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

To date, we have generated 236 RNA-Seq Datasets and 176 GeneChip Datasets which are submitted to GEO. Click on the "GEO Series Accessions" listed in the table to see the detail.

Study Sample No. Datasets GEO Series Accessions
Soybean
Transcriptome Profiling of Soybean Seed Compartments at Globular Stage Using Laser Microdissection (LCM) Embryo Proper 3 GSE57349
Endosperm 3
Seed Coat Endothelium 3
Seed Coat Epidermis 3
Seed Coat Hilium 3
Seed Coat Inner Integument 4
Seed Coat Outer Integument 3
Suspensor 3
Transcriptome Profiling of Soybean Seed Compartments at Heart Stage Using Laser Microdissection (LCM)
Embryo Proper 3 GSE57350
Endosperm 3
Seed Coat Endothelium 3
Seed Coat Epidermis 3
Seed Coat Hilium 3
Seed Coat Inner Integument 3
Seed Coat Outer Integument 3
Suspensor 3
Transcriptome Profiling of Soybean Seed Compartments at Cotyledon Stage Using Laser Microdissection (LCM)
Embryo Proper 3 GSE57606
Cotyledon 3
Axis 3
Endosperm 3
Seed Coat Endothelium 3
Seed Coat Inner Integument 3
Seed Coat Outer Integument 3
Seed Coat Hilum 3
Seed Coat Epidermis 3
Suspensor 3
Transcriptome Profiling of Soybean Seed Compartments at Early Maturation Stage Using Laser Microdissection (LCM)
Axis Epidermis 3 GSE46906
Axis Stele 3
Axis Vascular 3
Axis Parenchyma 3
Plumule 3
Root Tip 3
Shoot Meristem 3
Cotyledon Abaxial Parenchyma 3
Cotyledon Adaxial Parenchyma 3
Cotyledon Abaxial Epidermis 3
Cotyledon Adaxial Epidermis 3
Cotyledon Vascular Bundle 3
Endosperm 3
Hilum 3
Seed Coat Parenchyma 3
Seed Coat Hourglass 3
Seed Coat Palisade 3
Transcriptome Profiling of the Soybean Life Cycle Globular Stage Seeds 12 GSE29163
Heart Stage Seeds
Cotyledon Stage Seeds
Early Maturation Stage Seeds
Mid-Maturation Stage Seeds
Late Maturation Stage Seeds
Dry Seeds
Trifoliate leaves
Roots
Stems
Floral Buds
Whole seedlings six days after imbibition
Transcriptome Profiling of Soybean Seed Compartments Using Laser Microdissection (LCM)
Globular Stage Embryo Proper 3 GSE29162
Globular Stage Suspensor
Early Maturation Seed Coat Parenchyma
Transcriptome Profiling of Soybean Embryonic Cotyledon Before and After Germination
Mid-Maturation Cotyledon 3 GSE29134
Late-Maturation Cotyledon
Seedling Cotyledon
Transcriptome Profiling of Soybean Early Maturation Seed Parts
Embryonic Cotyledons 3 GSE37895
Embryonic Axis
Seed Coat
Arabidopsis
Transcriptome Profiling of Post Mature Green Seeds of Arabidopsis ddcc mutant and wild-type
ddcc mutant post mature green seeds 2 GSE76447
wild type post mature green seeds 2

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

Study Sample No. Datasets GEO Series Accessions
Small RNA Profiling of Soybean Seed Compartments at Globular Stage Using Laser Microdissection (LCM)
Embryo Proper 2 GSE57845
Endosperm 2
Inner Integument 2
Outer Integument 2
Hilum 2
Epidermis 2
Small RNA Profiling of Soybean Seed Compartments at Heart Stage Using Laser Microdissection (LCM)
Embryo Proper 2 GSE57874
Suspensor 2
Endosperm 2
Endothelium 2
Inner Integument 2
Outer Integument 2
Hilum 2
Seed Coat Epidermis 2
Small RNA Profiling of Soybean Seed Compartments at Cotyledon Stage Using Laser Microdissection (LCM)
Embryo Proper 2 GSE57883
Embryonic Axis 2
Embryonic Cotyledon 2
Endosperm 2
Inner Integument 2
Outer Integument 2
Hilum 2
Seed Coat Epidermis 2
Small RNA Profiling of Soybean Seed Compartments at Early Maturation Stage Using Laser Microdissection (LCM)
Axis Epidermis 2 GSE57906
Axis Stele 2
Axis Vascular 2
Axis Parenchyma 2
Plumule 2
Root Tip 2
Shoot Meristem 2
Cotyledon Abaxial Parenchyma 2
Cotyledon Adaxial Parenchyma 2
Cotyledon Abaxial Epidermis 2
Cotyledon Adaxial Epidermis 2
Cotyledon Vascular Bundle 2
Endosperm 2
Seed Coat Hilum 2
Seed Coat Parenchyma 2
Seed Coat Hourglass 2
Seed Coat Palisade 2
Small RNA Profiling of Soybean Early Maturation Seed Parts Embryonic Cotyledons 3 GSE37895
Embryonic Axis
Seed Coat

