and 100 mg.L-1 by water, respectively. Twenty DAG seedlings were sprayed with 25ml of 200 mg.L-1 PB, 100 mg.L-1 GA, or ethanol solvent (0.1% final concentration) as control at two days prior to the submergence. Plants were completely submerged and water depth was maintained at 100 cm for 0, 4, 8, 12, and 16 days in concrete tanks (180 cm in length, 120 cm in width and 100 cm in height), respectively.
GSE104035	GSM2788033	SRR6053400	paired-end	leaves	no_collect	Paclobutrazol (PB)	IR64	Transcriptomic analysis of gibberellic acid and paclobutrazol treated rice seedlings under submergence	Illumina HiSeq 2000	PB and GA stock solutions were made by pre-dissolving 300 mg and 150 mg powders in 2 mL 95% ethanol and then diluted to 200 mg.L-1 and 100 mg.L-1 by water, respectively. Twenty DAG seedlings were sprayed with 25ml of 200 mg.L-1 PB, 100 mg.L-1 GA, or ethanol solvent (0.1% final concentration) as control at two days prior to the submergence. Plants were completely submerged and water depth was maintained at 100 cm for 0, 4, 8, 12, and 16 days in concrete tanks (180 cm in length, 120 cm in width and 100 cm in height), respectively.
GSE104928	GSM2810186	SRR6168973	paired-end	leaves	Seedling_stage	none (control)	Caidao	Transcriptome analysis reveals important alkali-responsive genes and key pathways in rice under alkaline stress	Illumina HiSeq 2000	Fourteen days after germination, the seedlings of WD20342 and Caidao were subjected to control and alkaline stress treatment (marked as WDT and CDT, respectively). The seedlings of WD20342 and Caidao were kept grown on RO water served as controls (marked as WD and CD, respectively). For alkaline stress treatment, seedlings were transferred on their 96-well plates into containers filled with 0.5% Na2CO3 solution for 36h.
GSE104928	GSM2810187	SRR6168974	paired-end	leaves	Seedling_stage	none (control)	Caidao	Transcriptome analysis reveals important alkali-responsive genes and key pathways in rice under alkaline stress	Illumina HiSeq 2000	Fourteen days after germination, the seedlings of WD20342 and Caidao were subjected to control and alkaline stress treatment (marked as WDT and CDT, respectively). The seedlings of WD20342 and Caidao were kept grown on RO water served as controls (marked as WD and CD, respectively). For alkaline stress treatment, seedlings were transferred on their 96-well plates into containers filled with 0.5% Na2CO3 solution for 36h.
GSE104928	GSM2810188	SRR6168975	paired-end	leaves	Seedling_stage	none (control)	Caidao	Transcriptome analysis reveals important alkali-responsive genes and key pathways in rice under alkaline stress	Illumina HiSeq 2000	Fourteen days after germination, the seedlings of WD20342 and Caidao were subjected to control and alkaline stress treatment (marked as WDT and CDT, respectively). The seedlings of WD20342 and Caidao were kept grown on RO water served as controls (marked as WD and CD, respectively). For alkaline stress treatment, seedlings were transferred on their 96-well plates into containers filled with 0.5% Na2CO3 solution for 36h.
GSE104928	GSM2810189	SRR6168976	paired-end	leaves	Seedling_stage	0.5% Na2CO3 solution for 36h	Caidao	Transcriptome analysis reveals important alkali-responsive genes and key pathways in rice under alkaline stress	Illumina HiSeq 2000	Fourteen days after germination, the seedlings of WD20342 and Caidao were subjected to control and alkaline stress treatment (marked as WDT and CDT, respectively). The seedlings of WD20342 and Caidao were kept grown on RO water served as controls (marked as WD and CD, respectively). For alkaline stress treatment, seedlings were transferred on their 96-well plates into containers filled with 0.5% Na2CO3 solution for 36h.
GSE104928	GSM2810190	SRR6168977	paired-end	leaves	Seedling_stage	0.5% Na2CO3 solution for 36h	Caidao	Transcriptome analysis reveals important alkali-responsive genes and key pathways in rice under alkaline stress	Illumina HiSeq 2000	Fourteen days after germination, the seedlings of WD20342 and Caidao were subjected to control and alkaline stress treatment (marked as WDT and CDT, respectively). The seedlings of WD20342 and Caidao were kept grown on RO water served as controls (marked as WD and CD, respectively). For alkaline stress treatment, seedlings were transferred on their 96-well plates into containers filled with 0.5% Na2CO3 solution for 36h.
