GEO_accession GEO_ID sample_ID data_type tissue age control(0)/treatment(1) stimulus genotype title sequencer GSE134050 GSM3934460 SRR8659980 single-end seedling 10 days 1 5 mM Pcz then with 1 mM BL 1h Williams 82 Genome-Wide transcriptional profiling elucidating the effects of Brassinosteroid in Glycine max during early vegetative development Illumina HiSeq 2000 GSE134050 GSM3934463 SRR8659977 single-end seedling 10 days 1 5 mM Pcz with 1 mM BL for 8h Williams 82 Genome-Wide transcriptional profiling elucidating the effects of Brassinosteroid in Glycine max during early vegetative development Illumina HiSeq 2000 GSE134050 GSM3934466 SRR8659971 single-end seedling 10 days 1 5 mM Pcz Williams 82 Genome-Wide transcriptional profiling elucidating the effects of Brassinosteroid in Glycine max during early vegetative development Illumina HiSeq 2000 GSE134050 GSM3934469 SRR8659968 single-end seedling 10 days 1 5 mM Pcz with 10 nM BL Williams 82 Genome-Wide transcriptional profiling elucidating the effects of Brassinosteroid in Glycine max during early vegetative development Illumina HiSeq 2000 GSE134050 GSM3934472 SRR8659974 single-end seedling 10 days 0 mock treated Williams 82 Genome-Wide transcriptional profiling elucidating the effects of Brassinosteroid in Glycine max during early vegetative development Illumina HiSeq 2000 GSE129509 GSM3714641 SRR8868860 single-end nodule emerging 0 Emerging nodules Williams 82 Treanscriptomes of emering nodules, mature nodules, emerging lateral roots, and young lateral roots in soybean Illumina HiSeq 2000 GSE129509 GSM3714644 SRR8868863 single-end root 5-7 days after germination 0 Root segment above and below emerging nodules Williams 82 Treanscriptomes of emering nodules, mature nodules, emerging lateral roots, and young lateral roots in soybean Illumina HiSeq 2000 GSE129509 GSM3714647 SRR8868866 single-end nodule mature 1 Mature nodules Williams 82 Treanscriptomes of emering nodules, mature nodules, emerging lateral roots, and young lateral roots in soybean Illumina HiSeq 2000 GSE129509 GSM3714650 SRR8868869 single-end root 5-7 days after germination 1 Root segment above and below mature nodules Williams 82 Treanscriptomes of emering nodules, mature nodules, emerging lateral roots, and young lateral roots in soybean Illumina HiSeq 2000 GSE129509 GSM3714653 SRR8868872 single-end lateral_root emerging 0 Emerging lateral roots Williams 82 Treanscriptomes of emering nodules, mature nodules, emerging lateral roots, and young lateral roots in soybean Illumina HiSeq 2000 GSE129509 GSM3714656 SRR8868875 single-end root 5-7 days after germination 0 Root segment above and below emerging lateral roots Williams 82 Treanscriptomes of emering nodules, mature nodules, emerging lateral roots, and young lateral roots in soybean Illumina HiSeq 2000 GSE129509 GSM3714659 SRR8868878 single-end lateral_root young 1 Young lateral roots Williams 82 Treanscriptomes of emering nodules, mature nodules, emerging lateral roots, and young lateral roots in soybean Illumina HiSeq 2000 GSE129509 GSM3714662 SRR8868881 single-end root 5-7 days after germination 1 Root segment above and below young lateral roots Williams 82 Treanscriptomes of emering nodules, mature nodules, emerging lateral roots, and young lateral roots in soybean Illumina HiSeq 2000 GSE111799 GSM3039920 SRR6831048 paired-end leaf 20 days after germination 0 Zn sufficient Williams 82 Transcriptomic study of soybean (Glycine max) in response to zinc deficiency Illumina HiSeq 2000 GSE111799 GSM3039922 SRR6831050 paired-end leaf 20 days after germination 1 Zn deficient Williams 82 Transcriptomic study of soybean (Glycine max) in response to zinc deficiency Illumina HiSeq 2000 GSE111799 GSM3039924 SRR6831052 paired-end root 20 days after germination 0 Zn sufficient Williams 82 Transcriptomic study of soybean (Glycine max) in response to zinc deficiency Illumina HiSeq 2000 GSE111799 GSM3039926 SRR6831054 paired-end root 20 days after germination 1 Zn deficient Williams 82 Transcriptomic study of soybean (Glycine max) in response to zinc deficiency Illumina HiSeq 2000 GSE104286 GSM2794349 SRR6078270 paired-end leaf 18 days after germination 0 Pi sufficient Williams 82 Transcriptomic study of soybean (Glycine max) leaves in response to short-term phosphorus deficiency Illumina HiSeq 2000 GSE104286 GSM2794351 SRR6078272 paired-end leaf 18 days after germination 1 Pi deficient Williams 82 Transcriptomic study of soybean (Glycine max) leaves in response to short-term phosphorus deficiency Illumina HiSeq 2000 GSE117686 GSM3307252 SRR7601335 paired-end unifoliolate_leaf 2 weeks 0 cold treatment 0 hour Williams 82 RNAseq data of two week-old soybean leaves response to cold stress Illumina HiSeq 2000 GSE117686 GSM3307255 SRR7601338 paired-end unifoliolate_leaf 2 weeks 1 cold treatment 1 hour Williams 82 RNAseq data of two week-old soybean leaves response to cold stress Illumina HiSeq 2000 GSE117686 GSM3307258 SRR7601341 paired-end unifoliolate_leaf 2 weeks 1 cold treatment 24 hour Williams 82 RNAseq data of two week-old soybean leaves response to cold stress Illumina HiSeq 2000 GSE99571 GSM2646604 SRR5639237 single-end embryo developmental stage: cotyledon 0 Soybean Cotyledon-stage Embryo Williams 82 Gene Expression Changes during embryo and seed maturation, quiescence and germination in soybean Illumina HiSeq 2000 GSE99571 GSM2646607 SRR5639240 single-end embryo developmental stage: early maturation 0 Soybean Early Maturation-stage Embryo Williams 82 Gene Expression Changes during embryo and seed maturation, quiescence and germination in soybean Illumina HiSeq 2000 GSE99571 GSM2646610 SRR5639243 single-end embryo developmental stage: mid-maturation 0 Soybean Mid Maturation-stage Embryo Williams 82 Gene Expression Changes during embryo and seed maturation, quiescence and germination in soybean Illumina HiSeq 2000 GSE99571 GSM2646613 SRR5639246 single-end embryo developmental stage: late maturation 0 Soybean Late Maturation-stage Embryo Williams 82 Gene Expression Changes during embryo and seed maturation, quiescence and germination in soybean Illumina HiSeq 2000 GSE99571 GSM2646616 SRR5639249 single-end seed developmental stage: mature, dry seed 0 Soybean Dry Seed Williams 82 Gene Expression Changes during embryo and seed maturation, quiescence and germination in soybean Illumina HiSeq 2000 GSE99571 GSM2646619 SRR5639252 single-end seedling developmental stage: 8 day after seed sowing 0 Soybean Seedling 8 DAI Williams 82 Gene Expression Changes during embryo and seed maturation, quiescence and germination in soybean Illumina HiSeq 2000 GSE99109 GSM2633525 SRR5579276 single-end embryo_axis 4 weeks 0 Soybean Mid-Maturation Embryo Axis Williams 82 Gene Expression Changes in the Development of the Soybean Seed Mid-Maturation (B1) Stage Illumina HiSeq 2000 GSE99109 GSM2633528 SRR5579279 single-end cotyledon 4 weeks 0 Soybean Mid-Maturation Embryo Cotyledons Williams 82 Gene Expression Changes in the Development of the Soybean Seed Mid-Maturation (B1) Stage Illumina HiSeq 2000 GSE99109 GSM2633531 SRR5579282 single-end seed_coat 4 weeks 0 Soybean Mid-Maturation Seed Coat Williams 82 Gene Expression Changes in the Development of the Soybean Seed Mid-Maturation (B1) Stage Illumina HiSeq 2000 GSE99758 GSM2651551 SRR5655608 single-end leaf developmental stage: V2 (18 days old) 0 none Williams 82 Transcriptomes of 102 soybean accessions Illumina HiSeq 2500 GSE82240 GSM2187001 SRR3624076 paired-end stem none 1 infection: P. sojae inoculated Williams Fine mapping and candidate gene analysis of two loci conferring resistance to Phytophthora sojae in soybean Illumina HiScanSQ GSE82240 GSM2187002 SRR3624077 paired-end stem none 0 infection: mock-inoculated Williams Fine mapping and candidate gene analysis of two loci conferring resistance to Phytophthora sojae in soybean Illumina HiScanSQ GSE86201 GSM2297698 SRR4095538 single-end root 7 days 0 3 and 5 days post water incubation Williams 82 Investigation of the Fusarium virguliforme transcriptomes induced during infection of soybean roots suggests that enzymes with hydrolytic activities could play a major role in root necrosis Illumina Genome Analyzer II GSE86201 GSM2297699 SRR4095539 single-end root 7 days 0 10 and 24 days post water incubation Williams 82 Investigation of the Fusarium virguliforme transcriptomes induced during infection of soybean roots suggests that enzymes with hydrolytic activities could play a major role in root necrosis Illumina Genome Analyzer II GSE86201 GSM2297700 SRR4095540 single-end root 7 days 1 infected by conidial spores (pooled RNA samples at 3 and 5 days post infection) Williams 82 Investigation of the Fusarium virguliforme transcriptomes induced during infection of soybean roots suggests that enzymes with hydrolytic activities could play a major role in root necrosis Illumina Genome Analyzer II GSE86201 GSM2297701 SRR4095541 single-end root 7 days 1 infected by conidial spores (pooled RNA samples at 10 and 24 days post infection) Williams 82 Investigation of the Fusarium virguliforme transcriptomes induced during infection of soybean roots suggests that enzymes with hydrolytic activities could play a major role in root necrosis Illumina Genome Analyzer II GSE64620 GSM1575732 SRR1737979 single-end seed generation: 4th 1 764_B1,transgene: non-toxic Staphylococcus enterotoxin B Williams 82 Detection and Characterization of Gene Expression Differences in Transgenic Glycine max Seeds with RNAseq Illumina HiSeq 2000 GSE64620 GSM1575735 SRR1737982 single-end seed generation: 4th 1 764_H1,transgene: non-toxic Staphylococcus enterotoxin B Williams 82 Detection and Characterization of Gene Expression Differences in Transgenic Glycine max Seeds with RNAseq Illumina HiSeq 2000 GSE64620 GSM1575738 SRR1737985 single-end seed generation: 4th 1 764_K1,transgene: non-toxic Staphylococcus enterotoxin B Williams 82 Detection and Characterization of Gene Expression Differences in Transgenic Glycine max Seeds with RNAseq Illumina HiSeq 2000 GSE64620 GSM1575741 SRR1737988 single-end seed generation: 7th 1 ST77_D1,transgene: human thyroglobulin Williams 82 Detection and Characterization of Gene Expression Differences in Transgenic Glycine max Seeds with RNAseq Illumina HiSeq 2000 GSE64620 GSM1575744 SRR1737991 single-end seed generation: 7th 1 ST77_F1,transgene: human thyroglobulin Williams 82 Detection and Characterization of Gene Expression Differences in Transgenic Glycine max Seeds with RNAseq Illumina HiSeq 2000 GSE64620 GSM1575747 SRR1737994 single-end seed generation: 7th 1 ST77_J1,transgene: human thyroglobulin Williams 82 Detection and Characterization of Gene Expression Differences in Transgenic Glycine max Seeds with RNAseq Illumina HiSeq 2000 GSE64620 GSM1575750 SRR1737997 single-end seed generation: 3rd 1 ST111_B1,transgene: myelin-basic protein sigma conjugate Williams 82 Detection and Characterization of Gene Expression Differences in Transgenic Glycine max Seeds with RNAseq Illumina HiSeq 2000 GSE64620 GSM1575753 SRR1738000 single-end seed generation: 3rd 1 ST111_I1,transgene: myelin-basic protein sigma conjugate Williams 82 Detection and Characterization of Gene Expression Differences in Transgenic Glycine max Seeds with RNAseq Illumina HiSeq 2000 GSE64620 GSM1575756 SRR1738003 single-end seed generation: 3rd 1 ST111_K1,transgene: myelin-basic protein sigma conjugate Williams 82 Detection and Characterization of Gene Expression Differences in Transgenic Glycine max Seeds with RNAseq Illumina HiSeq 2000 GSE64620 GSM1575759 SRR1738006 single-end seed generation: n/a 0 WT_B1,transgene: none Williams 82 Detection and Characterization of Gene Expression Differences in Transgenic Glycine max Seeds with RNAseq Illumina HiSeq 2000 GSE64620 GSM1575762 SRR1738009 single-end seed generation: n/a 0 WT_H1,transgene: none Williams 82 Detection and Characterization of Gene Expression Differences in Transgenic Glycine max Seeds with RNAseq Illumina HiSeq 2000 GSE64620 GSM1575765 SRR1738012 single-end seed generation: n/a 0 WT_L1,transgene: none Williams 82 Detection and Characterization of Gene Expression Differences in Transgenic Glycine max Seeds with RNAseq Illumina HiSeq 2000 GSE64665 GSM1576581 SRR1740419 single-end root_meristematic_zone 4 days after plating 0 GmMZ1,root zone: Root meristematic zone Williams 82 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. GSE64665 GSM1576584 SRR1740422 single-end root_elongation_zone 4 days after plating 0 GmEZ1,root zone: Root elongation zone Williams 82 Conserved Molecular Program for Root Development in Diverse Plants Illumina HiSeq 2000 GSE64665 GSM1576587 SRR1740425 single-end root_differentiation_zone 4 days after plating 0 GmDZ1,root zone: Root differentiation zone Williams 82 Conserved Molecular Program for Root Development in Diverse Plants Illumina HiSeq 2000 GSE57252 GSM1377923 SRR1268082 single-end root developmental stage: V1 stage seedlings 0 control,0h Williams 82 Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress Illumina HiSeq 2000 GSE57252 GSM1377926 SRR1268085 single-end root developmental stage: V1 stage seedlings 1 dehydration treatment,1h Williams 82 Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress Illumina HiSeq 2000 GSE57252 GSM1377929 SRR1268088 single-end root developmental stage: V1 stage seedlings 1 dehydration treatment,6h Williams 82 Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress Illumina HiSeq 2000 GSE57252 GSM1377932 SRR1268091 single-end root developmental stage: V1 stage seedlings 1 dehydration treatment,12h Williams 82 Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress Illumina HiSeq 2000 GSE57252 GSM1377935 SRR1268094 single-end root developmental stage: V1 stage seedlings 1 salt treatment,1h Williams 82 Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress Illumina HiSeq 2000 GSE57252 GSM1377938 SRR1268097 single-end root developmental stage: V1 stage seedlings 1 salt treatment,6h Williams 82 Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress Illumina HiSeq 2000 GSE57252 GSM1377941 SRR1268100 single-end root developmental stage: V1 stage seedlings 1 salt treatment,12h Williams 82 Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress Illumina HiSeq 2000 GSE57606 GSM1385450 SRR1284502 single-end embryo seeds ranging 3.0-3.5mm in length 0 Soybean Cotyledon Stage Embryo Proper-Biological replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Cotyledon Stage Illumina HiSeq 2000 GSE57606 GSM1385453 SRR1284510 single-end embryo_axis seeds ranging 3.0-3.5mm in length 0 Soybean Cotyledon Stage Embryo Proper Axis-Biological replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Cotyledon Stage Illumina HiSeq 2000 GSE57606 GSM1385456 SRR1284518 single-end cotyledon seeds ranging 3.0-3.5mm in length 0 Soybean Cotyledon Stage Embryo Proper