Summary of All Project GenBank Submissions

Dataset Methylome mRNA Transcriptome smRNA Transcriptome Dataset GENECHIP
Total Reads ~ 12.0 ~ 4.4 ~ 2.7 No. Compartments 76
Total Bases ~ 1,195Gb ~ 250Gb ~ 136Gb No. GeneChip 166
No. Datasets 52 153 81 No. Datasets 76

Transcriptome Profiling of Soybean and Arabidopsis Seed Development Using RNA-Seq

Study Dataset No. Reads No. Bases GEO Accessions
Transcriptome Profiling of the Soybean Life Cycle
(GSE29163)
Globular Stage Seeds 89M 6.8Gb GSM721725
Heart Stage Seeds 40M 3.0Gb GSM721726
Cotyledon Stage Seeds 52M 4.0Gb GSM721727
Early Maturation Stage Seeds 123M 9.3Gb GSM721728
Mid-Maturation Stage Seeds 94M 4.7Gb GSM2734729
Late Maturation Stage Seeds 191M 9.5Gb GSM2734730
Dry Seeds 42M 3.2Gb GSM721729
Trifoliate leaves 45M 3.4Gb GSM721730
Roots 40M 3.0Gb GSM721731
Stems 19M 1.4Gb GSM721732
Floral Buds 59M 4.5Gb GSM721733
Whole seedlings six days after imbibition 33M 2.5Gb GSM721734
Transcriptome Profiling of Soybean Seed Compartments Using LCM
(GSE29162)
Globular Stage Embryo Proper 74M 5.6Gb GSM721717
Globular Stage Suspensor 68M 5.2Gb GSM721718
Early Maturation Seed Coat Parenchyma 73M 5.5Gb GSM721719
Transcriptome Profiling of Soybean Embryonic Cotyledon Before and After Germination
(GSE29134)
Mid-Maturation Cotyledon 49M 3.7Gb GSM721277
Late-Maturation Cotyledon 83M 6.3Gb GSM721278
Seedling Cotyledon 54M 4.1Gb GSM721280
Transcriptome Profiling of Soybean Early Maturation Seed Parts
(GSE37895)
Embryonic Cotyledons 24M 2.4Gb GSM1213856
Embryonic Axis 25M 2.5Gb GSM1213857
Seed Coat 21M 2.1Gb GSM1213855
Transcriptome Profiling of Soybean Seed Compartments at Early Maturation Stage Using LCM
(GSE46906)
Axis Epidermis (3 BRs) 88M 4.5Gb GSM1398252/GSM1398253/GSM1398254
Axis Stele (3 BRs) 82M 4.1Gb GSM1398262/GSM1398263/GSM1398264
Axis Vascular (3 BRs) 91M 4.5Gb GSM1123207/GSM1123208/GSM1398265
Axis Parenchyma (3 BRs) 102M 5.1Gb GSM1123204/GSM1123205/GSM1123206
Plumule (3 BRs) 75M 3.8Gb GSM1398255/GSM1398256/GSM1398257
Root Tip (3 BRs) 131M 6.6Gb GSM1123218/GSM1123219/GSM1398258
Shoot Meristem (3 BRs) 86M 4.2Gb GSM1398259/GSM1398260/GSM1398261
Cotyledon Abaxial Parenchyma (3 BRs) 121M 6.0Gb GSM1398266/GSM1398267/GSM1398268
Cotyledon Adaxial Parenchyma (3 BRs) 101M 5.1Gb GSM1398272/GSM1398273/GSM1398274
Cotyledon Abaxial Epidermis (3 BRs) 110M 5.5Gb GSM1123209/GSM1123210/GSM11232011
Cotyledon Adaxial Epidermis (3 BRs) 119M 5.9Gb GSM1398269/GSM1398270/GSM1398271
Cotyledon Vascular Bundle (3 BRs) 83M 4.2Gb GSM1123212/GSM1123213/GSM1123214
Endosperm (3 BRs) 96M 4.9Gb GSM1123214/GSM1398276/GSM1398277
Hilum (3 BRs) 118M 5.8Gb GSM1123215/GSM1123216/GSM1123217
