To date, we have generated 246 RNA-Seq Datasets and 238 GeneChip Datasets which are submitted to GEO. Click on the "GEO Series Accessions" listed in the tables to see the detail.
Transcriptome Profiling During Seed Development Using RNA-Seq
| Study | Sample | No. Datasets | GEO Series Accessions |
| Soybean | |||
| Soybean Seed Compartments at Globular Stage Using Laser Capture Microdissection (LCM) | Embryo Proper | 25 | GSE57349 |
| Suspensor | |||
| Endosperm | |||
| Seed Coat Endothelium | |||
| Seed Coat Epidermis | |||
| Seed Coat Hilium | |||
| Seed Coat Inner Integument | |||
| Seed Coat Outer Integument | |||
| Soybean Seed Compartments at Heart Stage Using Laser Capture Microdissection (LCM) |
Embryo Proper | 24 | GSE57350 |
| Suspensor | |||
| Endosperm | |||
| Seed Coat Endothelium | |||
| Seed Coat Epidermis | |||
| Seed Coat Hilium | |||
| Seed Coat Inner Integument | |||
| Seed Coat Outer Integument | |||
| Soybean Seed Compartments at Cotyledon Stage Using Laser Capture Microdissection (LCM) |
Embryo Proper | 30 | GSE57606 |
| Suspensor | |||
| Cotyledon | |||
| Axis | |||
| Endosperm | |||
| Seed Coat Endothelium | |||
| Seed Coat Inner Integument | |||
| Seed Coat Outer Integument | |||
| Seed Coat Hilum | |||
| Seed Coat Epidermis | |||
| Soybean Seed Compartments at Early Maturation Stage Using Laser Capture Microdissection (LCM) |
Axis Epidermis | 51 | GSE46906 |
| Axis Stele | |||
| Axis Vascular | |||
| Axis Parenchyma | |||
| Axis Plumule | |||
| Root Tip | |||
| Shoot Meristem | |||
| Cotyledon Abaxial Parenchyma | |||
| Cotyledon Adaxial Parenchyma | |||
| Cotyledon Abaxial Epidermis | |||
| Cotyledon Adaxial Epidermis | |||
| Cotyledon Vascular Bundle | |||
| Endosperm | |||
| Seed Coat Hilum | |||
| Seed Coat Parenchyma | |||
| Seed Coat Hourglass | |||
| Seed Coat Palisade | |||
| 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 | |||
| Soybean Seed Compartments Using Laser Capture Microdissection (LCM) |
Globular Stage Embryo Proper | 3 | GSE29162 |
| Globular Stage Suspensor | |||
| Early Maturation Seed Coat Parenchyma | |||
| Soybean Embryonic Cotyledon Before and After Germination |
Mid-Maturation Cotyledon | 3 | GSE29134 |
| Late-Maturation Cotyledon | |||
| Seedling Cotyledon | |||
| Soybean Early Maturation Seed Parts |
Embryonic Cotyledons | 3 | GSE37895 |
| Embryonic Axis | |||
| Seed Coat | |||
| Arabidopsis | |||
| Arabidopsis Post Mature Green Seeds of ddcc Mutant and wild-type |
ddcc Mutant Seeds at Post Mature Green Stage | 4 | GSE76447 |
| wild-type Seeds at Post Mature Green Stage | |||
| Arabidopsis Globular Embryo Regions Using Laser Capture Microdissection (LCM) |
Embryo Proper | 2 | GSE135393 |
| Suspensor | |||
| Scarlet Runner Bean | |||
| Scarlet Runner Bean Globular Embryo Regions Using Laser Capture Microdissection (LCM) |
Embryo Proper | 4 | GSE57537 |
| Suspensor | |||
| Common Bean | |||
| Common Bean Globular Embryo Regions Using Laser Capture Microdissection (LCM) |
Embryo Proper | 4 | GSE57537 |
| Suspensor | |||
Transcriptional Profiling of Soybean and Arabidopsis Seed Development Using GeneChip Arrays
| Study | Seed Compartment | No. Datasets | GEO Series Accessions |
| Soybean | |||
| Soybean Seed Compartments at Globular Stage Using Laser Capture Microdissection (LCM) |