Cotyledon-Biological replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Cotyledon Stage Illumina HiSeq 2000 GSE57606 GSM1385459 SRR1284522 single-end endosperm seeds ranging 3.0-3.5mm in length 0 Soybean Cotyledon Stage Endosperm-Biological replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Cotyledon Stage Illumina HiSeq 2000 GSE57606 GSM1385462 SRR1284527 single-end seed_coat seeds ranging 3.0-3.5mm in length 0 Soybean Cotyledon Stage Seed Coat Endothelium-Biological replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Cotyledon Stage Illumina HiSeq 2000 GSE57606 GSM1385465 SRR1284531 single-end seed_coat seeds ranging 3.0-3.5mm in length 0 Soybean Cotyledon Stage Seed Coat Epidermis-Biological replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Cotyledon Stage Illumina HiSeq 2000 GSE57606 GSM1385468 SRR1284535 single-end seed_coat seeds ranging 3.0-3.5mm in length 0 Soybean Cotyledon Stage Seed Coat Epidermis-Biological replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Cotyledon Stage Illumina HiSeq 2000 GSE57606 GSM1385471 SRR1284541 single-end seed_coat seeds ranging 3.0-3.5mm in length 0 Soybean Cotyledon Stage Seed Coat Inner Integument-Biological replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Cotyledon Stage Illumina HiSeq 2000 GSE57606 GSM1385474 SRR1284545 single-end seed_coat seeds ranging 3.0-3.5mm in length 0 Soybean Cotyledon Stage Seed Coat Outer Integument-Biological replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Cotyledon Stage Illumina HiSeq 2000 GSE57606 GSM1385477 SRR1284548 single-end suspensor seeds ranging 3.0-3.5mm in length 0 Soybean Cotyledon Stage Suspensor-Biological replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Cotyledon Stage Illumina HiSeq 2000 GSE57350 GSM1380799 SRR1272372 single-end embryo seed - heart stage 0 Soybean Heart Stage Embryo Proper-Biological replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Heart Stage Illumina HiSeq 2000 GSE57350 GSM1380802 SRR1272377 single-end endosperm seed - heart stage 0 Soybean Heart Stage Endosperm-Biological replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Heart Stage Illumina HiSeq 2000 GSE57350 GSM1380805 SRR1272383 single-end seed_coat seed - heart stage 0 Soybean Heart Stage Seed Coat Endothelium-Biological replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Heart Stage Illumina HiSeq 2000 GSE57350 GSM1380808 SRR1272388 single-end seed_coat seed - heart stage 0 Soybean Heart Stage Seed Coat Epidermis-Biological replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Heart Stage Illumina HiSeq 2000 GSE57350 GSM1380811 SRR1272393 single-end seed_coat seed - heart stage 0 Soybean Heart Stage Seed Coat Hilum-Biological replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Heart Stage Illumina HiSeq 2000 GSE57350 GSM1380814 SRR1272399 single-end seed_coat seed - heart stage 0 Soybean Heart Stage Seed Coat Inner Integument-Biological replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Heart Stage Illumina HiSeq 2000 GSE57350 GSM1380817 SRR1272404 single-end seed_coat seed - heart stage 0 Soybean Heart Stage Seed Coat Outer Integument-Biological replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Heart Stage Illumina HiSeq 2000 GSE57350 GSM1380820 SRR1272410 single-end suspensor seed - heart stage 0 Soybean Heart Stage Suspensor-Biological replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Heart Stage Illumina HiSeq 2000 GSE57349 GSM1380774 SRR1272329 single-end embryo seed - globular stage 0 Soybean Globular Stage Embryo Proper-Biological replicate 4 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Globular Stage Illumina HiSeq 2000 GSE57349 GSM1380777 SRR1272334 single-end endosperm seed - globular stage 0 Soybean Globular Stage Endosperm-Biological replicate 2 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Globular Stage Illumina HiSeq 2000 GSE57349 GSM1380780 SRR1272340 single-end seed_coat seed - globular stage 0 Soybean Globular Stage Seed Coat Endothelium-Biological replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Globular Stage Illumina HiSeq 2000 GSE57349 GSM1380783 SRR1272345 single-end seed_coat seed - globular stage 0 Soybean Globular Stage Seed Coat Epidermis-Biological replicate 4 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Globular Stage Illumina HiSeq 2000 GSE57349 GSM1380786 SRR1272350 single-end seed_coat seed - globular stage 0 Soybean Globular Stage Seed Coat Hilum-Biological replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Globular Stage Illumina HiSeq 2000 GSE57349 GSM1380789 SRR1272354 single-end seed_coat seed - globular stage 0 Soybean Globular Stage Seed Coat Inner Integument-Biological replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Globular Stage Illumina HiSeq 2000 GSE57349 GSM1380793 SRR1272361 single-end seed_coat seed - globular stage 0 Soybean Globular Stage Seed Coat Outer Integument-Biological replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Globular Stage Illumina HiSeq 2000 GSE57349 GSM1380796 SRR1272367 single-end suspensor seed - globular stage 0 Soybean Globular Stage Suspensor-Biological replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Globular Stage Illumina HiSeq 2000 GSE46096 GSM1398252 SRR1298602 single-end embryo_axis None 0 Soybean Early Maturation Axis Epidermis- biological replicate 2 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Early Maturation Stage Illumina HiSeq 2000 GSE46096 GSM1398255 SRR1298607 single-end plumule None 0 Soybean Early Maturation Axis Plumules- biological replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Early Maturation Stage Illumina HiSeq 2000 GSE46096 GSM1398258 SRR1298622 single-end root_tip None 0 Soybean Early Maturation Axis Root Tip- biological replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Early Maturation Stage Illumina HiSeq 2000 GSE46096 GSM1398259 SRR1298627 single-end embryo_axis None 0 Soybean Early Maturation Axis Shoot Apical Meristem- biological replicate 2 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Early Maturation Stage Illumina HiSeq 2000 GSE46096 GSM1398262 SRR1298633 single-end embryo_axis None 0 Soybean Early Maturation Axis Stele- biological replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Early Maturation Stage Illumina HiSeq 2000 GSE46096 GSM1398265 SRR1298647 single-end embryo_axis None 0 Soybean Early Maturation Axis Vasculature- biological replicate 4 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Early Maturation Stage Illumina HiSeq 2000 GSE46096 GSM1398266 SRR1298650 single-end cotyledon None 0 Soybean Early Maturation Cotyledon Abaxial Parenchyma- biological replicate 2 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Early Maturation Stage Illumina HiSeq 2000 GSE46096 GSM1398269 SRR1298657 single-end cotyledon None 0 Soybean Early Maturation Cotyledon Adaxial Epidermis- biological replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Early Maturation Stage Illumina HiSeq 2000 GSE46096 GSM1398272 SRR1298665 single-end cotyledon None 0 Soybean Early Maturation Cotyledon Adaxial Parenchyma- biological replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Early Maturation Stage Illumina HiSeq 2000 GSE46096 GSM1398275 SRR1298676 single-end cotyledon None 0 Soybean Early Maturation Cotyledon Vasculature- biological replicate 3 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Early Maturation Stage Illumina HiSeq 2000 GSE46096 GSM1398276 SRR1298678 single-end endosperm None 0 Soybean Early Maturation Endosperm- biological replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Early Maturation Stage Illumina HiSeq 2000 GSE46096 GSM1398278 SRR1298684 single-end seed_coat None 0 Soybean Early Maturation Seed Coat Palisade- biological replicate 4 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Early Maturation Stage Illumina HiSeq 2000 GSE46096 GSM1398279 SRR1298687 single-end seed_coat None 0 Soybean Early Maturation Seed Coat Parenchyma- biological replicate 2 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Early Maturation Stage Illumina HiSeq 2000 GSE29163 GSM2734729 SRR5906386 single-end seed mid-maturation-stage embryos 0 Soybean seeds containing mid-maturation-stage embryos Williams 82 Genome-Wide Transcript Profiling During Soybean Seed Development and Throughout the Soybean Life Cycle Illumina HiSeq 2000 GSE153951 GSM4659041 SRR12164947 single-end leaf None 0 control Magellan,PI595362 Combination of drought and heat in soybean plants Illumina NovaSeq 6000 GSE153951 GSM4659044 SRR12164950 single-end leaf None 1 water deficit Magellan,PI595362 Combination of drought and heat in soybean plants Illumina NovaSeq 6000 GSE153951 GSM4659047 SRR12164953 single-end leaf None 1 heat stress Magellan,PI595362 Combination of drought and heat in soybean plants Illumina NovaSeq 6000 GSE153951 GSM4659050 SRR12164956 single-end leaf None 1 water deficit and heat stress Magellan,PI595362 Combination of drought and heat in soybean plants Illumina NovaSeq 6000 GSE159910 GSM4850121 SRR12883241 paired-end leaf vegetative stage three (V3; 20 days after germination, DAG) 0 Wild Type 20 days 1 None GmNAC81 involved in leaf senecence and drought stress Illumina HiSeq 2500 GSE159910 GSM4850124 SRR12883244 paired-end leaf reproductive stage six (R6; 80 DAG) 0 Wild Type 80 days 1 None GmNAC81 involved in leaf senecence and drought stress Illumina HiSeq 2500 GSE146287 GSM4376739 SRR11219633 single-end seed_coat Extended hilum region of seed coats (10-25 mg seed weight stage) 1 SC Clark 63 (UC7_PI548532) 10-25 mg rep 1 UC7_PI548532 Overexpression of an ethylene-forming ACC Oxidase (ACO) gene precedes the Minute Hilum seed coat phenotype in Glycine max Illumina HiSeq 2000 GSE146287 GSM4376743 SRR11219637 single-end seed_coat Extended hilum region of seed coats (25-50 mg seed weight stage) 1 SC Clark 63 (UC7_PI548532) 25-50 mg rep 1 UC7_PI548532 Overexpression of an ethylene-forming ACC Oxidase (ACO) gene precedes the Minute Hilum seed coat phenotype in Glycine max Illumina HiSeq 2000 GSE146287 GSM4376747 SRR11219641 single-end seed_coat Extended hilum region of seed coats (50-100 mg seed weight stage) 1 SC Clark 63 (UC7_PI548532) 50-100 mg rep 1 UC7_PI548532 Overexpression of an ethylene-forming ACC Oxidase (ACO) gene precedes the Minute Hilum seed coat phenotype in Glycine max Illumina HiSeq 2000 GSE146287 GSM4376751 SRR11219645 single-end seed_coat Extended hilum region of seed coats (100-200 mg seed weight stage) 1 SC Clark 63 (UC7_PI548532) 100-200 mg rep 1 UC7_PI548532 Overexpression of an ethylene-forming ACC Oxidase (ACO) gene precedes the Minute Hilum seed coat phenotype in Glycine max Illumina HiSeq 2000 GSE146287 GSM4376753 SRR11219647 single-end seed_coat Whole seed coats (10-25 mg seed weight stage) 0 WS Clark 63 (UC7_PI548532) 10-25 mg rep 1 UC7_PI548532 Overexpression of an ethylene-forming ACC Oxidase (ACO) gene precedes the Minute Hilum seed coat phenotype in Glycine max Illumina HiSeq 2000 GSE146287 GSM4376755 SRR11219649 single-end seed_coat Whole seed coats (25-50 mg seed weight stage) 0 WS Clark 63 (UC7_PI548532) 25-50 mg rep 1 UC7_PI548532 Overexpression of an ethylene-forming ACC Oxidase (ACO) gene precedes the Minute Hilum seed coat phenotype in Glycine max Illumina HiSeq 2000 GSE146287 GSM4376757 SRR11219651 single-end seed_coat Whole seed coats (50-100 mg seed weight stage) 0 WS Clark 63 (UC7_PI548532) 50-100 mg rep 1 UC7_PI548532 Overexpression of an ethylene-forming ACC Oxidase (ACO) gene precedes the Minute Hilum seed coat phenotype in Glycine max Illumina HiSeq 2000 GSE158762 GSM4809930 SRR12743441 single-end leaf flowering 0 HN44-1 None Transcription analysis of different water use efficiency genotypes in soybean leaf BGISEQ-500 GSE158762 GSM4809933 SRR12743444 single-end leaf flowering 0 SN14-1 None Transcription analysis of different water use efficiency genotypes in soybean leaf BGISEQ-500 GSE141720 GSM4212367 SRR10640786 paired-end leaf 24 hours after infestation 0 24 hours mock Dongnong47_susceptible A genome-wide view of transcriptional responses during Aphis glycines Matsumura infestation in soybean Illumina HiSeq 2000 GSE141720 GSM4212370 SRR10640789 paired-end leaf 24 hours after infestation 1 24 hours after aphid infestation Dongnong47_susceptible A genome-wide view of transcriptional responses during Aphis glycines Matsumura infestation in soybean Illumina HiSeq 2000 GSE141720 GSM4212373 SRR10640792 paired-end leaf 48 hours after infestation 0 48 hours mock Dongnong47_susceptible A genome-wide view of transcriptional responses during Aphis glycines Matsumura infestation in soybean Illumina HiSeq 2000 GSE141720 GSM4212376 SRR10640795 paired-end leaf 48 hours after infestation 1 48 hours after aphid infestation Dongnong47_susceptible A genome-wide view of transcriptional responses during Aphis glycines Matsumura infestation in soybean Illumina HiSeq 2000 GSE141720 GSM4212379 SRR10640798 paired-end leaf 96 hours after infestation 0 96 hours mock Dongnong47_susceptible A genome-wide view of transcriptional responses during Aphis glycines Matsumura infestation in soybean Illumina HiSeq 2000 GSE141720 GSM4212382 SRR10640801 paired-end leaf 96 hours after infestation 1 96 hours after aphid infestation Dongnong47_susceptible A genome-wide view of transcriptional responses during Aphis glycines Matsumura infestation in soybean Illumina HiSeq 2000 GSE141720 GSM4212385 SRR10640804 paired-end leaf 24 hours after infestation 0 24 hours mock P203_antixenotic A genome-wide view of transcriptional responses during Aphis glycines Matsumura infestation in soybean Illumina HiSeq 2000 GSE141720 GSM4212388 SRR10640807 paired-end leaf 24 hours after infestation 1 24 hours after aphid infestation P203_antixenotic A genome-wide view of transcriptional responses during Aphis glycines Matsumura infestation in soybean Illumina HiSeq 2000 GSE141720 GSM4212391 SRR10640810 paired-end leaf 48 hours after infestation 0 48 hours mock P203_antixenotic A genome-wide view of transcriptional responses during Aphis glycines Matsumura infestation in soybean Illumina HiSeq 2000 GSE141720 GSM4212394 SRR10640813 paired-end leaf 48 hours after infestation 1 48 hours after aphid infestation P203_antixenotic A genome-wide view of transcriptional responses during Aphis glycines Matsumura infestation in soybean Illumina HiSeq 2000 GSE141720 GSM4212397 SRR10640816 paired-end leaf 96 hours after infestation 0 96 hours mock P203_antixenotic A genome-wide view of transcriptional responses during Aphis glycines Matsumura infestation in soybean Illumina HiSeq 2000 GSE141720 GSM4212400 SRR10640819 paired-end leaf 96 hours after infestation 1 96 hours after aphid infestation P203_antixenotic A genome-wide view of transcriptional responses during Aphis glycines Matsumura infestation in soybean Illumina HiSeq 2000 GSE141720 