Seed Coat Parenchyma (3 BRs) 70M 3.5Gb GSM1398279/GSM1398280/GSM1123225
Seed Coat Hourglass (3 BRs) 105M 5.2Gb GSM1123220/GSM1123221/GSM1123222
Seed Coat Palisade (3 BRs) 88M 4.4Gb GSM1123223/GSM1123224/GSM1398278
Transcriptome Profiling of Soybean Seed Compartments at Cotyledon Stage Using LCM
(GSE57606)
Embryo Proper (3 BRs) 74M 3.8Gb GSM1385450/GSM1385451/GSM1385452
Cotyledon (3 BRs) 98M 5.0Gb GSM1385456/GSM1385457/GSM1385458
Axis (3 BRs) 59M 3.0Gb GSM1385453/GSM1385454/GSM1385455
Endosperm (3 BRs) 64M 3.2Gb GSM1385459/GSM1385460/GSM1385461
Seed Coat Endothelium (3 BRs) 70M 3.5Gb GSM1385462/GSM1385463/GSM1385464
Seed Coat Inner Integument (3 BRs) 64M 3.2Gb GSM1385471/GSM1385472/GSM1385473
Seed Coat Outer Integument (3 BRs) 53M 2.7Gb GSM1385475/GSM1385476/GSM1385477
Seed Coat Hilum (3 BR) 65M 3.3Gb GSM1385468/GSM1385469/GSM1385460
Seed Coat Epidermis (3 BRs) 70M 3.5Gb GSM1385465/GSM1385466/GSM1385467
Suspensor (3 BRs) 58M 2.9Gb GSM1385477/GSM1385478/GSM1385479
Transcriptome Profiling of Soybean Seed Compartments at Heart Stage Using LCM
(GSE57350)
Embryo Proper (3 BRs) 56M 2.8Gb GSM1380799/GSM1380800/GSM1380801
Endosperm (3 BR) 53M 2.7Gb GSM1380802/GSM1380803/GSM1380804
Seed Coat Endothelium (3 BRs) 59M 3.0Gb GSM1380805/GSM1380806/GSM1380807
Seed Coat Epidermis (3 BRs) 73M 3.7Gb GSM1380808/GSM1380809/GSM1380810
Seed Coat Hilium (3 BRs) 63M 3.2Gb GSM1380811/GSM1380812/GSM1380813
Seed Coat Inner Integument (3 BRs) 54M 2.7Gb GSM1380814/GSM1380815/GSM1380816
Seed Coat Outer Integument (3 BRs) 53M 2.7Gb GSM1380817/GSM1380818/GSM1380819
Suspensor (3 BRs) 55M 2.8Gb GSM1380820/GSM1380821/GSM1380822
Transcriptome Profiling of Soybean Seed Compartments at Globular Stage Using LCM
(GSE57349)
Embryo Proper (3 BRs) 65M 3.3Gb GSM1380774/GSM1380775/GSM1380776
Endosperm (3 BR) 72M 3.7Gb GSM1380777/GSM1380778/GSM1380779
Seed Coat Endothelium (3 BRs) 63M 3.2Gb GSM1380780/GSM1380781/GSM1380782
Seed Coat Epidermis (3 BRs) 62M 3.1Gb GSM1380783/GSM1380784/GSM1380785
Seed Coat Hilium (3 BRs) 71M 3.6Gb GSM1380786/GSM1380787/GSM1380788
Seed Coat Inner Integument (4 BRs) 99M 5.0Gb GSM1380789/GSM1380790/GSM1380791/GSM1380792
Seed Coat Outer Integument (3 BRs) 66M 3.3Gb GSM1380793/GSM1380794/GSM1380795
Suspensor (3 BRs) 60M 3.0Gb GSM1380796/GSM1380797/GSM1380798
Transcriptome Profiling of Post Mature Green Seeds of Arabidopsis ddcc mutant and wild-type
(GSE76447)
ddcc mutant post mature green seeds (BR1) 11M 511.9Mb GSM2024779
ddcc mutant post mature green seeds (BR2) 7M 333Mb GSM2024780
wild type post mature green seeds (BR1) 11M 568Mb GSM2024781
wild type post mature green seeds (BR2) 11M 499Mb GSM2024782