GSE104928	GSM2810191	SRR6168978	paired-end	leaves	Seedling_stage	0.5% Na2CO3 solution for 36h	Caidao	Transcriptome analysis reveals important alkali-responsive genes and key pathways in rice under alkaline stress	Illumina HiSeq 2000	Fourteen days after germination, the seedlings of WD20342 and Caidao were subjected to control and alkaline stress treatment (marked as WDT and CDT, respectively). The seedlings of WD20342 and Caidao were kept grown on RO water served as controls (marked as WD and CD, respectively). For alkaline stress treatment, seedlings were transferred on their 96-well plates into containers filled with 0.5% Na2CO3 solution for 36h.
GSE104928	GSM2810192	SRR6168979	paired-end	leaves	Seedling_stage	none (control)	WD20342	Transcriptome analysis reveals important alkali-responsive genes and key pathways in rice under alkaline stress	Illumina HiSeq 2000	Fourteen days after germination, the seedlings of WD20342 and Caidao were subjected to control and alkaline stress treatment (marked as WDT and CDT, respectively). The seedlings of WD20342 and Caidao were kept grown on RO water served as controls (marked as WD and CD, respectively). For alkaline stress treatment, seedlings were transferred on their 96-well plates into containers filled with 0.5% Na2CO3 solution for 36h.
GSE104928	GSM2810193	SRR6168980	paired-end	leaves	Seedling_stage	none (control)	WD20342	Transcriptome analysis reveals important alkali-responsive genes and key pathways in rice under alkaline stress	Illumina HiSeq 2000	Fourteen days after germination, the seedlings of WD20342 and Caidao were subjected to control and alkaline stress treatment (marked as WDT and CDT, respectively). The seedlings of WD20342 and Caidao were kept grown on RO water served as controls (marked as WD and CD, respectively). For alkaline stress treatment, seedlings were transferred on their 96-well plates into containers filled with 0.5% Na2CO3 solution for 36h.
GSE104928	GSM2810194	SRR6168981	paired-end	leaves	Seedling_stage	none (control)	WD20342	Transcriptome analysis reveals important alkali-responsive genes and key pathways in rice under alkaline stress	Illumina HiSeq 2000	Fourteen days after germination, the seedlings of WD20342 and Caidao were subjected to control and alkaline stress treatment (marked as WDT and CDT, respectively). The seedlings of WD20342 and Caidao were kept grown on RO water served as controls (marked as WD and CD, respectively). For alkaline stress treatment, seedlings were transferred on their 96-well plates into containers filled with 0.5% Na2CO3 solution for 36h.
GSE104928	GSM2810195	SRR6168982	paired-end	leaves	Seedling_stage	0.5% Na2CO3 solution for 36h	WD20342	Transcriptome analysis reveals important alkali-responsive genes and key pathways in rice under alkaline stress	Illumina HiSeq 2000	Fourteen days after germination, the seedlings of WD20342 and Caidao were subjected to control and alkaline stress treatment (marked as WDT and CDT, respectively). The seedlings of WD20342 and Caidao were kept grown on RO water served as controls (marked as WD and CD, respectively). For alkaline stress treatment, seedlings were transferred on their 96-well plates into containers filled with 0.5% Na2CO3 solution for 36h.
GSE104928	GSM2810196	SRR6168983	paired-end	leaves	Seedling_stage	0.5% Na2CO3 solution for 36h	WD20342	Transcriptome analysis reveals important alkali-responsive genes and key pathways in rice under alkaline stress	Illumina HiSeq 2000	Fourteen days after germination, the seedlings of WD20342 and Caidao were subjected to control and alkaline stress treatment (marked as WDT and CDT, respectively). The seedlings of WD20342 and Caidao were kept grown on RO water served as controls (marked as WD and CD, respectively). For alkaline stress treatment, seedlings were transferred on their 96-well plates into containers filled with 0.5% Na2CO3 solution for 36h.
GSE104928	GSM2810197	SRR6168984	paired-end	leaves	Seedling_stage	0.5% Na2CO3 solution for 36h	WD20342	Transcriptome analysis reveals important alkali-responsive genes and key pathways in rice under alkaline stress	Illumina HiSeq 2000	Fourteen days after germination, the seedlings of WD20342 and Caidao were subjected to control and alkaline stress treatment (marked as WDT and CDT, respectively). The seedlings of WD20342 and Caidao were kept grown on RO water served as controls (marked as WD and CD, respectively). For alkaline stress treatment, seedlings were transferred on their 96-well plates into containers filled with 0.5% Na2CO3 solution for 36h.