GSM4212403 SRR10640822 paired-end leaf 24 hours after infestation 0 24 hours mock P746_antibiotic A genome-wide view of transcriptional responses during Aphis glycines Matsumura infestation in soybean Illumina HiSeq 2000 GSE141720 GSM4212406 SRR10640825 paired-end leaf 24 hours after infestation 1 24 hours after aphid infestation P746_antibiotic A genome-wide view of transcriptional responses during Aphis glycines Matsumura infestation in soybean Illumina HiSeq 2000 GSE141720 GSM4212409 SRR10640828 paired-end leaf 48 hours after infestation 0 48 hours mock P746_antibiotic A genome-wide view of transcriptional responses during Aphis glycines Matsumura infestation in soybean Illumina HiSeq 2000 GSE141720 GSM4212412 SRR10640831 paired-end leaf 48 hours after infestation 1 48 hours after aphid infestation P746_antibiotic A genome-wide view of transcriptional responses during Aphis glycines Matsumura infestation in soybean Illumina HiSeq 2000 GSE141720 GSM4212415 SRR10640834 paired-end leaf 96 hours after infestation 0 96 hours mock P746_antibiotic A genome-wide view of transcriptional responses during Aphis glycines Matsumura infestation in soybean Illumina HiSeq 2000 GSE141720 GSM4212418 SRR10640837 paired-end leaf 96 hours after infestation 1 96 hours after aphid infestation P746_antibiotic A genome-wide view of transcriptional responses during Aphis glycines Matsumura infestation in soybean Illumina HiSeq 2000 GSE131686 GSM3813939 SRR9113321 paired-end root_hair H2O treatment 24h 0 H2O treatment 24h Williams 82 Glyceollin transcription factor GmMYB29A2 is a regulator of soybean resistance to Phytophthora sojae Illumina HiSeq 1500 GSE131686 GSM3813943 SRR9113325 paired-end root_hair wall glucan elicitor (WGE) treatment 24h 1 wall glucan elicitor (WGE) treatment 24h Williams 82 Glyceollin transcription factor GmMYB29A2 is a regulator of soybean resistance to Phytophthora sojae Illumina HiSeq 1500 GSE131686 GSM3813947 SRR9113329 paired-end seed H2O treatment 48h 0 H2O treatment 48h Harosoy63 Glyceollin transcription factor GmMYB29A2 is a regulator of soybean resistance to Phytophthora sojae Illumina HiSeq 1500 GSE131686 GSM3813951 SRR9113333 paired-end seed wall glucan elicitor (WGE) treatment 48h 1 wall glucan elicitor (WGE) treatment 48h Harosoy63 Glyceollin transcription factor GmMYB29A2 is a regulator of soybean resistance to Phytophthora sojae Illumina HiSeq 1500 GSE135971 GSM4038723 SRR9995602 paired-end root 15 days 0 15 days_mocktissue Williams 82 Interactions of gene expression, alternative splicing, and DNA methylation in determining nodule identity Illumina HiSeq 2500 GSE135971 GSM4038726 SRR9995605 paired-end root 25 days 0 25 days_mocktissue Williams 82 Interactions of gene expression, alternative splicing, and DNA methylation in determining nodule identity Illumina HiSeq 2500 GSE135971 GSM4038729 SRR9995608 paired-end root 39 days 0 39 days_mocktissue Williams 82 Interactions of gene expression, alternative splicing, and DNA methylation in determining nodule identity Illumina HiSeq 2500 GSE135971 GSM4038732 SRR9995611 paired-end nodule 15 days 1 15 days_treattissue Williams 82 Interactions of gene expression, alternative splicing, and DNA methylation in determining nodule identity Illumina HiSeq 2500 GSE135971 GSM4038735 SRR9995614 paired-end nodule 25 days 1 25 days_treattissue Williams 82 Interactions of gene expression, alternative splicing, and DNA methylation in determining nodule identity Illumina HiSeq 2500 GSE135971 GSM4038738 SRR9995617 paired-end nodule 39 days 1 39 days_treattissue Williams 82 Interactions of gene expression, alternative splicing, and DNA methylation in determining nodule identity Illumina HiSeq 2500 GSE150157 GSM4525225 SRR11741785 single-end flower None 0 flower None Characterization of RNAs in soybean (Glycine max) Illumina HiSeq 2500 GSE150157 GSM4525226 SRR11741786 single-end leaf None 0 young leaf None Characterization of RNAs in soybean (Glycine max) Illumina HiSeq 2500 GSE150157 GSM4525227 SRR11741787 single-end seed None 0 seed early maturity stage 1 None Characterization of RNAs in soybean (Glycine max) Illumina HiSeq 2500 GSE150157 GSM4525228 SRR11741788 single-end seed None 0 seed early maturity stage 2 None Characterization of RNAs in soybean (Glycine max) Illumina HiSeq 2500 GSE150157 GSM4525229 SRR11741789 single-end seed None 0 seed cotyledon stage None Characterization of RNAs in soybean (Glycine max) Illumina HiSeq 2500 GSE150157 GSM4525230 SRR11741790 single-end pod None 0 one cm pod None Characterization of RNAs in soybean (Glycine max) Illumina HiSeq 2500 GSE150157 GSM4525231 SRR11741791 single-end pod None 0 pod shell 10DAF None Characterization of RNAs in soybean (Glycine max) Illumina HiSeq 2500 GSE150157 GSM4525232 SRR11741792 single-end pod None 0 pod shell 14DAF None Characterization of RNAs in soybean (Glycine max) Illumina HiSeq 2500 GSE150157 GSM4525233 SRR11741793 single-end nodule None 0 nodule None Characterization of RNAs in soybean (Glycine max) Illumina HiSeq 2500 GSE150157 GSM4525234 SRR11741794 single-end root None 0 root None Characterization of RNAs in soybean (Glycine max) Illumina HiSeq 2500 GSE150157 GSM4525235 SRR11741795 single-end anther None 0 anther, rep 1 None Characterization of RNAs in soybean (Glycine max) Illumina HiSeq 2500 GSE150157 GSM4525236 SRR11741796 single-end ovary None 0 ovary, rep 1 None Characterization of RNAs in soybean (Glycine max) Illumina HiSeq 2500 GSE150157 GSM4525237 SRR11741797 single-end flower None 0 unopened flower, rep 1 None Characterization of RNAs in soybean (Glycine max) Illumina HiSeq 2500 GSE150157 GSM4525238 SRR11741798 single-end flower None 0 open flower, rep 1 None Characterization of RNAs in soybean (Glycine max) Illumina HiSeq 2500 GSE150157 GSM4525239 SRR11741799 single-end leaf None 0 soybean leaf V3 rep1 None Characterization of RNAs in soybean (Glycine max) Illumina HiSeq 2500 GSE150157 GSM4525240 SRR11741800 single-end leaf None 0 soybean leaf V3 rep2 None Characterization of RNAs in soybean (Glycine max) Illumina HiSeq 2500 GSE137263 GSM4074067 SRR10098755 paired-end leaf 0 hours 0 0 hours post mosaic virus (SMV) strain G7 (SMV-G7) inoculation sampled L29 (Rsv3-genotype resistant ) A Transcriptional Regulatory Network of Rsv3-mediated Extreme Resistance Against Soybean Mosaic Virus Illumina HiSeq 4000 GSE137263 GSM4074070 SRR10098758 paired-end leaf 2 hours 1 2 hours post mosaic virus (SMV) strain G7 (SMV-G7) inoculation sampled L29 (Rsv3-genotype resistant ) A Transcriptional Regulatory Network of Rsv3-mediated Extreme Resistance Against Soybean Mosaic Virus Illumina HiSeq 4000 GSE137263 GSM4074072 SRR10098760 paired-end leaf 4 hours 1 4 hours post mosaic virus (SMV) strain G7 (SMV-G7) inoculation sampled L29 (Rsv3-genotype resistant ) A Transcriptional Regulatory Network of Rsv3-mediated Extreme Resistance Against Soybean Mosaic Virus Illumina HiSeq 4000 GSE137263 GSM4074074 SRR10098762 paired-end leaf 6 hours 1 6 hours post mosaic virus (SMV) strain G7 (SMV-G7) inoculation sampled L29 (Rsv3-genotype resistant ) A Transcriptional Regulatory Network of Rsv3-mediated Extreme Resistance Against Soybean Mosaic Virus Illumina HiSeq 4000 GSE137263 GSM4074076 SRR10098764 paired-end leaf 8 hours 1 8 hours post mosaic virus (SMV) strain G7 (SMV-G7) inoculation sampled L29 (Rsv3-genotype resistant ) A Transcriptional Regulatory Network of Rsv3-mediated Extreme Resistance Against Soybean Mosaic Virus Illumina HiSeq 4000 GSE137263 GSM4074078 SRR10098766 paired-end leaf 0 hours 0 0 hours post mosaic virus (SMV) strain G7 (SMV-G7) inoculation sampled Williams 82 (rsv3-genotype susceptible ) A Transcriptional Regulatory Network of Rsv3-mediated Extreme Resistance Against Soybean Mosaic Virus Illumina HiSeq 4000 GSE137263 GSM4074080 SRR10098768 paired-end leaf 2 hours 1 2 hours post mosaic virus (SMV) strain G7 (SMV-G7) inoculation sampled Williams 82 (rsv3-genotype susceptible ) A Transcriptional Regulatory Network of Rsv3-mediated Extreme Resistance Against Soybean Mosaic Virus Illumina HiSeq 4000 GSE137263 GSM4074082 SRR10098770 paired-end leaf 4 hours 1 4 hours post mosaic virus (SMV) strain G7 (SMV-G7) inoculation sampled Williams 82 (rsv3-genotype susceptible ) A Transcriptional Regulatory Network of Rsv3-mediated Extreme Resistance Against Soybean Mosaic Virus Illumina HiSeq 4000 GSE137263 GSM4074084 SRR10098772 paired-end leaf 6 hours 1 6 hours post mosaic virus (SMV) strain G7 (SMV-G7) inoculation sampled Williams 82 (rsv3-genotype susceptible ) A Transcriptional Regulatory Network of Rsv3-mediated Extreme Resistance Against Soybean Mosaic Virus Illumina HiSeq 4000 GSE137263 GSM4074086 SRR10098774 paired-end leaf 8 hours 1 8 hours post mosaic virus (SMV) strain G7 (SMV-G7) inoculation sampled Williams 82 (rsv3-genotype susceptible ) A Transcriptional Regulatory Network of Rsv3-mediated Extreme Resistance Against Soybean Mosaic Virus Illumina HiSeq 4000 GSE130138 GSM3732705 SRR8937687 paired-end root 8 days 0 noninfected TN09-16(Soybean cyst nematode susceptible) Identification of introduced and stably inherited DNA methylation variants in soybean associated with soybean cyst nematode parasitism [RNA-seq] Illumina HiSeq 2500 GSE130138 GSM3732708 SRR8937690 paired-end root 8 days 1 soybean cyst nematode(SCN)_infected TN09-16(Soybean cyst nematode susceptible) Identification of introduced and stably inherited DNA methylation variants in soybean associated with soybean cyst nematode parasitism [RNA-seq] Illumina HiSeq 2500 GSE130138 GSM3732711 SRR8937693 paired-end root 8 days 0 noninfected TN09-29(Soybean cyst nematode resistant) Identification of introduced and stably inherited DNA methylation variants in soybean associated with soybean cyst nematode parasitism [RNA-seq] Illumina HiSeq 2500 GSE130138 GSM3732714 SRR8937696 paired-end root 8 days 1 soybean cyst nematode(SCN)_infected TN09-29(Soybean cyst nematode resistant) Identification of introduced and stably inherited DNA methylation variants in soybean associated with soybean cyst nematode parasitism [RNA-seq] Illumina HiSeq 2500 GSE139303 GSM4137628 SRR10337249 paired-end leaf V1 stage 0 mock treated with MgCl2 Soybean (Glycine max (L.) Merr.) L76-1988 RNA-seq analysis of distal gene expression changes during nodulation Illumina HiSeq 3000 GSE139303 GSM4137631 SRR10337252 paired-end leaf V1 stage 1 sample treated with Bradyrhizobium japonicum USDA122 Soybean (Glycine max (L.) Merr.) L76-1988 RNA-seq analysis of distal gene expression changes during nodulation Illumina HiSeq 3000 GSE139303 GSM4137634 SRR10337255 paired-end leaf V1 stage 1 sample treated with Sinorhizobium fredii USDA257 Soybean (Glycine max (L.) Merr.) L76-1988 RNA-seq analysis of distal gene expression changes during nodulation Illumina HiSeq 3000 GSE94228 GSM2471308 SRR5210841 paired-end unifoliolate_leaf 11-day old 0 ZT0_rep1 Williams 82 Circadian transcriptome of soybean unifoliolate leaves Illumina HiSeq 4000 GSE94228 GSM2471309 SRR5210844 paired-end unifoliolate_leaf 11-day old 1 ZT4_rep1 Williams 82 Circadian transcriptome of soybean unifoliolate leaves Illumina HiSeq 4000 GSE94228 GSM2471310 SRR5210847 paired-end unifoliolate_leaf 11-day old 1 ZT8_rep1 Williams 82 Circadian transcriptome of soybean unifoliolate leaves Illumina HiSeq 4000 GSE94228 GSM2471311 SRR5210850 paired-end unifoliolate_leaf 11-day old 1 ZT12_rep1 Williams 82 Circadian transcriptome of soybean unifoliolate leaves Illumina HiSeq 4000 GSE94228 GSM2471312 SRR5210853 paired-end unifoliolate_leaf 11-day old 1 ZT16_rep1 Williams 82 Circadian transcriptome of soybean unifoliolate leaves Illumina HiSeq 4000 GSE94228 GSM2471313 SRR5210856 paired-end unifoliolate_leaf 11-day old 1 ZT20_rep1 Williams 82 Circadian transcriptome of soybean unifoliolate leaves Illumina HiSeq 4000 GSE94228 GSM2471314 SRR5210859 paired-end unifoliolate_leaf 11-day old 1 ZT24_rep1 Williams 82 Circadian transcriptome of soybean unifoliolate leaves Illumina HiSeq 4000 GSE94228 GSM2471315 SRR5210862 paired-end unifoliolate_leaf 11-day old 1 ZT28_rep1 Williams 82 Circadian transcriptome of soybean unifoliolate leaves Illumina HiSeq 4000 GSE94228 GSM2471316 SRR5210865 paired-end unifoliolate_leaf 11-day old 1 ZT32_rep1 Williams 82 Circadian transcriptome of soybean unifoliolate leaves Illumina HiSeq 4000 GSE94228 GSM2471317 SRR5210868 paired-end unifoliolate_leaf 11-day old 1 ZT36_rep1 Williams 82 Circadian transcriptome of soybean unifoliolate leaves Illumina HiSeq 4000 GSE94228 GSM2471318 SRR5210871 paired-end unifoliolate_leaf 11-day old 1 ZT40_rep1 Williams 82 Circadian transcriptome of soybean unifoliolate leaves Illumina HiSeq 4000 GSE94228 GSM2471319 SRR5210874 paired-end unifoliolate_leaf 11-day old 1 ZT44_rep1 Williams 82 Circadian transcriptome of soybean unifoliolate leaves Illumina HiSeq 4000 GSE123655 GSM3508915 SRR8312553 single-end cotyledon 5-6mg 0 cotyledon from 5-6mg immature seeds Williams (PI548631) Williams RNA-Seq Samples from Various Organ and Developmental Stages Illumina HiSeq 2000 GSE123655 GSM3508916 SRR8312554 single-end cotyledon 200-300mg desiccating 0 Cotyledon without embryo axis from 200-300 mg yellow, desiccating seed Williams (PI548631) Williams RNA-Seq Samples from Various Organ and Developmental Stages Illumina HiSeq 2000 GSE123655 GSM3508917 SRR8312555 single-end cotyledon Mature dry seed 0 Cotyledon from mature dry seed Williams (PI548631) Williams RNA-Seq Samples from Various Organ and Developmental Stages Illumina HiSeq 2000 GSE123655 GSM3508918 SRR8312556 single-end embryo_axis 300-400mg desiccating 0 embryo axis dissected from 300-400 mg yellow, desiccating seed Williams (PI548631) Williams RNA-Seq Samples from Various Organ and Developmental Stages Illumina HiSeq 2000 GSE123655 GSM3508919 SRR8312557 single-end embryo_axis 200-300mg desiccating 0 embryo axis dissected from 200-300 mg yellow, desiccating seed Williams (PI548631) Williams RNA-Seq Samples from Various Organ and Developmental Stages Illumina HiSeq 2000 GSE123655 GSM3508920 SRR8312558 single-end seed_coat 200-300mg desiccating 0 seed coat dissected from 200-300 mg yellow desiccating seed Williams (PI548631) Williams RNA-Seq Samples from Various Organ and Developmental Stages Illumina HiSeq 2000 GSE123655 GSM3508921 SRR8312559 single-end seed_coat Mature dry seed 0 seed coat dissected from mature dry seed Williams (PI548631) Williams RNA-Seq Samples from Various Organ and Developmental Stages Illumina HiSeq 2000 GSE123655 GSM3508922 SRR8312560 single-end seed_coat 5-6mg 0 seed coat dissected from 5-6mg immature seed Williams (PI548631) Williams RNA-Seq Samples from Various Organ and Developmental Stages Illumina HiSeq 2000 GSE123655 GSM3508924 SRR8312561 single-end root 5 days 0 seedling roots from 5 day greenhouse grown seedlings Williams (PI548631) Williams RNA-Seq Samples