Small RNA Profiling During Soybean Seed Development Using Small RNA-Seq

Study Dataset No. Reads No. Bases GEO Accessions
Small RNA Profiling of Soybean Early Maturation Seed Parts
(GSE37895)
Embryonic Cotyledons 53M 2.7Gb GSM1213859
Embryonic Axis 53M 2.7Gb GSM1213860
Seed Coat 53M 2.7Gb GSM1213858
Small RNA Profiling of Soybean Seed Compartments at Early Maturation Stage Using LCM
(GSE57906)
Axis Epidermis (2 BRs) 35M 1.8Gb GSM1397256/GSM1397257/
Axis Stele (2 BRs) 43M 2.1Gb GSM1397266/GSM1397267
Axis Vascular (2 BRs) 72M 3.6Gb GSM1397268/GSM1397269
Axis Parenchyma (2 BRs) 36M 1.8Gb GSM1397260/GSM1397261
Plumule (2 BRs) 52M 2.6Gb GSM1397258/GSM1397259
Root Tip (2 BRs) 82M 4.1Gb GSM1397262/GSM1397263
Shoot Meristem (2 BRs) 73M 3.6Gb GSM1397264/GSM1397265
Cotyledon Abaxial Parenchyma (2 BRs) 54M 2.7Gb GSM1397272/GSM1397273
Cotyledon Adaxial Parenchyma (2 BRs) 53M 2.7Gb GSM1397276/GSM1397277
Cotyledon Abaxial Epidermis (2 BRs) 59M 2.9Gb GSM1397270/GSM1397271
Cotyledon Adaxial Epidermis (2 BRs) 59M 2.9Gb GSM1397274/GSM1397275
Cotyledon Vascular Bundle (2 BRs) 80M 4.0Gb GSM1397278/GSM1397279
Endosperm (2 BRs) 115M 5.8Gb GSM1397280/GSM1397281
Hilum (2 BRs) 89M 4.4Gb GSM1397284/GSM1397285
Seed Coat Parenchyma (2 BRs) 36M 1.8Gb GSM1397288/GSM1397289
Seed Coat Hourglass (2 BRs) 60M 3.0Gb GSM1397282/GSM1397283
Seed Coat Palisade (2 BRs) 58M 2.9Gb GSM1397286/GSM1397287
Small RNA Profiling of Soybean Seed Compartments at Cotyledon Stage Using LCM
(GSE57883)
Embryo Proper (2 BRs) 84M 4.2Gb GSM1396335/GSM1396336
Embryonic Axis (2 BRs) 27M 1.3Gb GSM1396337/GSM1396338
Embryonic Cotyledon (2 BRs) 40M 2.0Gb GSM1396339/GSM1396340
Endosperm (2 BRs) 107M 5.3Gb GSM1396341/GSM1396342
Inner Integument (2 BRs) 115M 5.7Gb GSM1396347/GSM1396348
Outer Integument (2 BRs) 58M 2.9Gb GSM1396349/GSM1396350
Hilum (2 BRs) 44M 2.2Gb GSM1396345/GSM1396346
Seed Coat Epidermis (2 BRs) 84M 4.1Gb GSM1396343/GSM1396344
Small RNA Profiling of Soybean Seed Compartments at Heart Stage Using LCM
(GSE57874)
Embryo Proper (2 BRs) 51M 2.5Gb GSM1396278/GSM1396279
Suspensor (2 BRs) 82M 4.1Gb GSM1396288/GSM1396289
Endosperm (2 BRs) 53M 2.6Gb GSM1396280/GSM1396281
Endothelium (2 BRs) 97M 4.8Gb GSM1396276/GSM1396277
Inner Integument (2 BRs) 62M 3.1Gb GSM1396284/GSM1396285
Outer Integument (2 BRs) 63M 3.1Gb GSM1396286/GSM1396287
Hilum (2 BRs) 103M 5.1Gb GSM1695750/GSM1695751
Seed Coat Epidermis (2 BRs) 69M 3.4Gb GSM1396282/GSM1396283
Small RNA Profiling of Soybean Seed Compartments at Globular Stage Using LCM
(GSE57845)
Embryo Proper (2 BRs) 60M 3.0Gb GSM1695746/GSM1695747
Endosperm (2 BRs) 57M 2.8Gb GSM1394967/GSM1394968
Inner Integument (2 BRs) 77M 3.8Gb GSM1394971/GSM1394972
Outer Integument (2 BRs) 58M 2.9Gb GSM1394973/GSM1394974
Hilum (2 BRs) 73M 3.6Gb GSM1394969/GSM1394970
Epidermis (2 BRs) 54M 2.7Gb GSM1695748/GSM1695749

Note: M - Million; Gb- Gigabyte; BR - Biological Replicate; LCM - Laser Microdissection

Methylome Profiling of Soybean Seed Development Using Bisulfite Sequencing (BS-Seq)

