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. Y 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. Y 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 Y 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. Y 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. Y GSE115371 GSM3176788 SRR7265400 single-end coleoptile no_collect 2dA 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. N GSE115371 GSM3176791 SRR7265403 single-end coleoptile no_collect 2dN 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. N GSE115371 GSM3176794 SRR7265406 single-end coleoptile no_collect 3dA 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. N GSE115371 GSM3176797 SRR7265409 single-end coleoptile no_collect 3dN 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. N GSE115371 GSM3176800 SRR7265412 single-end coleoptile no_collect 4dA 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. N GSE115371 GSM3176803 SRR7265415 single-end coleoptile no_collect 4dN 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. N GSE115371 GSM3176806 SRR7265418 single-end coleoptile no_collect 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. N 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. N GSE115371 GSM3176761 SRR7265373 single-end embryo no_collect dry seed 0 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. Y GSE115371 GSM3176764 SRR7265376 single-end embryo no_collect 1hA 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. N GSE115371 GSM3176767 SRR7265379 single-end embryo no_collect 1hN 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. N GSE115371 GSM3176770 SRR7265382 single-end embryo no_collect 3hA 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. N GSE115371 GSM3176773 SRR7265385 single-end embryo no_collect 3hN 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. N GSE115371 GSM3176776 SRR7265388 single-end embryo no_collect 12hA 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. N GSE115371 GSM3176779 SRR7265391 single-end embryo no_collect 12hN 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. N GSE115371 GSM3176782 SRR7265394 single-end embryo no_collect 24hA 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. N GSE115371 GSM3176785 SRR7265397 single-end embryo no_collect 24hN 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. N 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 Y 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. Y 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. N 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. N 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. N 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. N 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. N 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. N 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. N 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. Y GSE121269 GSM3430618 SRR8060835 paired-end leaf 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. N GSE122887 GSM3487669 SRR8240824 paired-end leaf 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. Y GSE76051 GSM1973422 SRR3015592 paired-end leaf 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. N GSE75131 GSM1943702 SRR2922622 single-end leaf 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. N GSE67588 GSM1650074 SRR1952778 single-end leaf 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. N GSE67588 GSM1650080 SRR1952784 single-end leaf 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. N GSE67588 GSM1650083 SRR1952787 single-end leaf 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. N GSE67588 GSM1650086 SRR1952790 single-end leaf 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. N GSE67588 GSM1650089 SRR1952793 single-end leaf 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. N GSE67588 GSM1650092 SRR1952796 single-end leaf 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. N GSE67588 GSM1650095 SRR1952799 single-end leaf 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. N GSE67588 GSM1650098 SRR1952802 single-end leaf 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. N GSE67588 GSM1650101 SRR1952805 single-end leaf 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. N GSE67588 GSM1650104 SRR1952808 single-end leaf 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. N GSE65025 GSM1585996 SRR1761788 single-end leaf 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. N GSE65024 GSM1585988 SRR1761780 single-end leaf 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. N GSE65022 GSM1585980 SRR1761528 single-end leaf 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. N GSE38480 GSM943197 SRR504365 single-end leaf 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 N GSE108504 GSM2902389 SRR6417964 paired-end leaf 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. N GSE108504 GSM2902392 SRR6417967 paired-end leaf 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. N GSE78972 GSM2082857 SRR3209769 single-end leaf 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. N GSE78972 GSM2082861 SRR3209773 single-end leaf 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. N GSE78972 GSM2082865 SRR3209777 single-end leaf 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. N GSE78972 GSM2082866 SRR3209778 single-end leaf 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. N GSE126961 GSM3618871 SRR8611900 paired-end leaf 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. N GSE126961 GSM3618880 SRR8611909 paired-end leaf 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. N GSE106150 GSM2830514 SRR6216698 paired-end leaf 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. N GSE56463 GSM1361893 SRR1213692 single-end leaf 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. N GSE56463 GSM1361894 SRR1213693 single-end leaf 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. N GSE109341 GSM2940029 SRR6502085 single-end leaf 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. N GSE109341 GSM2940032 SRR6502088 single-end leaf 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. N GSE109341 GSM2940041 SRR6502097 single-end leaf 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. N GSE109341 GSM2940044 SRR6502100 single-end leaf 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. N GSE101734 GSM2714232 SRR5856927 paired-end leaf 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. N GSE101734 GSM2714235 SRR5856930 paired-end leaf 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. N GSE101734 GSM2714238 SRR5856933 paired-end leaf 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. N GSE101734 GSM2714241 SRR5856936 paired-end leaf 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. N GSE104035 GSM2788025 SRR6053392 paired-end leaf 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. N GSE104035 GSM2788028 SRR6053395 paired-end leaf 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. N GSE104035 GSM2788031 SRR6053398 paired-end leaf 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. N GSE104928 GSM2810186 SRR6168973 paired-end leaf 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. N GSE104928 GSM2810189 SRR6168976 paired-end leaf 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. N GSE104928 GSM2810192 SRR6168979 paired-end leaf 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. N GSE104928 GSM2810195 SRR6168982 paired-end leaf 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. N 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. Y 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. N 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. N 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. N 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. N 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. N 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. N 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. N 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. N 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. N 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. N 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. N 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. N 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). N 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). Y 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). N 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. Y 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. N 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. N 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. N 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. N 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. N 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. N 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. N 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. N 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. N 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. N 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. N 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. N 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. N 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. N 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. N 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. N 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. N 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. N 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. N 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. N 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. Y 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. Y 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. Y GSE108782 GSM2913197 SRR6441554 paired-end seedling 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﹝ N 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 N GSE74465 GSM1921121 SRR2857719 paired-end seedling 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. N 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. N 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. N 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. Y 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. N 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. N 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). N 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). N 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). N 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). N 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. N 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. N 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. N 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. N 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. N 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. N 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. N 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. N 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. N 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. N GSE90493 GSM2402820 SRR5052708 single-end shoot_apical_meristem 6_week_old 0_days_after_shift 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. Y GSE90493 GSM2402823 SRR5052711 single-end shoot_apical_meristem 6_week_old 4_days_after_shift 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. N GSE90493 GSM2402828 SRR5052716 single-end shoot_apical_meristem 6_week_old 8_days_after_shift 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. N GSE90493 GSM2402833 SRR5052721 single-end shoot_apical_meristem 6_week_old 12_days_after_shift 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. N GSE62554 GSM1528766 SRR1617549 single-end shoot_apical_meristem 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. N 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). N 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). N 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). N 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. Y 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. N 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. N 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. N