from Various Organ and Developmental Stages Illumina HiSeq 2000 GSE123655 GSM3508925 SRR8312562 single-end leaf Adult 0 1-1.5 inch rolled (furled) trifoliates from adult plants Williams (PI548631) Williams RNA-Seq Samples from Various Organ and Developmental Stages Illumina HiSeq 2000 GSE118749 GSM3346370 SRR7718941 single-end root_hair 276 hours after sowing 0 root hair cells_276 hrs after sowing Williams 82 Characterization of the transcriptional changes during soybean root hair cell development. Illumina HiSeq 2000 GSE118749 GSM3346373 SRR7718944 single-end root_hair 288 hours after sowing 0 root hair cells_288 hrs after sowing Williams 82 Characterization of the transcriptional changes during soybean root hair cell development. Illumina HiSeq 2000 GSE118749 GSM3346376 SRR7718947 single-end root_hair 312 hours after sowing 0 root hair cells_312 hrs after sowing Williams 82 Characterization of the transcriptional changes during soybean root hair cell development. Illumina HiSeq 2000 GSE93322 GSM2451227 SRR5163161 single-end seedling 2-week old 0 WT,mock treatment for 6 hrs GmSIN1 wildtype Transgenic and conventional cultivar comparison in response to salt stress Illumina HiSeq 2000 GSE93322 GSM2451231 SRR5163165 single-end seedling 2-week old 1 WT NaCl,150 mM NaCl treatment for 6 hrs GmSIN1 wildtype Transgenic and conventional cultivar comparison in response to salt stress Illumina HiSeq 2000 GSE133574 GSM3912455 SRR9622344 paired-end root 30 hours 0 wild type Williams 82 Dynamic changes in genome-wide histone methylation and gene expression of soybean roots in response to salt stress (RNA-seq dataset) Illumina MiSeq GSE133574 GSM3912458 SRR9622347 paired-end root 30 hours 1 salt-treated Williams 82 Dynamic changes in genome-wide histone methylation and gene expression of soybean roots in response to salt stress (RNA-seq dataset) Illumina MiSeq GSE130010 GSM3729240 SRR8926860 paired-end pod Pods after 18 days flowering 0 High pod shattering force soybean G1_015 Transcriptome analysis of differentially expressed genes in different pod dehiscence characteristics of soybean Illumina HiSeq 2500 GSE130010 GSM3729241 SRR8926861 paired-end pod Pods after 18 days flowering 0 High pod shattering force soybean G1_018 Transcriptome analysis of differentially expressed genes in different pod dehiscence characteristics of soybean Illumina HiSeq 2500 GSE130010 GSM3729242 SRR8926862 paired-end pod Pods after 18 days flowering 0 High pod shattering force soybean G1_044 Transcriptome analysis of differentially expressed genes in different pod dehiscence characteristics of soybean Illumina HiSeq 2500 GSE130010 GSM3729243 SRR8926863 paired-end pod Pods after 18 days flowering 0 High pod shattering force soybean G1_060 Transcriptome analysis of differentially expressed genes in different pod dehiscence characteristics of soybean Illumina HiSeq 2500 GSE130010 GSM3729244 SRR8926864 paired-end pod Pods after 18 days flowering 0 High pod shattering force soybean G1_071 Transcriptome analysis of differentially expressed genes in different pod dehiscence characteristics of soybean Illumina HiSeq 2500 GSE130010 GSM3729245 SRR8926865 paired-end pod Pods after 18 days flowering 1 Low pod shattering force soybean G2_038 Transcriptome analysis of differentially expressed genes in different pod dehiscence characteristics of soybean Illumina HiSeq 2500 GSE130010 GSM3729246 SRR8926866 paired-end pod Pods after 18 days flowering 1 Low pod shattering force soybean G2_055 Transcriptome analysis of differentially expressed genes in different pod dehiscence characteristics of soybean Illumina HiSeq 2500 GSE130010 GSM3729247 SRR8926867 paired-end pod Pods after 18 days flowering 1 Low pod shattering force soybean G2_072 Transcriptome analysis of differentially expressed genes in different pod dehiscence characteristics of soybean Illumina HiSeq 2500 GSE130010 GSM3729248 SRR8926868 paired-end pod Pods after 18 days flowering 1 Low pod shattering force soybean G2_092 Transcriptome analysis of differentially expressed genes in different pod dehiscence characteristics of soybean Illumina HiSeq 2500 GSE130010 GSM3729249 SRR8926869 paired-end pod Pods after 18 days flowering 1 Low pod shattering force soybean G2_109 Transcriptome analysis of differentially expressed genes in different pod dehiscence characteristics of soybean Illumina HiSeq 2500 GSE129320 GSM3704502 SRR8847715 single-end root None 1 low pH,pH=4.2 None Complex regulatory mechanisms underlying mineral nutrient acquisition in soybean roots responsive to low pH stress BGISEQ-500 GSE129320 GSM3704505 SRR8847718 single-end root None 0 high pH,pH=5.8 None Complex regulatory mechanisms underlying mineral nutrient acquisition in soybean roots responsive to low pH stress BGISEQ-500 GSE125103 GSM3562775 SRR8427366 single-end root 30 day post aphid infestation 1 treatment_soybean cyst nematode(SCN)_30d Williams 82 Transcriptome profiling of interaction effects of soybean cyst nematodes and soybean aphids on soybean Illumina HiSeq 3000 GSE125103 GSM3562778 SRR8427369 single-end root 30 day post aphid infestation 1 treatment_Aphid_30d Williams 82 Transcriptome profiling of interaction effects of soybean cyst nematodes and soybean aphids on soybean Illumina HiSeq 3000 GSE125103 GSM3562781 SRR8427364 single-end root 30 day post aphid infestation 1 treatment_soybean cyst nematode(SCN) and Aphid_30d Williams 82 Transcriptome profiling of interaction effects of soybean cyst nematodes and soybean aphids on soybean Illumina HiSeq 3000 GSE125103 GSM3562784 SRR8427371 single-end root 30 day post aphid infestation 1 treatment_soybean cyst nematode(SCN)_30d H. glycines resistant (MN1806CN)] cultivars Transcriptome profiling of interaction effects of soybean cyst nematodes and soybean aphids on soybean Illumina HiSeq 3000 GSE125103 GSM3562787 SRR8427385 single-end root 30 day post aphid infestation 1 treatment_Aphid_30d H. glycines resistant (MN1806CN)] cultivars Transcriptome profiling of interaction effects of soybean cyst nematodes and soybean aphids on soybean Illumina HiSeq 3000 GSE125103 GSM3562790 SRR8427388 single-end root 30 day post aphid infestation 1 treatment_soybean cyst nematode(SCN) and Aphid_30d H. glycines resistant (MN1806CN)] cultivars Transcriptome profiling of interaction effects of soybean cyst nematodes and soybean aphids on soybean Illumina HiSeq 3000 GSE125103 GSM3562793 SRR8427391 single-end root 30 day post aphid infestation 0 control_30d H. glycines resistant (MN1806CN)] cultivars Transcriptome profiling of interaction effects of soybean cyst nematodes and soybean aphids on soybean Illumina HiSeq 3000 GSE125103 GSM3562798 SRR8427406 single-end root 5 day post aphid infestation 1 treatment_soybean cyst nematode(SCN)_5d Williams 82 Transcriptome profiling of interaction effects of soybean cyst nematodes and soybean aphids on soybean Illumina HiSeq 3000 GSE125103 GSM3562801 SRR8427403 single-end root 5 day post aphid infestation 1 treatment_Aphid_5d Williams 82 Transcriptome profiling of interaction effects of soybean cyst nematodes and soybean aphids on soybean Illumina HiSeq 3000 GSE125103 GSM3562804 SRR8427398 single-end root 5 day post aphid infestation 1 treatment_soybean cyst nematode(SCN) and Aphid_5d Williams 82 Transcriptome profiling of interaction effects of soybean cyst nematodes and soybean aphids on soybean Illumina HiSeq 3000 GSE125103 GSM3562807 SRR8427379 single-end root 5 day post aphid infestation 1 treatment_soybean cyst nematode(SCN)_5d H. glycines resistant (MN1806CN)] cultivars Transcriptome profiling of interaction effects of soybean cyst nematodes and soybean aphids on soybean Illumina HiSeq 3000 GSE125103 GSM3562810 SRR8427378 single-end root 5 day post aphid infestation 1 treatment_Aphid_5d H. glycines resistant (MN1806CN)] cultivars Transcriptome profiling of interaction effects of soybean cyst nematodes and soybean aphids on soybean Illumina HiSeq 3000 GSE125103 GSM3562813 SRR8427373 single-end root 5 day post aphid infestation 1 treatment_soybean cyst nematode(SCN) and Aphid_5d H. glycines resistant (MN1806CN)] cultivars Transcriptome profiling of interaction effects of soybean cyst nematodes and soybean aphids on soybean Illumina HiSeq 3000 GSE125103 GSM3562816 SRR8427396 single-end root 5 day post aphid infestation 0 control_5d H. glycines resistant (MN1806CN)] cultivars Transcriptome profiling of interaction effects of soybean cyst nematodes and soybean aphids on soybean Illumina HiSeq 3000 GSE129626 GSM3717543 SRR8848027 single-end leaf Day1 0 11A_Control_Susceptible_Day1 LD12-15838R Characterization of induced susceptibility effects on soybean- soybean aphid interactions NextSeq 500 GSE129626 GSM3717544 SRR8848028 single-end leaf Day11 0 11C_Control_Susceptible_Day11 LD12-15838R Characterization of induced susceptibility effects on soybean- soybean aphid interactions NextSeq 500 GSE129626 GSM3717545 SRR8848025 single-end leaf Day1 0 12A_Control_Resistant_Day1 LD12-15813Ra Characterization of induced susceptibility effects on soybean- soybean aphid interactions NextSeq 500 GSE129626 GSM3717546 SRR8848026 single-end leaf Day11 0 12C_Control_Resistant_Day11 LD12-15813Ra Characterization of induced susceptibility effects on soybean- soybean aphid interactions NextSeq 500 GSE129626 GSM3717547 SRR8848031 single-end leaf Day11 1 1C_No Inducer_15 biotype1_Day11 LD12-15838R Characterization of induced susceptibility effects on soybean- soybean aphid interactions NextSeq 500 GSE129626 GSM3717548 SRR8848032 single-end leaf Day1 1 4A_50 biotype 2_15 biotype1_Day1 LD12-15838R Characterization of induced susceptibility effects on soybean- soybean aphid interactions NextSeq 500 GSE129626 GSM3717549 SRR8848029 single-end leaf Day11 1 4C_50 biotype 2_15 biotype1_Day11 LD12-15838R Characterization of induced susceptibility effects on soybean- soybean aphid interactions NextSeq 500 GSE129626 GSM3717550 SRR8848030 single-end leaf Day11 1 5C_No Inducer_15 biotype1_Day11 LD12-15813Ra Characterization of induced susceptibility effects on soybean- soybean aphid interactions NextSeq 500 GSE129626 GSM3717551 SRR8848023 single-end leaf Day1 1 8A_50 biotype2_15 biotype1_Day1 LD12-15813Ra Characterization of induced susceptibility effects on soybean- soybean aphid interactions NextSeq 500 GSE129626 GSM3717552 SRR8848024 single-end leaf Day11 1 8C_50 biotype2_15 biotype1_Day11 LD12-15813Ra Characterization of induced susceptibility effects on soybean- soybean aphid interactions NextSeq 500 GSE112584 GSM3073252 SRR6924895 paired-end seedling 9 days after treatment 0 control_ph5.8_9days Harosoy 63 Identification of a NAC Transcription Factor for the Elicitation of Glyceollin Biosynthesis in Soybean Reveals a Conserved Phytoalexin Regulatory Pathway Illumina HiSeq 1500 GSE112584 GSM3073255 SRR6924898 paired-end seedling 9 days after treatment 1 treatment_ph3_9days Harosoy 63 Identification of a NAC Transcription Factor for the Elicitation of Glyceollin Biosynthesis in Soybean Reveals a Conserved Phytoalexin Regulatory Pathway Illumina HiSeq 1500 GSE112584 GSM3073258 SRR6924901 paired-end seedling 6 days after treatment 0 control_ph5.8_6days Harosoy 63 Identification of a NAC Transcription Factor for the Elicitation of Glyceollin Biosynthesis in Soybean Reveals a Conserved Phytoalexin Regulatory Pathway Illumina HiSeq 1500 GSE112584 GSM3073261 SRR6924904 paired-end seedling 6 days after treatment 1 treatment_ph3_6days Harosoy 63 Identification of a NAC Transcription Factor for the Elicitation of Glyceollin Biosynthesis in Soybean Reveals a Conserved Phytoalexin Regulatory Pathway Illumina HiSeq 1500 GSE103490 GSM2772382 SRR6006869 paired-end leaf germination day 30 0 DN50_rep1 None GmRAV1 regulates regeneration of root and adventitious buds by cytokinin in Arabidopsis and soybean Illumina HiSeq 2000 GSE114878 GSM3152839 SRR7213989 paired-end leaf 8:00 0 biological replicate 1 - 8:00 93B15 mRNA sequencing of field-grown Glycine max whole leaflets at four time points Illumina HiSeq 2000 GSE114878 GSM3152843 SRR7213993 paired-end leaf 11:00 0 biological replicate 1 - 11:00 93B15 mRNA sequencing of field-grown Glycine max whole leaflets at four time points Illumina HiSeq 2000 GSE114878 GSM3152847 SRR7213997 paired-end leaf 14:00 0 biological replicate 1 - 14:00 93B15 mRNA sequencing of field-grown Glycine max whole leaflets at four time points Illumina HiSeq 2000 GSE114878 GSM3152851 SRR7214001 paired-end leaf 17:00 0 biological replicate 1 - 17:00 93B15 mRNA sequencing of field-grown Glycine max whole leaflets at four time points Illumina HiSeq 2000 GSE122915 GSM3488014 SRR8241878 paired-end leaf 20 days after germination 0 GmBR16_20_DAG_1 GmBR16 Genes induced by senescence in soybean Illumina HiSeq 2500 GSE122915 GSM3488017 SRR8241881 paired-end leaf 80 days after germination 0 GmBR16_80_DAG_1 GmBR16 Genes induced by senescence in soybean Illumina HiSeq 2500 GSE116593 GSM3243555 SRR7468248 paired-end nodule 25 days 0 HP,phosphorus conccentration: 500 mM None Genome wide transcriptome analysis reveals complex regulatory mechanisms underlying phosphate homeostasis in soybean nodules HiSeq X Ten GSE116593 GSM3243558 SRR7468251 paired-end nodule 25 days 1 LP,phosphorus conccentration:25 mM None Genome wide transcriptome analysis reveals complex regulatory mechanisms underlying phosphate homeostasis in soybean nodules HiSeq X Ten GSE114448 GSM3141910 SRR7172314 single-end stem 4 weeks 0 non infected resistant soybean stem None Global transcriptome analysis of resistant and susceptible soybean lines following Sclerotinia sclerotiorum infection Illumina HiSeq 2500 GSE114448 GSM3141913 SRR7172317 single-end stem 4 weeks 1 resistant soybean stem 24 hours post sclerotinia infection None Global transcriptome analysis of resistant and susceptible soybean lines following Sclerotinia sclerotiorum infection Illumina HiSeq 2500 GSE114448 GSM3141916 SRR7172320 single-end stem 4 weeks 1 resistant soybean stem 48 hours post sclerotinia infection None Global transcriptome analysis of resistant and susceptible soybean lines following Sclerotinia sclerotiorum infection Illumina HiSeq 2500 GSE114448 GSM3141919 SRR7172323 single-end stem 4 weeks 1 resistant soybean stem 96 hours post sclerotinia infection None Global transcriptome analysis of resistant and susceptible soybean lines following Sclerotinia sclerotiorum infection Illumina HiSeq 2500 GSE114448 GSM3141922 SRR7172326 single-end stem 4 weeks 0 non infected susceptible soybean stem None Global transcriptome analysis of resistant and susceptible soybean lines following Sclerotinia sclerotiorum infection Illumina HiSeq 2500 GSE114448 GSM3141925 SRR7172329 single-end stem 4 weeks 1 susceptible soybean stem 24 hours post sclerotinia infection None Global transcriptome analysis of resistant and susceptible soybean