Study Dataset No. Reads No. Bases GEO Accessions
Methylation Changes During Soybean Seed Development
(GSE34637)
Globular Stage Seeds 297M 27.9Gb GSM852274
Cotyledon Stage Seeds 276M 27.6Gb GSM1392187
Early Maturation Stage Seeds 268M 25.4Gb GSM852275
Mid-Maturation Stage Seeds (BR1) 284M 28.4Gb GSM2417602
Mid-Maturation Stage Seeds (BR2) 52M 5.2Gb GSM2417603
Late-Maturation Stage Seeds (BR1) 144M 14.4Gb GSM852278
Late-Maturation Stage Seeds (BR2) 194M 19.4Gb GSM1707337
Late-Maturation Stage Seeds (BR3) 233M 23.3Gb GSM1707338
Pre-dormancy Stage 1 Seeds 182M 18.2Gb GSM1707336
Pre-dormancy Stage 2 Seeds 190M 19.0Gb GSM1707335
Dry Seeds (BR1) 382M 38.2Gb GSM852279
Dry Seeds (BR2) 195M 19.5Gb GSM1707334
6DAI Cotyledon (BR1) 151M 12.9Gb GSM1008197
6DAI Cotyledon (BR2) 206M 20.6Gb GSM1707341
6DAI Cotyledon (BR3) 198M 19.8Gb GSM1707342
6DAI Seedling (BR1) 207M 17.9Gb GSM1008196
6DAI Seedling (BR2) 211M 21.1Gb GSM1707339
6DAI Seedling (BR3) 193M 19.3Gb GSM1707340
Methylation Changes in Soybean Early Maturation Seed Compartments Using LCM
(GSE37893)
Seed Coat Parenchyma 334M 33.4Gb GSM1388205
Seed Coat Palisade 286M 28.6Gb GSM1388204
Cotyledon Abaxial Parenchyma 196M 19.6Gb GSM929624
Cotyledon Adaxial Parenchyma 245M 24.5Gb GSM929625
Axis Parenchyma 195M 19.5Gb GSM1397517
Axis Plumule 205M 20.5Gb GSM1397518
Axis Root Tip 218M 21.8Gb GSM1397519
Axis Vascular 190M 19.0Gb GSM1397520
Seed Coat 213M 21.3Gb GSM2417600
Embryonic Cotyledon 206M 20.6Gb GSM2417601
Methylation Changes in Soybean Early Maturation Seed Parts
(GSE37895)
Embryonic Cotyledons 393M 39.3Gb GSM929633
Embryonic Axis 350M 35.0Gb GSM929634
Seed Coat (BR1) 294M 29.4Gb GSM2417691
Seed Coat (BR2) 263M 26.3Gb GSM2417692
Methylation Changes in Soybean Mid-Maturation Seed Parts
(GSE41601)
Embryonic Cotyledons 273M 27.3Gb GSM1008126
Embryonic Axis 457M 45.7Gb GSM1023628
Seed Coat 250M 25.0Gb GSM1008125
Methylation Changes in Soybean Cotyledons Seed Parts
(GSE57762)
Embryonic Cotyledons 276M 27.6Gb GSM1388176
Embryonic Axis 275M 27.5Gb GSM1388177
Seed Coat 270M 27.0Gb GSM1388175

Methylome Profiling of Arabidopsis Seed Development Using Bisulfite Sequencing (BS-Seq)

Study Dataset No. Reads No. Bases GEO Accessions
Methylation Changes in Mature Green Stage Seed Parts (GSE57755) Embryo 123M 12.3Gb GSM1388112
Seed Coat 172M 17.2Gb GSM1388111
Methylation Changes in Arabidopsis Seed Development (GSE68132) Globular Stage Seeds 206M 20.6Gb GSM1664380
Linear Cotyledon Stage Seeds 191M 19.1Gb GSM1664381
Mature Green Stage Seeds 189M 18.9Gb GSM1664382
Post Mature Green Stage Seeds 227M 22.7Gb GSM1664383
Dry Seeds 215M 21.5Gb GSM1664384
Leaf 170M 17.0Gb GSM1664385
Methylation Profile of post mature green stage seed and dry seed from Arabidopsis ddcc mutant (GSE68131) ddcc mutant dry seeds 232M 23.2Gb GSM1664376
ddcc mutant post mature green seeds 191M 19.1Gb GSM2319711
ddcc mutant leaf 228M 22.8Gb GSM1664377
wild type dry seeds 220M 22.0Gb GSM1664378
wild type post mature green seeds 188M 18.8Gb GSM2319712
wild type leaf 234M 23.4Gb GSM1664379

Note: M - Million; Gb- Gigabyte; BR - Biological Replicate; LCM - Laser Microdissection

DNA-Protein Binding Profiling of Seed Tissue-Specific Transcription Factors Using Chromatin Immunoprecipitation (ChIP) Assays with Sequencing (ChIP-Seq)

TF or Histone Marker Seed Stage Seed Region or Subregion No. Datasets GEO Series Accessions
LEC1 Cotyledon Embryo 4 GSE99882
Early-Maturation Embryo 8
Mid-Maturation Embryo 4

Transcriptome Profiling of Seed Development Using GeneChip Arrays

Study Seed Stage No. Compartments Studied No. GeneChip Experiments GEO Series Accessions
Transcriptome Profiling of Soybean Seed Compartments Using LCM
Globular 8 24 GSE6414
Heart 8 19 GSE7511
Cotyledon 8 16 GSE7881
Early Maturation 16 32 GSE8112
Transcriptome Profiling of Arabidopsis Seed Compartments Using LCM
Pre-globular 6 12 GSE12402
Globular 7 15 GSE11262
Heart 6 14 GSE15160
Linear Cotyledon 6 12 GSE12403
Bending Cotyledon 5 10 GSE20039
Mature Green 6 12 GSE15165
Transcript Profiling of Arabidopsis Plant Life Cycle
(GSE680)

Note: LCM - Laser Microdissection;