Transcriptome Profiling of Soybean and Arabidopsis Seed Development Using GeneChip Arrays

Study Seed Stage No. Samples No. Datasets GEO Series Accessions
Soybean
Transcriptome Profiling of Soybean Seed Compartments Using aser Microdissection (LCM)
Globular 10 28 GSE6414
Heart 10 23 GSE7511
Cotyledon 9 18 GSE7881
Early Maturation 17 34 GSE8112
Arabidopsis
Transcriptome Profiling of Arabidopsis Seed Compartments Using aser Microdissection (LCM)
Pre-globular 7 14 GSE12402
Globular 8 17 GSE11262
Heart 6 14 GSE15160
Linear Cotyledon 7 14 GSE12403
Bending Cotyledon 7 14 GSE20039
Mature Green 7 14 GSE15165

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

To date, we have generated 52 BS-Seq Datasets which are submitted to GEO. Click on the "GEO Series Accessions" listed in the table to see the detail.

Study Sample No. Datasets GEO Series Accessions
Soybean
Methylation Changes During Soybean Seed Development
Globular Stage Seeds 1 GSE34637
Cotyledon Stage Seeds 1
Early Maturation Stage Seeds 1
Mid-Maturation Stage Seeds 2
Late-Maturation Stage Seeds (BR1) 3
Pre-dormancy Stage 1 Seeds 1
Pre-dormancy Stage 2 Seeds 1
Dry Seeds 2
6DAI Cotyledon 3
6DAI Seedling 3
Methylation Changes in Soybean Early Maturation Seed Compartments Using Laser Microdissection (LCM)
Seed Coat Parenchyma 10 GSE37893
Seed Coat Palisade
Cotyledon Abaxial Parenchyma
Cotyledon Adaxial Parenchyma
Axis Parenchyma
Axis Plumule
Axis Root Tip
Axis Vascular
Seed Coat
Embryonic Cotyledon
Methylation Changes in Soybean Early Maturation Seed Parts
Embryonic Cotyledons 4 GSE37895
Embryonic Axis
Seed Coat
Methylation Changes in Soybean Mid-Maturation Seed Parts
Embryonic Cotyledons 3 GSE41601
Embryonic Axis
Seed Coat
Methylation Changes in Soybean Cotyledons Seed Parts
Embryonic Cotyledons 3 GSE57762
Embryonic Axis
Seed Coat
Arabidopsis
Methylation Changes in Arabidopsis Mature Green Stage Seed Parts Embryo 2 GSE57755
Seed Coat
Methylation Changes in Arabidopsis Seed Development Globular Stage Seeds 6 GSE68132
Linear Cotyledon Stage Seeds
Mature Green Stage Seeds
Post Mature Green Stage Seeds
Dry Seeds
Leaf
Methylation Profile of post mature green stage seed and dry seed from Arabidopsis ddcc mutant ddcc mutant dry seeds 6 GSE68131
ddcc mutant post mature green seeds
ddcc mutant leaf
wild type dry seeds
wild type post mature green seeds
wild type leaf

DNA-Protein Interaction Profiling Using Chromatin Immunoprecipitation (ChIP) Assays with Sequencing (ChIP-Seq)

To date, we have generated 126 ChIP-Seq Datasets and submitted all to GEO. Click on the "GEO Series Accessions" listed in the table to see the detail.

TF or Histone Marker Seed Stage Seed Region or Subregion No. Datasets GEO Series Accessions
Soybean
LEC1 Cotyledon Embryo 4 GSE99882
Early-Maturation Embryo 8
Mid-Maturation Embryo 4
ABI3 Early-Maturation Embryo 4 GSE101649
Mid-Maturation Embryo 12 GSE101648, GSE140700
AREB3 Early-Maturation Embryo 10 GSE140699, GSE101672
bZIP67 Early-Maturation Embryo 6 GSE140701, GSE101672
Mid-Maturation Embryo 4 GSE101663
AGL62 Globular Endosperm 2 GSE135265
WOX9 Globular Suspensor 4 GSE135267
Heart Suspensor 4
YAB1 Globular Embryo Proper 4 GSE135278
GRF5 Early-Maturation Embryo 4 GSE152313
HB22 Early-Maturation Embryo 6 GSE152314
WRI1 Early-Maturation Embryo 4 GSE152310
H3K4me3 and H3K27me3 Cotyledon Embryo 6 GSE114879
Early-Maturation Embryo 6
Mid-Maturation Embryo 6
Late-Maturation Embryo 6
Seedling Seedling 6
Scarlet Runner Bean
WOX9 Globular Suspensor 4 GSE153644
Arabidopsis
LEC1 Bent Cotyledon Embryo 4 GSE99587
Seedling Seedling 8 GSE99529