lines following Sclerotinia sclerotiorum infection Illumina HiSeq 2500 GSE114448 GSM3141928 SRR7172332 single-end stem 4 weeks 1 susceptible soybean stem 48 hours post sclerotinia infection None Global transcriptome analysis of resistant and susceptible soybean lines following Sclerotinia sclerotiorum infection Illumina HiSeq 2500 GSE114448 GSM3141931 SRR7172335 single-end stem 4 weeks 1 susceptible soybean stem 96 hours post sclerotinia infection None Global transcriptome analysis of resistant and susceptible soybean lines following Sclerotinia sclerotiorum infection Illumina HiSeq 2500 GSE101692 GSM2712234 SRR5852804 single-end seed seed length 2-4 mm 0 3MWT-Stage1-Rep1_re-analyzed None Inference of transcription regulatory network in low phytic acid soybean seeds Illumina HiSeq 2000 GSE101692 GSM2712237 SRR5852807 single-end seed seed length 4-6 mm 0 3MWT-Stage2-Rep1_re-analyzed None Inference of transcription regulatory network in low phytic acid soybean seeds Illumina HiSeq 2000 GSE101692 GSM2712240 SRR5852810 single-end seed seed length 6-8 mm 0 3MWT-Stage3-Rep1_re-analyzed None Inference of transcription regulatory network in low phytic acid soybean seeds Illumina HiSeq 2000 GSE101692 GSM2712243 SRR5852813 single-end seed seed length 8-10 mm 0 3MWT-Stage4-Rep1_re-analyzed None Inference of transcription regulatory network in low phytic acid soybean seeds Illumina HiSeq 2000 GSE101692 GSM2712246 SRR5852816 single-end seed seed length 10-12 mm mm 0 3MWT-Stage5-Rep1_re-analyzed None Inference of transcription regulatory network in low phytic acid soybean seeds Illumina HiSeq 2000 GSE101692 GSM2712264 SRR5852834 single-end seed seed length 2-4 mm 0 1MWT-Stage1-Rep1 None Inference of transcription regulatory network in low phytic acid soybean seeds Illumina HiSeq 2000 GSE101692 GSM2712267 SRR5852837 single-end seed seed length 4-6 mm 0 1MWT-Stage2-Rep1 None Inference of transcription regulatory network in low phytic acid soybean seeds Illumina HiSeq 2000 GSE101692 GSM2712270 SRR5852840 single-end seed seed length 6-8 mm 0 1MWT-Stage3-Rep1 None Inference of transcription regulatory network in low phytic acid soybean seeds Illumina HiSeq 2000 GSE101692 GSM2712273 SRR5852843 single-end seed seed length 8-10 mm 0 1MWT-Stage4-Rep1 None Inference of transcription regulatory network in low phytic acid soybean seeds Illumina HiSeq 2000 GSE101692 GSM2712276 SRR5852846 single-end seed seed length 10-12 mm mm 0 1MWT-Stage5-Rep1 None Inference of transcription regulatory network in low phytic acid soybean seeds Illumina HiSeq 2000 GSE85714 GSM2282102 SRR4036063 paired-end leaf 28 Days after planting (R2 growth stage) 1 Line T295H_SterileAP1.1 T295H Molecular Analysis of Sink Limited Soybeans Illumina HiSeq 2500 GSE85714 GSM2282105 SRR4036066 paired-end leaf 35 days after planting 0 Line T295H_Sterile_Control2.1 T295H Molecular Analysis of Sink Limited Soybeans Illumina HiSeq 2500 GSE85714 GSM2282108 SRR4036069 paired-end leaf 35 days after planting 1 Line T295H_Sterile2.1 T295H Molecular Analysis of Sink Limited Soybeans Illumina HiSeq 2500 GSE85714 GSM2282111 SRR4036072 paired-end leaf 63 days after planting 0 Line T295H_Sterile_Control3.1 T295H Molecular Analysis of Sink Limited Soybeans Illumina HiSeq 2500 GSE85714 GSM2282114 SRR4036075 paired-end leaf 63 days after planting 1 Line T295H_Sterile3.1 T295H Molecular Analysis of Sink Limited Soybeans Illumina HiSeq 2500 GSE85714 GSM2282117 SRR4036078 paired-end leaf 38 days after planting (R2 growth stage) 1 Line Williams 82_AP1.1 Williams 82 Molecular Analysis of Sink Limited Soybeans Illumina HiSeq 2500 GSE85714 GSM2282120 SRR4036081 paired-end leaf 45 days after planting 0 Line Williams 82_Depodding_Control2.1 Williams 82 Molecular Analysis of Sink Limited Soybeans Illumina HiSeq 2500 GSE85714 GSM2282123 SRR4036084 paired-end leaf 45 days after planting 1 Line Williams 82_Depodding2.1 Williams 82 Molecular Analysis of Sink Limited Soybeans Illumina HiSeq 2500 GSE85714 GSM2282126 SRR4036087 paired-end leaf 54 days after planting 0 Line Williams 82_Depodding_Control3.1 Williams 82 Molecular Analysis of Sink Limited Soybeans Illumina HiSeq 2500 GSE85714 GSM2282129 SRR4036090 paired-end leaf 54 days after planting 1 Line Williams 82_Depodding3.1 Williams 82 Molecular Analysis of Sink Limited Soybeans Illumina HiSeq 2500 GSE85714 GSM2282132 SRR4036093 paired-end leaf 64 days after planting 0 Line Williams 82_Depodding_Control4.1 Williams 82 Molecular Analysis of Sink Limited Soybeans Illumina HiSeq 2500 GSE85714 GSM2282135 SRR4036096 paired-end leaf 64 days after planting 1 Line Williams 82_Depodding5.1 Williams 82 Molecular Analysis of Sink Limited Soybeans Illumina HiSeq 2500 GSE85714 GSM2282138 SRR4036099 paired-end leaf 76 days after planting 0 Line Williams 82_Depodding_Control5.1 Williams 82 Molecular Analysis of Sink Limited Soybeans Illumina HiSeq 2500 GSE85714 GSM2282141 SRR4036102 paired-end leaf 76 days after planting 1 Line Williams 82_Depodding4.1 Williams 82 Molecular Analysis of Sink Limited Soybeans Illumina HiSeq 2500 GSE94366 GSM2474145 SRR5221832 paired-end seed seeds after 13 days flowering 1 Cultivated soybean df12 None Characterizing seed weight related genes through transcriptome analyses of wild and cultivated soybeans Illumina HiSeq 2500 GSE94366 GSM2474146 SRR5221833 paired-end seed seeds after 13 days flowering 1 Cultivated soybean df14 None Characterizing seed weight related genes through transcriptome analyses of wild and cultivated soybeans Illumina HiSeq 2500 GSE94366 GSM2474147 SRR5221834 paired-end seed seeds after 13 days flowering 1 Cultivated soybean df17 None Characterizing seed weight related genes through transcriptome analyses of wild and cultivated soybeans Illumina HiSeq 2500 GSE94366 GSM2474148 SRR5221835 paired-end seed seeds after 13 days flowering 1 Cultivated soybean df36 None Characterizing seed weight related genes through transcriptome analyses of wild and cultivated soybeans Illumina HiSeq 2500 GSE94366 GSM2474149 SRR5221836 paired-end seed seeds after 13 days flowering 1 Cultivated soybean df3 None Characterizing seed weight related genes through transcriptome analyses of wild and cultivated soybeans Illumina HiSeq 2500 GSE94366 GSM2474150 SRR5221837 paired-end seed seeds after 13 days flowering 1 Cultivated soybean df43 None Characterizing seed weight related genes through transcriptome analyses of wild and cultivated soybeans Illumina HiSeq 2500 GSE94366 GSM2474151 SRR5221838 paired-end seed seeds after 13 days flowering 0 Wild soybean ys16 None Characterizing seed weight related genes through transcriptome analyses of wild and cultivated soybeans Illumina HiSeq 2500 GSE94366 GSM2474152 SRR5221839 paired-end seed seeds after 13 days flowering 0 Wild soybean ys17 None Characterizing seed weight related genes through transcriptome analyses of wild and cultivated soybeans Illumina HiSeq 2500 GSE94366 GSM2474153 SRR5221840 paired-end seed seeds after 13 days flowering 0 Wild soybean ys1 None Characterizing seed weight related genes through transcriptome analyses of wild and cultivated soybeans Illumina HiSeq 2500 GSE94366 GSM2474154 SRR5221841 paired-end seed seeds after 13 days flowering 0 Wild soybean ys23 None Characterizing seed weight related genes through transcriptome analyses of wild and cultivated soybeans Illumina HiSeq 2500 GSE94366 GSM2474155 SRR5221842 paired-end seed seeds after 13 days flowering 0 Wild soybean ys26 None Characterizing seed weight related genes through transcriptome analyses of wild and cultivated soybeans Illumina HiSeq 2500 GSE94366 GSM2474156 SRR5221843 paired-end seed seeds after 13 days flowering 0 Wild soybean ys29 None Characterizing seed weight related genes through transcriptome analyses of wild and cultivated soybeans Illumina HiSeq 2500 GSE94366 GSM2474157 SRR5221844 paired-end seed seeds after 13 days flowering 0 Wild soybean ys34 None Characterizing seed weight related genes through transcriptome analyses of wild and cultivated soybeans Illumina HiSeq 2500 GSE86608 GSM2306783 SRR4209737 single-end leaf None 0 F1 hybrid rep 1 Clayton F1 hybrid Changes in Gene Expression between Soybean F1 Hybrids and their Parents are Associated with Agronomically Valuable Traits NextSeq 500 GSE86608 GSM2306787 SRR4209749 single-end leaf None 1 NMS4-44-329 rep 1 Clayton Parent with G soja in pedigree Changes in Gene Expression between Soybean F1 Hybrids and their Parents are Associated with Agronomically Valuable Traits NextSeq 500 GSE86608 GSM2306791 SRR4209761 single-end leaf None 1 N7103 rep 1 Clayton recurrent G. max parent Changes in Gene Expression between Soybean F1 Hybrids and their Parents are Associated with Agronomically Valuable Traits NextSeq 500 GSE86608 GSM2306795 SRR4209773 single-end leaf None 0 F1 hybrid rep 1 Caswell F1 hybrid Changes in Gene Expression between Soybean F1 Hybrids and their Parents are Associated with Agronomically Valuable Traits NextSeq 500 GSE86608 GSM2306799 SRR4209785 single-end leaf None 1 NMS4-44-329 rep 1 Caswell Parent with G soja in pedigree Changes in Gene Expression between Soybean F1 Hybrids and their Parents are Associated with Agronomically Valuable Traits NextSeq 500 GSE86608 GSM2306803 SRR4209797 single-end leaf None 1 N7103 rep 1 Caswell recurrent G. max parent Changes in Gene Expression between Soybean F1 Hybrids and their Parents are Associated with Agronomically Valuable Traits NextSeq 500 GSE98199 GSM2589116 SRR5481101 single-end seed stage 7.1 0 seeds harvested at stage 7.1 BRS284 Expression profiling of Glycine max seed maturation by high throughput sequencing Illumina HiSeq 2500 GSE98199 GSM2589117 SRR5481110 single-end seed stage 7.2 0 seeds harvested at stage 7.2, replica 1 BRS284 Expression profiling of Glycine max seed maturation by high throughput sequencing Illumina HiSeq 2500 GSE98199 GSM2589119 SRR5481131 single-end seed stage 7.2 0 seeds harvested at stage 7.2 and dried, replica 1 BRS284 Expression profiling of Glycine max seed maturation by high throughput sequencing Illumina HiSeq 2500 GSE98199 GSM2589121 SRR5481155 single-end seed stage 7.3 0 seeds harvested at stage 7.3 BRS284 Expression profiling of Glycine max seed maturation by high throughput sequencing Illumina HiSeq 2500 GSE98199 GSM2589122 SRR5481161 single-end seed stage 8.1 0 seeds harvested at stage 8.1 BRS284 Expression profiling of Glycine max seed maturation by high throughput sequencing Illumina HiSeq 2500 GSE98199 GSM2589123 SRR5481167 single-end seed stage 8.2 0 seeds harvested at stage 8.2 BRS284 Expression profiling of Glycine max seed maturation by high throughput sequencing Illumina HiSeq 2500 GSE98199 GSM2589124 SRR5481173 single-end seed stage 8.3 0 seeds harvested at stage 8.3 BRS284 Expression profiling of Glycine max seed maturation by high throughput sequencing Illumina HiSeq 2500 GSE98199 GSM2589125 SRR5481182 single-end seed stage 9 0 seeds harvested at stage 9, replica 1 BRS284 Expression profiling of Glycine max seed maturation by high throughput sequencing Illumina HiSeq 2500 GSE83481 GSM2204137 SRR3680368 paired-end embryo_axis None 0 dry BRS284 Large-scale analysis of soybean embryonic axis in five time points during germination Illumina HiSeq 2000 GSE83481 GSM2204139 SRR3680378 paired-end embryo_axis None 1 3 hours after imbibition BRS284 Large-scale analysis of soybean embryonic axis in five time points during germination Illumina HiSeq 2000 GSE83481 GSM2204142 SRR3680393 paired-end embryo_axis None 1 6 hours after imbibition BRS284 Large-scale analysis of soybean embryonic axis in five time points during germination Illumina HiSeq 2000 GSE83481 GSM2204144 SRR3680403 paired-end embryo_axis None 1 12 hours after imbibition BRS284 Large-scale analysis of soybean embryonic axis in five time points during germination Illumina HiSeq 2000 GSE83481 GSM2204145 SRR3680408 paired-end embryo_axis None 1 24 hours after imbibition BRS284 Large-scale analysis of soybean embryonic axis in five time points during germination Illumina HiSeq 2000 GSE67779 GSM1655665 SRR1965003 single-end leaf 0h 0 no aphids,susceptible None Identification of Soybean Genes Differentially Regulated in Near Isogenic Lines Differing in Resistance to Aphid Infestation Illumina HiSeq 2000 GSE67779 GSM1655666 SRR1965004 single-end leaf 4h 1 4h after aphid infestation,susceptible None Identification of Soybean Genes Differentially Regulated in Near Isogenic Lines Differing in Resistance to Aphid Infestation Illumina HiSeq 2000 GSE67779 GSM1655667 SRR1965005 single-end leaf 8h 1 8h after aphid infestation,susceptible None Identification of Soybean Genes Differentially Regulated in Near Isogenic Lines Differing in Resistance to Aphid Infestation Illumina HiSeq 2000 GSE67779 GSM1655668 SRR1965006 single-end leaf 24h 1 24h after aphid infestation,susceptible None Identification of Soybean Genes Differentially Regulated in Near Isogenic Lines Differing in Resistance to Aphid Infestation Illumina HiSeq 2000 GSE67779 GSM1655669 SRR1965007 single-end leaf 48h 1 48h after aphid infestation,susceptible None Identification of Soybean Genes Differentially Regulated in Near Isogenic Lines Differing in Resistance to Aphid Infestation Illumina HiSeq 2000 GSE66861 GSM1633404 SRR1914574 paired-end seedling 72 hpi 0 control,72 hours post inoculation None Transcriptome profiles in compatible and incompatible interactions between soybean and Fusarium oxysporum Illumina HiSeq 2500 GSE66861 GSM1633407 SRR1914577 paired-end seedling 96 hpi 0 control,96 hours post inoculation None Transcriptome profiles in compatible and incompatible interactions between soybean and Fusarium oxysporum Illumina HiSeq 2500 GSE66861 GSM1633410 SRR1914580 paired-end seedling 72 hpi 1 72 hours post FO36 non-pathogenic fusarium oxysporum inoculation None Transcriptome profiles in compatible and incompatible interactions between soybean and Fusarium oxysporum Illumina HiSeq 2500 GSE66861 GSM1633413 SRR1914583 paired-end seedling 96 hpi 1 96 hours post FO36 non-pathogenic fusarium oxysporum inoculation None Transcriptome profiles in compatible and incompatible interactions between soybean and Fusarium oxysporum Illumina HiSeq 2500 GSE66861 GSM1633416 SRR1914586 paired-end seedling 72 hpi 1 72 hours post FO40 pathogenic fusarium oxysporum inoculation None Transcriptome profiles in compatible and incompatible interactions between soybean and Fusarium oxysporum Illumina HiSeq 2500 GSE66861 GSM1633419 SRR1914589 paired-end seedling 96 hpi 1 96 hours post FO40 pathogenic fusarium oxysporum inoculation None Transcriptome profiles in compatible and incompatible interactions between soybean and Fusarium oxysporum Illumina HiSeq 2500 GSE59076 GSM1426228 SRR1506089 single-end leaf 30 minute increments starting 5 hours after introduction of ozone 0 25ppb ozone,control,1 time point None RNA-seq analysis