Embryo Proper | 28 | GSE6414 |
| Suspensor | |||
| Endosperm | |||
| Seed Coat Endothelium | |||
| Seed Coat Epidermis | |||
| Seed Coat Hilium | |||
| Seed Coat Inner Integument | |||
| Seed Coat Outer Integument | |||
| Soybean Seed Compartments at Heart Stage Using Laser Capture Microdissection (LCM) |
Embryo Proper | 23 | GSE7511 |
| Suspensor | |||
| Endosperm | |||
| Seed Coat Endothelium | |||
| Seed Coat Epidermis | |||
| Seed Coat Hilium | |||
| Seed Coat Inner Integument | |||
| Seed Coat Outer Integument | |||
| Soybean Seed Compartments at Cotyledon Stage Using Laser Capture Microdissection (LCM) |
Embryo Proper | 18 | GSE7881 |
| Suspensor | |||
| Endosperm | |||
| Seed Coat Endothelium | |||
| Seed Coat Epidermis | |||
| Seed Coat Hilium | |||
| Seed Coat Inner Integument | |||
| Seed Coat Outer Integument | |||
| Soybean Seed Compartments at Early Maturation Stage Using Laser Capture Microdissection (LCM) |
Axis Epidermis | 34 | GSE8112 |
| Axis Vascular Bundle | |||
| Axis Parenchyma | |||
| Axis Plumule | |||
| Root Meristem | |||
| Shoot Meristem | |||
| Cotyledon Abaxial Parenchyma | |||
| Cotyledon Adaxial Parenchyma | |||
| Cotyledon Abaxial Epidermis | |||
| Cotyledon Adaxial Epidermis | |||
| Cotyledon Vascular Bundle | |||
| Endosperm | |||
| Seed Coat Hilum | |||
| Seed Coat Parenchyma | |||
| Seed Coat Hourglass | |||
| Seed Coat Palisade | |||
| Arabidopsis | |||
| Arabidopsis Seed Compartments at Pre-globular Stage Using Laser Capture Microdissection (LCM) |
Embryo Proper | 14 | GSE12402 |
| Micropylar Endosperm | |||
| Peripheral Endosperm | |||
| Chalazal Endosperm | |||
| Chalazal Seed Coat | |||
| General Seed Coat | |||
| Whole Seed | |||
| Arabidopsis Seed Compartments at Globular Stage Using Laser Capture Microdissection (LCM) |
Embryo Proper | 17 | GSE11262 |
| Suspensor | |||
| Micropylar Endosperm | |||
| Peripheral Endosperm | |||
| Chalazal Endosperm | |||
| Chalazal Seed Coat | |||
| General Seed Coat | |||
| Whole Seed | |||
| Arabidopsis Seed Compartments at Heart Stage Using Laser Capture Microdissection (LCM) |
Embryo Proper | 16 | GSE15160 |
| Micropylar Endosperm | |||
| Peripheral Endosperm | |||
| Chalazal Endosperm | |||
| Chalazal Seed Coat | |||
| General Seed Coat | |||
| Whole Seed | |||
| Arabidopsis Seed Compartments at Linear Cotyledon Stage Using Laser Capture Microdissection (LCM) |
Embryo Proper | 14 | GSE12403 |
| Micropylar Endosperm | |||
| Peripheral Endosperm | |||
| Chalazal Endosperm | |||
| Chalazal Seed Coat | |||
| General Seed Coat | |||
| Whole Seed | |||
| Arabidopsis Seed Compartments at Bending Cotyledon Stage Using Laser Capture Microdissection (LCM) |
Embryo Proper | 14 | GSE20039 |
| Micropylar Endosperm | |||
| Peripheral Endosperm | |||
| Chalazal Endosperm | |||
| Chalazal Seed Coat | |||
| General Seed Coat | |||
| Whole Seed | |||
| Arabidopsis Seed Compartments at Mature Green Stage Using Laser Capture Microdissection (LCM) |
Embryo Proper | 14 | GSE15165 |
| Micropylar Endosperm | |||
| Peripheral Endosperm | |||
| Chalazal Endosperm | |||
| Chalazal Seed Coat | |||
| General Seed Coat | |||
| Whole Seed | |||
| Transcript Profiling of Arabidopsis Plant Life Cycle |