reveals genetic response and tolerance mechanisms to ozone exposure in soybean Illumina HiSeq 2000 GSE59076 GSM1426230 SRR1506091 single-end leaf 30 minute increments starting 5 hours after introduction of ozone 1 75ppb ozone,treatment,1 time point None RNA-seq analysis reveals genetic response and tolerance mechanisms to ozone exposure in soybean Illumina HiSeq 2000 GSE59076 GSM1426232 SRR1506093 single-end leaf 30 minute increments starting 5 hours after introduction of ozone 0 25ppb ozone,control,2 time point None RNA-seq analysis reveals genetic response and tolerance mechanisms to ozone exposure in soybean Illumina HiSeq 2000 GSE59076 GSM1426234 SRR1506095 single-end leaf 30 minute increments starting 5 hours after introduction of ozone 1 75ppb ozone,treatment,2 time point None RNA-seq analysis reveals genetic response and tolerance mechanisms to ozone exposure in soybean Illumina HiSeq 2000 GSE59076 GSM1426236 SRR1506097 single-end leaf 30 minute increments starting 5 hours after introduction of ozone 1 75ppb ozone,treatment,3 time point None RNA-seq analysis reveals genetic response and tolerance mechanisms to ozone exposure in soybean Illumina HiSeq 2000 GSE59076 GSM1426239 SRR1506100 single-end leaf 30 minute increments starting 5 hours after introduction of ozone 0 25ppb ozone,control,3 time point None RNA-seq analysis reveals genetic response and tolerance mechanisms to ozone exposure in soybean Illumina HiSeq 2000 GSE59076 GSM1426241 SRR1506102 single-end leaf 30 minute increments starting 5 hours after introduction of ozone 0 25ppb ozone,control,4 time point None RNA-seq analysis reveals genetic response and tolerance mechanisms to ozone exposure in soybean Illumina HiSeq 2000 GSE59076 GSM1426243 SRR1506104 single-end leaf 30 minute increments starting 5 hours after introduction of ozone 1 75ppb ozone,treatment,4 time point None RNA-seq analysis reveals genetic response and tolerance mechanisms to ozone exposure in soybean Illumina HiSeq 2000 GSE75575 GSM1959602 SRR5352361 single-end seed seed length: 2-4 mm 0 3MWT-Stage1,2-4mm-Rep1 None Genome-wide transcriptome analyses of developing seeds from low and normal phytic acid soybean lines Illumina HiSeq 2000 GSE75575 GSM1959605 SRR5352364 single-end seed seed length: 4-6 mm 0 3MWT-Stage2,4-6 mm-Rep1 None Genome-wide transcriptome analyses of developing seeds from low and normal phytic acid soybean lines Illumina HiSeq 2000 GSE75575 GSM1959608 SRR5352367 single-end seed seed length: 6-8 mm 0 3MWT-Stage3,6-8 mm-Rep1 None Genome-wide transcriptome analyses of developing seeds from low and normal phytic acid soybean lines Illumina HiSeq 2000 GSE75575 GSM1959611 SRR5352370 single-end seed seed length: 8-10 mm 0 3MWT-Stage4,8-10 mm-Rep1 None Genome-wide transcriptome analyses of developing seeds from low and normal phytic acid soybean lines Illumina HiSeq 2000 GSE75575 GSM1959614 SRR5352373 single-end seed seed length: 10-12 mm 0 3MWT-Stage5,10-12 mm-Rep1 None Genome-wide transcriptome analyses of developing seeds from low and normal phytic acid soybean lines Illumina HiSeq 2000 GSE69469 GSM1701586 SRR2048167 paired-end leaf developmental stage: V1 1 ZT0_8h_water_deficit BR16 Daytime soybean transcriptome fluctuations during water deficit stress Illumina HiSeq 2000 GSE69469 GSM1701589 SRR2048170 paired-end leaf developmental stage: V1 0 ZT0_8h_control BR16 Daytime soybean transcriptome fluctuations during water deficit stress Illumina HiSeq 2000 GSE69469 GSM1701592 SRR2048173 paired-end leaf developmental stage: V1 1 ZT4_12h_water_deficit BR16 Daytime soybean transcriptome fluctuations during water deficit stress Illumina HiSeq 2000 GSE69469 GSM1701595 SRR2048176 paired-end leaf developmental stage: V1 0 ZT4_12h_control BR16 Daytime soybean transcriptome fluctuations during water deficit stress Illumina HiSeq 2000 GSE69469 GSM1701598 SRR2048179 paired-end leaf developmental stage: V1 1 ZT8_16h_water_deficit BR16 Daytime soybean transcriptome fluctuations during water deficit stress Illumina HiSeq 2000 GSE69469 GSM1701601 SRR2048182 paired-end leaf developmental stage: V1 0 ZT8_16h_control BR16 Daytime soybean transcriptome fluctuations during water deficit stress Illumina HiSeq 2000 GSE69469 GSM1701604 SRR2048185 paired-end leaf developmental stage: V1 1 ZT12_20h_water_deficit BR16 Daytime soybean transcriptome fluctuations during water deficit stress Illumina HiSeq 2000 GSE69469 GSM1701607 SRR2048188 paired-end leaf developmental stage: V1 0 ZT12_20h_control BR16 Daytime soybean transcriptome fluctuations during water deficit stress Illumina HiSeq 2000 GSE69469 GSM1701610 SRR2048191 paired-end leaf developmental stage: V1 1 ZT16_24h_water_deficit BR16 Daytime soybean transcriptome fluctuations during water deficit stress Illumina HiSeq 2000 GSE69469 GSM1701615 SRR2048196 paired-end leaf developmental stage: V1 0 ZT16_24h_control BR16 Daytime soybean transcriptome fluctuations during water deficit stress Illumina HiSeq 2000 GSE69469 GSM1701616 SRR2048197 paired-end leaf developmental stage: V1 1 ZT20_4h_water_deficit BR16 Daytime soybean transcriptome fluctuations during water deficit stress Illumina HiSeq 2000 GSE69469 GSM1701619 SRR2048200 paired-end leaf developmental stage: V1 0 ZT20_4h_control BR16 Daytime soybean transcriptome fluctuations during water deficit stress Illumina HiSeq 2000 GSE61857 GSM1515813 SRR1592286 paired-end cotyledon 4 days after planting 0 Cotyledon_Stage1_rep1 None Gene Expression Profiling of Glycine max Cotyledons and Trifoliate Leaves to Determine Genes Associated with Senescence Illumina HiScanSQ GSE61857 GSM1515816 SRR1592289 paired-end cotyledon 15 days after planting 0 Cotyledon_Stage2_rep1 None Gene Expression Profiling of Glycine max Cotyledons and Trifoliate Leaves to Determine Genes Associated with Senescence Illumina HiScanSQ GSE61857 GSM1515819 SRR1592292 paired-end cotyledon 27 days after planting 0 Cotyledon_Stage3_rep1 None Gene Expression Profiling of Glycine max Cotyledons and Trifoliate Leaves to Determine Genes Associated with Senescence Illumina HiScanSQ GSE61857 GSM1515822 SRR1592295 paired-end leaf V3 Stage 0 Leaf_Stage1_rep1 None Gene Expression Profiling of Glycine max Cotyledons and Trifoliate Leaves to Determine Genes Associated with Senescence Illumina HiSeq 2500 GSE61857 GSM1515825 SRR1592298 paired-end leaf 2 weeks after V3 stage 0 Leaf_Stage3_rep1 None Gene Expression Profiling of Glycine max Cotyledons and Trifoliate Leaves to Determine Genes Associated with Senescence Illumina HiSeq 2500 GSE61857 GSM1515828 SRR1592301 paired-end leaf 4 weeks after V3 stage 0 Leaf_Stage5_rep1 None Gene Expression Profiling of Glycine max Cotyledons and Trifoliate Leaves to Determine Genes Associated with Senescence Illumina HiSeq 2500 GSE61857 GSM1515831 SRR1592304 paired-end leaf 6 weeks after V3 stage 0 Leaf_Stage7_rep1 None Gene Expression Profiling of Glycine max Cotyledons and Trifoliate Leaves to Determine Genes Associated with Senescence Illumina HiSeq 2500 GSE61857 GSM1515834 SRR1592307 paired-end leaf 7 weeks after V3 stage 0 Leaf_Stage8_rep1 None Gene Expression Profiling of Glycine max Cotyledons and Trifoliate Leaves to Determine Genes Associated with Senescence Illumina HiSeq 2500 GSE42550 GSM1044984 SRR620376 single-end cotyledon 1 day after imbibition 0 R76_Germinating_Cotyledons_Stage1_BR1 Williams Transcription factors and glyoxylate cycle genes prominent in the transition of soybean cotyledons to the first functional leaves of the seedling Illumina HiSeq 2000 GSE42550 GSM1044986 SRR620378 single-end cotyledon 2 day after imbibition 0 R77_Germinating_Cotyledons_Stage2_BR1 Williams Transcription factors and glyoxylate cycle genes prominent in the transition of soybean cotyledons to the first functional leaves of the seedling Illumina HiSeq 2000 GSE42550 GSM1044988 SRR620380 single-end cotyledon 2-3 days after planting 0 R78_Germinating_Cotyledons_Stage3_BR1 Williams Transcription factors and glyoxylate cycle genes prominent in the transition of soybean cotyledons to the first functional leaves of the seedling Illumina HiSeq 2000 GSE42550 GSM1044990 SRR620382 single-end cotyledon 3-4 days after planting 0 R79_Germinating_Cotyledons_Stage4_BR1 Williams Transcription factors and glyoxylate cycle genes prominent in the transition of soybean cotyledons to the first functional leaves of the seedling Illumina HiSeq 2000 GSE42550 GSM1044992 SRR620384 single-end cotyledon 4-5 days after planting 0 R80_Germinating_Cotyledons_Stage5_BR1 Williams Transcription factors and glyoxylate cycle genes prominent in the transition of soybean cotyledons to the first functional leaves of the seedling Illumina HiSeq 2000 GSE42550 GSM1044994 SRR620386 single-end cotyledon 5-6 days after planting 0 R81_Germinating_Cotyledons_Stage6_BR1 Williams Transcription factors and glyoxylate cycle genes prominent in the transition of soybean cotyledons to the first functional leaves of the seedling Illumina HiSeq 2000 GSE42550 GSM1044996 SRR620388 single-end cotyledon 6-7 days after planting 0 R82_Germinating_Cotyledons_Stage7_BR1 Williams Transcription factors and glyoxylate cycle genes prominent in the transition of soybean cotyledons to the first functional leaves of the seedling Illumina HiSeq 2000 GSE49097 GSM1193705 SRR942068 single-end leaf None 1 high vapor pressure deficit(VPD) Hutchesen Genes Differentially Expressed in Slow Wilting Phenotypes under a High Vapor Pressure Deficit Illumina HiSeq 2000 GSE49097 GSM1193706 SRR942069 single-end leaf None 1 high vapor pressure deficit(VPD) PI471938 Genes Differentially Expressed in Slow Wilting Phenotypes under a High Vapor Pressure Deficit Illumina HiSeq 2000 GSE49097 GSM1193707 SRR942070 single-end leaf None 1 high vapor pressure deficit(VPD) PI416937 Genes Differentially Expressed in Slow Wilting Phenotypes under a High Vapor Pressure Deficit Illumina HiSeq 2000 GSE49097 GSM1193708 SRR942071 single-end leaf None 1 high vapor pressure deficit(VPD) PI416937 Genes Differentially Expressed in Slow Wilting Phenotypes under a High Vapor Pressure Deficit Illumina HiSeq 2000 GSE49097 GSM1193709 SRR942072 single-end leaf None 1 high vapor pressure deficit(VPD) PI471938 Genes Differentially Expressed in Slow Wilting Phenotypes under a High Vapor Pressure Deficit Illumina HiSeq 2000 GSE49097 GSM1193710 SRR942073 single-end leaf None 1 high vapor pressure deficit(VPD) Hutchesen Genes Differentially Expressed in Slow Wilting Phenotypes under a High Vapor Pressure Deficit Illumina HiSeq 2000 GSE49097 GSM1193711 SRR942074 single-end leaf None 0 low vapor pressure deficit(VPD) Hutchesen Genes Differentially Expressed in Slow Wilting Phenotypes under a High Vapor Pressure Deficit Illumina HiSeq 2000 GSE49097 GSM1193712 SRR942075 single-end leaf None 0 low vapor pressure deficit(VPD) PI471938 Genes Differentially Expressed in Slow Wilting Phenotypes under a High Vapor Pressure Deficit Illumina HiSeq 2000 GSE49097 GSM1193713 SRR942076 single-end leaf None 0 low vapor pressure deficit(VPD) PI416937 Genes Differentially Expressed in Slow Wilting Phenotypes under a High Vapor Pressure Deficit Illumina HiSeq 2000 GSE49097 GSM1193714 SRR942077 single-end leaf None 0 low vapor pressure deficit(VPD) Hutchesen Genes Differentially Expressed in Slow Wilting Phenotypes under a High Vapor Pressure Deficit Illumina HiSeq 2000 GSE49097 GSM1193715 SRR942078 single-end leaf None 0 low vapor pressure deficit(VPD) PI416937 Genes Differentially Expressed in Slow Wilting Phenotypes under a High Vapor Pressure Deficit Illumina HiSeq 2000 GSE49097 GSM1193716 SRR942079 single-end leaf None 0 low vapor pressure deficit(VPD) PI471938 Genes Differentially Expressed in Slow Wilting Phenotypes under a High Vapor Pressure Deficit Illumina HiSeq 2000 GSE54903 GSM1326387 SRR1168173 single-end seed_coat 50-100mg seed weight stage 0 Clark_standard Clark RNA-Seq Profiling of a Defective Seed Coat Mutation in Glycine max Reveals Differential Expression of Proline Rich and Other Cell Wall Protein Transcripts Illumina HiSeq 2000 GSE54903 GSM1326388 SRR1168174 single-end seed_coat 100-200mg seed weight stage 0 Clark_standard Clark RNA-Seq Profiling of a Defective Seed Coat Mutation in Glycine max Reveals Differential Expression of Proline Rich and Other Cell Wall Protein Transcripts Illumina Genome Analyzer II GSE54903 GSM1326389 SRR1168175 single-end seed_coat 400-500mg seed weight stage 0 Clark_standard Clark RNA-Seq Profiling of a Defective Seed Coat Mutation in Glycine max Reveals Differential Expression of Proline Rich and Other Cell Wall Protein Transcripts Illumina HiSeq 2000 GSE54903 GSM1326393 SRR1168179 single-end seed_coat 50-100mg seed weight stage 0 Harosoy_standard Harosoy RNA-Seq Profiling of a Defective Seed Coat Mutation in Glycine max Reveals Differential Expression of Proline Rich and Other Cell Wall Protein Transcripts Illumina HiSeq 2000 GSE54903 GSM1326394 SRR1168180 single-end seed_coat 100-200mg seed weight stage 0 Harosoy_standard Harosoy RNA-Seq Profiling of a Defective Seed Coat Mutation in Glycine max Reveals Differential Expression of Proline Rich and Other Cell Wall Protein Transcripts Illumina Genome Analyzer II GSE54903 GSM1326395 SRR1168181 single-end seed_coat 400-500mg seed weight stage 0 Harosoy_standard Harosoy RNA-Seq Profiling of a Defective Seed Coat Mutation in Glycine max Reveals Differential Expression of Proline Rich and Other Cell Wall Protein Transcripts Illumina HiSeq 2000 GSE48524 GSM1180272 SRR925830 paired-end stem None 1 P. sojae inoculated Williams Comparative Transcriptomics of Soybean Near Isogenic Lines in Response to Phytophthora Sojae Illumina HiScanSQ GSE48524 GSM1180273 SRR925831 paired-end stem None 1 P. sojae inoculated Rps1-a Comparative Transcriptomics of Soybean Near Isogenic Lines in Response to Phytophthora Sojae Illumina HiScanSQ GSE48524 GSM1180277 SRR925835 paired-end stem None 1 P. sojae inoculated Rps3-a Comparative Transcriptomics of Soybean Near Isogenic Lines in Response to Phytophthora Sojae Illumina HiScanSQ GSE48524 GSM1180280 SRR925838 paired-end stem None 1 P. sojae inoculated Rps4 Comparative Transcriptomics of Soybean Near Isogenic Lines in Response to Phytophthora Sojae Illumina HiScanSQ GSE48524 GSM1180281 SRR925839 paired-end stem None 1 P. sojae inoculated Rps5 Comparative Transcriptomics of Soybean Near Isogenic Lines in Response to Phytophthora Sojae Illumina HiScanSQ GSE48524 GSM1180282 SRR925840 paired-end stem None 1 P. sojae inoculated Rps6 Comparative Transcriptomics of Soybean Near Isogenic Lines in Response to Phytophthora Sojae Illumina HiScanSQ GSE48524 GSM1180283 SRR925841 paired-end stem None 0 mock-inoculated Williams Comparative Transcriptomics of Soybean Near Isogenic Lines in Response to Phytophthora Sojae Illumina HiScanSQ GSE48524 GSM1180284 SRR925842 paired-end stem None 0 mock-inoculated Rps1-a Comparative Transcriptomics of Soybean Near Isogenic Lines in Response to Phytophthora Sojae Illumina HiScanSQ GSE48524 GSM1180288 SRR925846 paired-end stem None 0 mock-inoculated Rps3-a Comparative Transcriptomics of Soybean Near Isogenic Lines in Response to Phytophthora Sojae Illumina HiScanSQ GSE48524 GSM1180291 SRR925849 paired-end stem None 0 mock-inoculated Rps4 Comparative Transcriptomics of Soybean Near Isogenic Lines in Response to Phytophthora Sojae Illumina HiScanSQ GSE48524 GSM1180292 SRR925850 paired-end stem None 0 mock-inoculated Rps5 Comparative Transcriptomics of Soybean Near Isogenic Lines in Response to Phytophthora Sojae Illumina HiScanSQ GSE48524 GSM1180293 SRR925851 paired-end stem None 0 mock-inoculated Rps6 Comparative Transcriptomics of Soybean Near Isogenic Lines in Response to Phytophthora Sojae Illumina HiScanSQ GSE46153 GSM1125101 SRR830182 paired-end embryo 5 days post initial seed size of 3-4 mm long 0 Day 5, rep 1 Williams 82 Metabolic and Transcriptional Reprogramming in Developing Soybean (Glycine max) Embryos Illumina HiSeq 2000 GSE46153 GSM1125104 SRR830185 paired-end embryo 10 days post initial seed size of 3-4 mm long 0 Day 10, rep 1 Williams 82 Metabolic and Transcriptional Reprogramming in Developing Soybean (Glycine max) Embryos Illumina HiSeq 2000 GSE46153 GSM1125107 SRR830188 paired-end embryo 15 days post initial seed size of 3-4 mm long 0 Day 15, rep 1 Williams 82 Metabolic and Transcriptional Reprogramming in Developing Soybean (Glycine max) Embryos Illumina HiSeq 2000 GSE46153 GSM1125110 SRR830191 paired-end embryo 20 days post initial seed size of 3-4 mm long 0 Day 20, rep 1 Williams 82 Metabolic and Transcriptional Reprogramming in Developing Soybean (Glycine max) Embryos Illumina HiSeq 2000 GSE46153 GSM1125113 SRR830194 paired-end embryo 25 days post initial seed size of 3-4 mm long 0 Day 25, rep 1 Williams 82 Metabolic and Transcriptional Reprogramming in Developing Soybean (Glycine max) Embryos Illumina HiSeq 2000 GSE46153 GSM1125116 SRR830197 paired-end embryo 30 days post initial seed size of 3-4 mm long 0 Day 30, rep 1 Williams 82 Metabolic and Transcriptional Reprogramming in Developing Soybean (Glycine max) Embryos Illumina HiSeq 2000 GSE46153 GSM1125119 SRR830200 paired-end embryo 35 days post initial seed size of 3-4 mm long 0 Day 35, rep 1 Williams 82 Metabolic and Transcriptional Reprogramming in Developing Soybean (Glycine max) Embryos Illumina HiSeq 2000 GSE46153 GSM1125122 SRR830203 paired-end embryo 40 days post initial seed size of 3-4 mm long 0 Day 40, rep 1 Williams 82 Metabolic and Transcriptional Reprogramming in Developing Soybean (Glycine max) Embryos Illumina HiSeq 2000 GSE46153 GSM1125125 SRR830206 paired-end embryo 45 days post initial seed size of 3-4 mm long 0 Day 45, rep 1 Williams 82 Metabolic and Transcriptional Reprogramming in Developing Soybean (Glycine max) Embryos Illumina HiSeq 2000 GSE46153 GSM1125128 SRR830209 paired-end embryo 55 days post initial seed size of 3-4 mm long 0 Day 55, rep 1 Williams 82 Metabolic and Transcriptional Reprogramming in Developing Soybean (Glycine max) Embryos Illumina HiSeq 2000 GSE42871 GSM1056094 SRR639162 paired-end seed 4 days after flowering 0 fresh frozen, no purification Williams 43 Using RNA-Seq to Profile Soybean Seed Development from Fertilization to Maturity Illumina Genome Analyzer II GSE42871 GSM1056096 SRR639164 paired-end seed 12-14 days after flowering 0 fresh frozen, no purification Williams 43 Using RNA-Seq to Profile Soybean Seed Development from Fertilization to Maturity Illumina Genome Analyzer II GSE42871 GSM1056098 SRR639166 single-end seed 22-24 days after flowering 0 fresh frozen, no purification Williams 43 Using RNA-Seq to Profile Soybean Seed Development from Fertilization to Maturity Illumina HiSeq 2000 GSE42871 GSM1056100 SRR639168 paired-end seed 5-6mg fresh weight 0 fresh frozen, no purification Williams 43 Using RNA-Seq to Profile Soybean Seed Development from Fertilization to Maturity Illumina Genome Analyzer II GSE42871 GSM1056102 SRR639170 single-end cotyledon 100-200mg fresh weight 0 lyophilized, purification: Qiagen Rneasy Midi kit Williams 43 Using RNA-Seq to Profile Soybean Seed Development from Fertilization to Maturity Illumina Genome Analyzer II GSE42871 GSM1056104 SRR639172 paired-end cotyledon 400-500mg fresh weight 0 lyophilized, purification: Qiagen Rneasy Midi kit Williams 43 Using RNA-Seq to Profile Soybean Seed Development from Fertilization to Maturity Illumina Genome Analyzer II GSE42871 GSM1056106 SRR639174 paired-end seed dry mature seed 0 room temperature, purification: Qiagen Rneasy Midi kit Williams 43 Using RNA-Seq to Profile Soybean Seed Development from Fertilization to Maturity Illumina Genome Analyzer II GSE42871 GSM1056108 SRR639176 single-end cotyledon 5-6mg fresh weight 0 fresh frozen Williams 43 Using RNA-Seq to Profile Soybean Seed Development from Fertilization to Maturity Illumina HiSeq 2000 GSE29163 GSM721725 SRR203351 single-end seed globular-stage embryo 0 Soybean seeds containing globular-stage embryos Williams 82 Genome-Wide Transcript Profiling During Soybean Seed Development and Throughout the Soybean Life Cycle Illumina HiSeq 2000 GSE29163 GSM721726 SRR203354 single-end seed heart-stage embryo 0 Soybean seeds containing heart-stage embryos Williams 82 Genome-Wide Transcript Profiling During Soybean Seed Development and Throughout the Soybean Life Cycle Illumina HiSeq 2000 GSE29163 GSM721727 SRR203356 single-end seed cotyledon-stage embryo 0 Soybean seeds containing cotyledon-stage embryos Williams 82 Genome-Wide Transcript Profiling During Soybean Seed Development and Throughout the Soybean Life Cycle Illumina HiSeq 2000 GSE29163 GSM721728 SRR203358 single-end seed early maturation-stage embryo 0 Soybean seeds containing early-maturation stage seeds Williams 82 Genome-Wide Transcript Profiling During Soybean Seed Development and Throughout the Soybean Life Cycle Illumina HiSeq 2000 GSE29163 GSM721729 SRR203361 single-end seed dry 0 Dry seeds Williams 82 Genome-Wide Transcript Profiling During Soybean Seed Development and Throughout the Soybean Life Cycle Illumina HiSeq 2000 GSE29163 GSM721730 SRR203363 single-end leaf None 0 Trifoliate leaves Williams 82 Genome-Wide Transcript Profiling During Soybean Seed Development and Throughout the Soybean Life Cycle Illumina HiSeq 2000 GSE29163 GSM721731 SRR203364 single-end root None 0 Roots Williams 82 Genome-Wide Transcript Profiling During Soybean Seed Development and Throughout the Soybean Life Cycle Illumina HiSeq 2000 GSE29163 GSM721732 SRR203365 single-end stem None 0 Stems Williams 82 Genome-Wide Transcript Profiling During Soybean Seed Development and Throughout the Soybean Life Cycle Illumina HiSeq 2000 GSE29163 GSM721733 SRR203366 single-end flower_bud None 0 Floral buds Williams 82 Genome-Wide Transcript Profiling During Soybean Seed Development and Throughout the Soybean Life Cycle Illumina HiSeq 2000 GSE29163 GSM721734 SRR203368 single-end seedling 6 days after imbibition 0 Whole seedlings six days after imbibition Williams 82 Genome-Wide Transcript Profiling During Soybean Seed Development and Throughout the Soybean Life Cycle Illumina HiSeq 2000 GSE46096 GSM1123204 SRR827653 single-end embryo_axis seeds ranging 6.0-7.0mm in length 0 Soybean Early Maturation Axis Parenchyma-Biological replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Early Maturation Stage Illumina HiSeq 2000 GSE46096 GSM1123207 SRR827657 single-end embryo_axis seeds ranging 6.0-7.0mm in length 0 Soybean Early Maturation Axis Vasculature-Biological replicate 2 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Early Maturation Stage Illumina HiSeq 2000 GSE46096 GSM1123209 SRR827666 single-end cotyledon seeds ranging 6.0-7.0mm in length 0 Soybean Early Maturation Cotyledon Abaxial Epidermis-Biological replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Early Maturation Stage Illumina HiSeq 2000 GSE46096 GSM1123212 SRR827672 single-end cotyledon seeds ranging 6.0-7.0mm in length 0 Soybean Early Maturation Cotyledon Vasculature-Biological replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Early Maturation Stage Illumina HiSeq 2000 GSE46096 GSM1123214 SRR827675 single-end endosperm seeds ranging 6.0-7.0mm in length 0 Soybean Early Maturation Endosperm-Biological replicate 3 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Early Maturation Stage Illumina HiSeq 2000 GSE46096 GSM1123215 SRR827677 single-end seed_coat seeds ranging 6.0-7.0mm in length 0 Soybean Early Maturation Seed Coat Hilum-Biological Replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Early Maturation Stage Illumina HiSeq 2000 GSE46096 GSM1123218 SRR827681 single-end root_tip seeds ranging 6.0-7.0mm in length 0 Soybean Early Maturation Root Tip-Biological replicate 2 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Early Maturation Stage Illumina HiSeq 2000 GSE46096 GSM1123220 SRR827687 single-end seed_coat seeds ranging 6.0-7.0mm in length 0 Soybean Early Maturation Seed Coat Hourglass-Biological Replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Early Maturation Stage Illumina HiSeq 2000 GSE46096 GSM1123223 SRR827693 single-end seed_coat seeds ranging 6.0-7.0mm in length 0 Soybean Early Maturation Seed Coat Palisade-Biological Replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Early Maturation Stage Illumina HiSeq 2000 GSE46096 GSM1123225 SRR827697 single-end seed_coat seeds ranging 6.0-7.0mm in length 0 Soybean Early Maturation Seed Coat Parenchyma-Biological Replicate 1 Williams 82 Gene Expression Changes in the Development of the Soybean Seed-Early Maturation Stage Illumina HiSeq 2000 GSE34875 GSM856142 SRR394316 single-end root 14 days after germination 0 mRNA-seq of roots cultivar Heinong44 Analysis of soybean DNA methylomes shows CHH hypermethylation enhances gene expression in cotyledons of developing seeds Illumina Genome Analyzer IIx GSE34875 GSM856143 SRR394317 single-end stem 14 days after germination 0 mRNA-seq of stems cultivar Heinong44 Analysis of soybean DNA methylomes shows CHH hypermethylation enhances gene expression in cotyledons of developing seeds Illumina Genome Analyzer IIx GSE34875 GSM856144 SRR394318 single-end leaf 14 days after germination 0 mRNA-seq of leaves cultivar Heinong44 Analysis of soybean DNA methylomes shows CHH hypermethylation enhances gene expression in cotyledons of developing seeds Illumina Genome Analyzer IIx GSE34875 GSM856145 SRR394319 single-end cotyledon 20 days after flowering 0 mRNA-seq of cotyledons cultivar Heinong44 Analysis of soybean DNA methylomes shows CHH hypermethylation enhances gene expression in cotyledons of developing seeds Illumina Genome Analyzer IIx GSE37895 GSM1213857 SRR955406 single-end embryo_axis Early maturation-stage 0 Early maturation-stage embryonic axis [RNA-seq] Williams 82 Methylation Changes in Soybean Early Maturation Seed Parts Illumina HiSeq 2000 GSE114074 GSM3132197 SRR7124207 single-end leaf None 0 mRNA gmax FC33243 Anderson FC33243 Anderson Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132198 SRR7124208 single-end leaf None 0 mRNA gmax PI548360 Korean PI548360 Korean Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132199 SRR7124209 single-end leaf None 0 mRNA gmax PI548362 Lincoln PI548362 Lincoln Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132200 SRR7124210 single-end leaf None 0 mRNA gmax PI548379 Mandarin PI548379 Mandarin Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132201 SRR7124211 single-end leaf None 0 mRNA gmax PI548391 Mukden PI548391 Mukden Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132202 SRR7124212 single-end leaf None 0 mRNA gmax PI548406 Richland PI548406 Richland Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132203 SRR7124213 single-end leaf None 0 mRNA gmax PI548456 Haberlandt PI548456 Haberlandt Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132204 SRR7124214 single-end leaf None 0 mRNA gmax PI548477 Ogden PI548477 Ogden Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132205 SRR7124215 single-end leaf None 0 mRNA gmax PI548484 Ralsoy PI548484 Ralsoy Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132206 SRR7124216 single-end leaf None 0 mRNA gmax PI548485 Roanoke PI548485 Roanoke Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132207 SRR7124217 single-end leaf None 0 mRNA gmax PI548488 S-100 PI548488 S-100 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132208 SRR7124218 single-end leaf None 0 mRNA gmax PI508266 Young PI508266 Young Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132209 SRR7124219 single-end leaf None 0 mRNA gmax PI548493 Tokyo PI548493 Tokyo Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132210 SRR7124220 single-end leaf None 0 mRNA gmax PI548505 Amcor PI548505 Amcor Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132211 SRR7124221 single-end leaf None 0 mRNA gmax PI548510 Beeson PI548510 Beeson Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132212 SRR7124222 single-end leaf None 0 mRNA gmax PI548512 Century PI548512 Century Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132213 SRR7124223 single-end leaf None 0 mRNA gmax PI548516 Blackhawk PI548516 Blackhawk Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132214 SRR7124224 single-end leaf None 0 mRNA gmax PI548517 Bonus PI548517 Bonus Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132215 SRR7124225 single-end leaf None 0 mRNA gmax PI548523 Pella PI548523 Pella Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132216 SRR7124226 single-end leaf None 0 mRNA gmax PI548527 Calland PI548527 Calland Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132217 SRR7124227 single-end leaf None 0 mRNA gmax PI548530 Chippewa PI548530 Chippewa Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132218 SRR7124228 single-end leaf None 0 mRNA gmax PI548533 Clark PI548533 Clark Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132219 SRR7124229 single-end leaf None 0 mRNA gmax PI518671 Williams82 PI518671 Williams 82 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132220 SRR7124230 single-end leaf None 0 mRNA gmax PI548540 Corsoy PI548540 Corsoy Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132221 SRR7124231 single-end leaf None 0 mRNA gmax PI548542 Cumberland PI548542 Cumberland Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132222 SRR7124232 single-end leaf None 0 mRNA gmax PI548543 Oakland PI548543 Oakland Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132223 SRR7124233 single-end leaf None 0 mRNA gmax PI548545 Merit PI548545 Merit Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132224 SRR7124234 single-end leaf None 0 mRNA gmax PI548555 Douglas PI548555 Douglas Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132225 SRR7124235 single-end leaf None 0 mRNA gmax PI548562 Ford PI548562 Ford Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132226 SRR7124236 single-end leaf None 0 mRNA gmax PI548570 Harcor PI548570 Harcor Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132227 SRR7124237 single-end leaf None 0 mRNA gmax PI548573 Harosoy PI548573 Harosoy Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132228 SRR7124238 single-end leaf None 0 mRNA gmax PI548574 Shelby PI548574 Shelby Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132229 SRR7124239 single-end leaf None 0 mRNA gmax PI548577 Hawkeye PI548577 Hawkeye Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132230 SRR7124240 single-end leaf None 0 mRNA gmax PI518673 Lawrence PI518673 Lawrence Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132231 SRR7124241 single-end leaf None 0 mRNA gmax PI548586 Kent PI548586 Kent Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132232 SRR7124242 single-end leaf None 0 mRNA gmax PI548603 Perry PI548603 Perry Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132233 SRR7124243 single-end leaf None 0 mRNA gmax PI548628 Wayne PI548628 Wayne Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132234 SRR7124244 single-end leaf None 0 mRNA gmax PI548631 Williams PI548631 Williams Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132235 SRR7124245 single-end leaf None 0 mRNA gmax PI548632 Woodworth PI548632 Woodworth Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132236 SRR7124246 single-end leaf None 0 mRNA gmax PI548634 Zane PI548634 Zane Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132237 SRR7124247 single-end leaf None 0 mRNA gmax PI548654 Hill PI548654 Hill Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132238 SRR7124248 single-end leaf None 0 mRNA gmax PI548657 Jackson PI548657 Jackson Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132239 SRR7124249 single-end leaf None 0 mRNA gmax PI548975 Centennial PI548975 Centennial Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132240 SRR7124250 single-end leaf None 0 mRNA gmax PI548980 Hood PI548980 Hood Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132241 SRR7124251 single-end leaf None 0 mRNA gmax PI548298 A.K.