wild-type Ovule | 30 | GSE680 |
| wild-type 24-hr Seed | |||
| wild-type Globular Stage Seed | |||
| wild-type Linear Cotyledon Stage Seed | |||
| wild-type Mature Green Stage Seed | |||
| wild-type Post-Mature Green Stage Seed | |||
| wild-type Mid-Maturation Stage Seed | |||
| wild-type Late-Maturation Stage Seed | |||
| wild-type Seedling | |||
| wild-type Floral Bud | |||
| wild-type Rosette Leaf | |||
| wild-type Root | |||
| wild-type Stem | |||
| lec1 Floral Bud | |||
| lec1 Rosette Leaf | |||
| lec1 Root | |||
| lec1 Stem | |||
| Transcript Profiling of Arabidopsis Seed Development in LEAFY COTYLEDON1 (LEC1) Mutants |
lec1 24-hr Seed | 14 | GSE1051 |
| lec1 Globular Stage Seed | |||
| lec1 Linear Cotyledon Stage Seed | |||
| lec1 Mature Green Stage Seed | |||
| lec1 Post-Mature Green Stage Seed | |||
| lec1 Mid-Maturation Stage Seed | |||
| mRNA Changes Following Induction of LEC1 Activity in Arabidopsis Seedlings |
lec1 8-days Seedling with Induction | 4 | GSE99528 |
| lec1 8-days Seedling without Induction |
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 Capture Microdissection (LCM) |
Embryo Proper | 12 | GSE57845 |
| Endosperm | |||
| Inner Integument | |||
| Outer Integument | |||
| Hilum | |||
| Epidermis | |||
| Small RNA Profiling of Soybean Seed Compartments at Heart Stage Using Laser Capture Microdissection (LCM) |
Embryo Proper | 16 | GSE57874 |
| Suspensor | |||
| Endosperm | |||
| Endothelium | |||
| Inner Integument | |||
| Outer Integument | |||
| Hilum | |||
| Seed Coat Epidermis | |||
| Small RNA Profiling of Soybean Seed Compartments at Cotyledon Stage Using Laser Capture Microdissection (LCM) |
Embryo Proper | 16 | GSE57883 |
| Embryonic Axis | |||
| Embryonic Cotyledon | |||
| Endosperm | |||
| Inner Integument | |||
| Outer Integument | |||
| Hilum | |||
| Seed Coat Epidermis | |||
| Small RNA Profiling of Soybean Seed Compartments at Early Maturation Stage Using Laser Capture Microdissection (LCM) |
Axis Epidermis | 34 | GSE57906 |
| Axis Stele | |||
| Axis Vascular | |||
| Axis Parenchyma | |||
| Plumule | |||
| Root Tip | |||
| Shoot Meristem | |||
| Cotyledon Abaxial Parenchyma | |||
| Cotyledon Adaxial Parenchyma | |||
| Cotyledon Abaxial Epidermis | |||
| Cotyledon Adaxial Epidermis | |||
| Cotyledon Vascular Bundle | |||
| Endosperm | |||
| Seed Coat Hilum | |||
| Seed Coat Parenchyma | |||
| Seed Coat Hourglass | |||
| Seed Coat Palisade | |||
| Small RNA Profiling of Soybean Early Maturation Seed Parts |
Embryonic Cotyledons | 3 | GSE37895 |
| Embryonic Axis | |||
| Seed Coat | |||
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.
Methylome Profiling of Soybean and Arabidopsis Seed Development Using Bisulfite Sequencing (BS-Seq)
| 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 |
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.
DNA-Protein Interaction Profiling Using Chromatin Immunoprecipitation (ChIP) Assays with Sequencing (ChIP-Seq)
| Transcription Factor 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 | GSE135268 |
| GRF5 | Early-Maturation | Embryo | 4 | GSE152313 |
| HB22 | Early-Maturation | Embryo | 6 | GSE152314 |
| WRI1 | Early-Maturation | Embryo | 4 | GSE152310 |
| H3K4me3 & 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 | |