(Harrow) PI548298 A.K.(Harrow) Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132242 SRR7124252 single-end leaf None 0 mRNA gmax PI548983 Tracy PI548983 Tracy Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132243 SRR7124253 single-end leaf None 0 mRNA gmax PI548986 Brim PI548986 Brim Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132244 SRR7124254 single-end leaf None 0 mRNA gmax PI548987 Dare PI548987 Dare Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132245 SRR7124255 single-end leaf None 0 mRNA gmax PI548988 Pickett PI548988 Pickett Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132246 SRR7124256 single-end leaf None 0 mRNA gmax PI548989 Ransom PI548989 Ransom Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132247 SRR7124257 single-end leaf None 0 mRNA gmax PI553039 Davis PI553039 Davis Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132248 SRR7124258 single-end leaf None 0 mRNA gmax PI553046 Gasoy17 PI553046 Gasoy17 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132249 SRR7124259 single-end leaf None 0 mRNA gmax PI572239 Holladay PI572239 Holladay Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132250 SRR7124260 single-end leaf None 0 mRNA gmax PI617045 NC-Roy PI617045 NC-Roy Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132251 SRR7124261 single-end leaf None 0 mRNA gmax PI630984 5601T PI630984 5601T Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132252 SRR7124262 single-end leaf None 0 mRNA gmax PI548311 Capital PI548311 Capital Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132253 SRR7124263 single-end leaf None 0 mRNA gmax PI641156 NC-Raleigh PI641156 NC-Raleigh Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132254 SRR7124264 single-end leaf None 0 mRNA gmax PI88788 unnamed PI88788 unnamed Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132255 SRR7124265 single-end leaf None 0 mRNA gmax PI548318 Dunfield PI548318 Dunfield Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132256 SRR7124266 single-end leaf None 0 mRNA gmax PI548348 Illini PI548348 Illini Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132257 SRR7124267 single-end leaf None 0 mRNA gmax PI548356 Kanro PI548356 Kanro Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132258 SRR7124268 paired-end leaf None 0 mRNA gmax NAM02 TN05-3027 NAM02 TN05-3027 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132259 SRR7124269 paired-end leaf None 0 mRNA gmax NAM03 4J105-3-4 NAM03 4J105-3-4 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132260 SRR7124270 paired-end leaf None 0 mRNA gmax NAM04 5M20-2-5-2 NAM04 5M20-2-5-2 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132261 SRR7124271 paired-end leaf None 0 mRNA gmax NAM05 CL0J095-4-6 NAM05 CL0J095-4-6 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132262 SRR7124272 paired-end leaf None 0 mRNA gmax NAM06 CL0J173-6-8 NAM06 CL0J173-6-8 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132263 SRR7124273 paired-end leaf None 0 mRNA gmax NAM08 HS6-3976 NAM08 HS6-3976 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132264 SRR7124274 paired-end leaf None 0 mRNA gmax NAM09 Prohio NAM09 Prohio Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132265 SRR7124275 paired-end leaf None 0 mRNA gmax NAM10 LD00-3309 NAM10 LD00-3309 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132266 SRR7124276 paired-end leaf None 0 mRNA gmax NAM11 LD01-5907 NAM11 LD01-5907 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132267 SRR7124277 paired-end leaf None 0 mRNA gmax NAM12 LD02-4485 NAM12 LD02-4485 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132268 SRR7124278 paired-end leaf None 0 mRNA gmax NAM13 LD02-9050 NAM13 LD02-9050 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132269 SRR7124279 paired-end leaf None 0 mRNA gmax NAM14 Magellan NAM14 Magellan Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132270 SRR7124280 paired-end leaf None 0 mRNA gmax NAM15 Maverick NAM15 Maverick Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132271 SRR7124281 paired-end leaf None 0 mRNA gmax NAM17 S06-13640 NAM17 S06-13640 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132272 SRR7124282 paired-end leaf None 0 mRNA gmax NAM18 NE3001 NAM18 NE3001 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132273 SRR7124283 paired-end leaf None 0 mRNA gmax NAM22 Skylla NAM22 Skylla Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132274 SRR7124284 paired-end leaf None 0 mRNA gmax NAM23 U03-100612 NAM23 U03-100612 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132275 SRR7124285 paired-end leaf None 0 mRNA gmax NAM24 LG03-2979 NAM24 LG03-2979 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132276 SRR7124286 paired-end leaf None 0 mRNA gmax NAM25 LG03-3191 NAM25 LG03-3191 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132277 SRR7124287 paired-end leaf None 0 mRNA gmax NAM26 LG04-4717 NAM26 LG04-4717 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132278 SRR7124288 paired-end leaf None 0 mRNA gmax NAM27 LG05-4292 NAM27 LG05-4292 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132279 SRR7124289 paired-end leaf None 0 mRNA gmax NAM28 LG05-4317 NAM28 LG05-4317 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132280 SRR7124290 paired-end leaf None 0 mRNA gmax NAM29 LG05-4464 NAM29 LG05-4464 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132281 SRR7124291 paired-end leaf None 0 mRNA gmax NAM30 LG05-4832 NAM30 LG05-4832 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132282 SRR7124292 paired-end leaf None 0 mRNA gmax NAM31 LG90-2550 NAM31 LG90-2550 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132283 SRR7124293 paired-end leaf None 0 mRNA gmax NAM32 LG92-1255 NAM32 LG92-1255 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132284 SRR7124294 paired-end leaf None 0 mRNA gmax NAM33 LG94-1128 NAM33 LG94-1128 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132285 SRR7124295 paired-end leaf None 0 mRNA gmax NAM34 LG94-1906 NAM34 LG94-1906 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132286 SRR7124296 paired-end leaf None 0 mRNA gmax NAM36 LG97-7012 NAM36 LG97-7012 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132287 SRR7124297 paired-end leaf None 0 mRNA gmax NAM37 LG98-1605 NAM37 LG98-1605 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132288 SRR7124298 paired-end leaf None 0 mRNA gmax NAM38 LG00-3377 NAM38 LG00-3377 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132289 SRR7124299 paired-end leaf None 0 mRNA gmax NAM39 LG04-6000 NAM39 LG04-6000 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132290 SRR7124300 paired-end leaf None 0 mRNA gmax NAM40 PI398.881 NAM40 PI398.881 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132291 SRR7124301 paired-end leaf None 0 mRNA gmax NAM41 PI427.136 NAM41 PI427.136 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132292 SRR7124302 paired-end leaf None 0 mRNA gmax NAM42 PI437.169B NAM42 PI437.169B Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132293 SRR7124303 paired-end leaf None 0 mRNA gmax NAM46 PI507.681B NAM46 PI507.681B Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132294 SRR7124304 paired-end leaf None 0 mRNA gmax NAM48 PI518.751 NAM48 PI518.751 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132295 SRR7124305 paired-end leaf None 0 mRNA gmax NAM50 PI561.370 NAM50 PI561.370 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132296 SRR7124306 paired-end leaf None 0 mRNA gmax NAM54 PI404.188A NAM54 PI404.188A Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132297 SRR7124307 paired-end leaf None 0 mRNA gmax NAM64 PI574.486 NAM64 PI574.486 Epigenomics of Glycine max Illumina HiSeq 2000 GSE114074 GSM3132298 SRR7124308 paired-end leaf None 0 mRNA gmax NAM IA3023 NAM IA3023 Epigenomics of Glycine max Illumina HiSeq 2000 GSE94299 GSM2472701 SRR5220366 single-end cotyledon 24 hours 0 mRNA 24h-2,4-D rep1,40 mg/l of 2,4 D medium, Embryo Initiation Jack Genome-Wide Reinforcement of DNA Methylation Occurs during Somatic Embryogenesis in Soybean Illumina HiSeq 2500 GSE94299 GSM2472704 SRR5220369 single-end cotyledon 24 hours 0 mRNA 24h+2,4-D rep1,40 mg/l of 2,4 D medium, Embryo Initiation Jack Genome-Wide Reinforcement of DNA Methylation Occurs during Somatic Embryogenesis in Soybean Illumina HiSeq 2500 GSE94299 GSM2472707 SRR5220372 single-end embryo 6 weeks 0 mRNA 6 wk globular rep1,20 mg/l of 2,4 D medium, Embryo Maintenance Jack Genome-Wide Reinforcement of DNA Methylation Occurs during Somatic Embryogenesis in Soybean Illumina HiSeq 2500 GSE94299 GSM2472710 SRR5220375 single-end embryo 6 weeks 0 mRNA 6 wk diff rep1,20 mg/l of 2,4 D medium, Embryo Maintenance Jack Genome-Wide Reinforcement of DNA Methylation Occurs during Somatic Embryogenesis in Soybean Illumina HiSeq 2500 GSE94299 GSM2472713 SRR5220378 single-end embryo 10 weeks + 4 days 0 mRNA 4-day subculture rep1,20 mg/l of 2,4 D medium, Embryo Maintenance Jack Genome-Wide Reinforcement of DNA Methylation Occurs during Somatic Embryogenesis in Soybean Illumina HiSeq 2500 GSE94299 GSM2472716 SRR5220381 single-end embryo 6 months 0 mRNA 6 mo globular rep1,20 mg/l of 2,4 D medium, Embryo Maintenance Jack Genome-Wide Reinforcement of DNA Methylation Occurs during Somatic Embryogenesis in Soybean Illumina HiSeq 2500 GSE94299 GSM2472719 SRR5220384 single-end embryo 12 months 0 mRNA 12 mo globular,20 mg/l of 2,4 D medium, Embryo Maintenance Jack Genome-Wide Reinforcement of DNA Methylation Occurs during Somatic Embryogenesis in Soybean Illumina HiSeq 2500 GSE94299 GSM2472720 SRR5220385 single-end embryo 12 months 0 mRNA 12 mo dif,20 mg/l of 2,4 D medium, Embryo Maintenance Jack Genome-Wide Reinforcement of DNA Methylation Occurs during Somatic Embryogenesis in Soybean Illumina HiSeq 2500 GSE94299 GSM2472721 SRR5220386 single-end embryo 8 year 0 mRNA 8 yr globular,20 mg/l of 2,4 D medium, Embryo Maintenance Jack Genome-Wide Reinforcement of DNA Methylation Occurs during Somatic Embryogenesis in Soybean Illumina HiSeq 2500 GSE69571 GSM1704039 SRR2051082 paired-end leaf 4 hours 0 control None Identifying salt stress-responsive miRNAs and their targets in soybean Illumina HiSeq 2000 GSE69571 GSM1704043 SRR2051086 paired-end leaf 4 hours 1 salt stress None Identifying salt stress-responsive miRNAs and their targets in soybean Illumina HiSeq 2000 GSE77796 GSM2059583 SRR3160561 paired-end leaf 14 days post-inoculation 0 Rsv1_Mock_RNA-seq Rsv1-genotype soybean,PI96983 Deep Sequencing Leads to the Identification of Eukaryotic Translation Initiation Factor 5A as a Key Element in Rsv1-Mediated Lethal Systemic Hypersensitive Response to Soybean Mosaic Virus Infection in Soybean Illumina MiSeq GSE77796 GSM2059584 SRR3160563 paired-end leaf 14 days post-inoculation 1 Rsv1_SMV-L_RNA-seq Rsv1-genotype soybean,PI96983 Deep Sequencing Leads to the Identification of Eukaryotic Translation Initiation Factor 5A as a Key Element in Rsv1-Mediated Lethal Systemic Hypersensitive Response to Soybean Mosaic Virus Infection in Soybean Illumina MiSeq GSE77796 GSM2059585 SRR3160565 paired-end leaf 14 days post-inoculation 1 Rsv1_SMV-G7_RNA-seq Rsv1-genotype soybean,PI96983 Deep Sequencing Leads to the Identification of Eukaryotic Translation Initiation Factor 5A as a Key Element in Rsv1-Mediated Lethal Systemic Hypersensitive Response to Soybean Mosaic Virus Infection in Soybean Illumina MiSeq GSE76636 GSM2029561 SRR3090710 paired-end leaf 14 days post-inoculation 0 Williams82_Mock_RNA-seq Williams 82,Susceptible Genome-wide investigation using sRNA-seq, degradome-seq and transcriptome-seq reveals regulatory networks of microRNAs and their target genes in soybean during Soybean mosaic virus infection Illumina MiSeq GSE76636 GSM2029562 SRR3090711 paired-end leaf 14 days post-inoculation 1 Williams82_SMV-L_RNA-seq Williams 82,Susceptible Genome-wide investigation using sRNA-seq, degradome-seq and transcriptome-seq reveals regulatory networks of microRNAs and their target genes in soybean during Soybean mosaic virus infection Illumina MiSeq GSE76636 GSM2029563 SRR3090712 paired-end leaf 14 days post-inoculation 1 Williams82_SMV-LRB_RNA-seq Williams 82,Susceptible Genome-wide investigation using sRNA-seq, degradome-seq and transcriptome-seq reveals regulatory networks of microRNAs and their target genes in soybean during Soybean mosaic virus infection Illumina MiSeq GSE76636 GSM2029564 SRR3090713 paired-end leaf 14 days post-inoculation 1 Williams82_SMV-G7_RNA-seq Williams 82,Susceptible Genome-wide investigation using sRNA-seq, degradome-seq and transcriptome-seq reveals regulatory networks of microRNAs and their target genes in soybean during Soybean mosaic virus infection Illumina MiSeq