GEO DataSets

(Submitter supplied) We obtained early-senescence (ES)- and late-senescence (LS)-type F7 plants from a cross between a hybrid (Glycine max × Glycine soja) and the Glycine max cultivar. The ES-type plants presented the reproductive (R2) growth stage at 50 days after sowing (DAS) and the R7 growth stage at 95 DAS, whereas the LS-type plants presented the beginning of the R1 and R6 growth stages at 50 and 95 DAS, respectively. more...

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15008

2 Samples

Download data: TXT

(Submitter supplied) Research conducted, including the rationale: Weeds reduce yield in soybeans through incompletely defined mechanisms. The effects of weeds on the soybean transcriptome were evaluated in field conditions during four separate gR1.fastqing seasons. Methods: RNASeq data were collected from 6 biological samples of soybeans gR1.fastqing with or without weeds. Weed species and the methods to maintain weed free controls varied between years to mitigate treatment effects and to allow detection of general soybeans weed responses. more...

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15008

12 Samples

Download data: TXT

(Submitter supplied) Background: To elucidate features of seed development, we investigated the transcriptome of a soybean isoline from the germplasm collection that contained an introgressed allele known as minute hilum (mi) which confers a smaller hilum region where the seed attaches to the pod and also results in seed coat cracking surrounding the hilum region. Results: RNAs were extracted from immature seed from an extended hilum region (i.e., the hilum and a small ring of tissue surrounding the hilum in which the cracks form) at three different developmental stages:10-25, 25-50 and 50-100 mg seed fresh weight in two independent replicates for each stage. more...

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15008

20 Samples

Download data: XLSX

(Submitter supplied) Soybean aphid is one of the major limiting factors for soybean production. However, the mechanism for aphid resistance in soybean is remain enigmatic, very little information is available about the different mechanisms between antibiosis and antixenosis genotypes. Here we dissected aphid infestation into three stages and used genome-wide gene expression profiling to investigate the underlying aphid-plant interaction mechanisms. more...

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15008

54 Samples

Download data: TXT

(Submitter supplied) 1 RNA-Seq sample from Clark (PI548532) from seed coats of 100-200mg immature seeds

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15008

1 Sample

Download data: XLS

(Submitter supplied) Modern plant breeding increasingly relies on genomic information to guide crop improvement. Although some genes are characterized, additional tools are needed to effectively identify and characterize novel genes associated with crop traits. To meet this need, the mPing element from rice was developed as an activation tag designed to induce overexpression of nearby genes. Addition of promoter sequences to mPing resulted in a decrease in overall transposition rate, however, this effect was negated by using a hyperactive version of mPing called mmPing20. more...

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15008

4 Samples

Download data: CSV, TXT

(Submitter supplied) 11 RNA-Seq samples from Williams (PI548631), with a variety of tissues especially immature seeds represented; 1 sample is from Williams 55, i mutation with black seed coat (PI547881)

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL15008 GPL11192

12 Samples

Download data: XLSX

(Submitter supplied) Root hair cells growth under contolled conditions harvested at 3 different time points (276, 288 and 312 hours after sowing). For each time point, 3 biological replicates have been produced

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL22410 GPL15008

9 Samples

Download data: TXT

(Submitter supplied) Transcription Factors are bound to the nucleosome-depleted region or open chormatin. ATAC-Seq can help us to dissect the interactions among TFs which are important for soybean seed development.

Organism:

Glycine max

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL15008

4 Samples

Download data: TXT

(Submitter supplied) Soybean is one of the main sources of oil worldwide. Salinity severely affect its yield. GmSIN1 is a NAC transcription factor coding gene. Its overexpression (OE) transgenic lines greatly improved the yield in both common and saline fields. This study focuses on founding changes genes between GmSIN1 OE transgenic seedlings and control seedlings under salt stress or non-salt stress conditions. Illumina Solexa sequencing platform was used for the comparative analysis of transcriptome profiles in the roots and leaves of GmSIN1 OE transgenic seedlings and WEI6823 (control) seedlings under mock or 150 mM NaCl treatment for 6 hrs.

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15008

8 Samples

Download data: TXT

(Submitter supplied) Transcriptome profiling is performed to reveal how Brassinosteroids (BRs) play a crucial role for plant vegetative growth and reproductive development.

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15008

15 Samples

Download data: XLSX

(Submitter supplied) Symbiotic legume nodules and lateral roots arise away from the root meristem via dedifferentiation events. While these organs share some morphological and developmental similarities, whether legume nodules are modified lateral roots is an open question. We dissected emerging nodules (EN), mature nodules (MN), emerging lateral roots (ELR) and young lateral roots (YLR), and constructed strand-specific RNAseq libraries using polyA-enriched RNA preparations. more...

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15008

24 Samples

Download data: CSV

(Submitter supplied) We conducted a genome-wide transcriptomic analysis in soybean leaves and roots treated with zinc (Zn) deficiency using RNA sequencing (RNA-seq) technology. Two biological replicates of RNA-seq were included for Zn-sufficient leaves (ZSL), Zn-deficient leaves (ZDL), Zn-sufficient roots (ZSR), and Zn-deficient roots (ZDR). Therefore a total of eight libraries were constructed. Using a 2-fold change and a P-value ≤0.05 as the cut-off for selecting the differentially expressed transcripts, we globally identified Zn-deficiency responsive genes. more...

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15008

8 Samples

Download data: XLSX

(Submitter supplied) Purpose: The goals of this study are to identify what gene GmRAV1 was related to. RNA-Sequencing experiments were designed between GmRAV1-ox soybeans and DN50 soybeans. Methods: Leaves mRNA of 30-day-old DN50 and GmRAV1-ox soybeans were used by RNA sequencing using Illumina HiSeqTM2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. more...

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15008

6 Samples

Download data: XLS

(Submitter supplied) We conducted a genome-wide transcriptomic analysis in soybean leaves treated with a short-term (24 h) Pi-deficiency using RNA sequencing (RNA-seq) technology. Two biological replicates of RNA-seq were included for both Pi-sufficient leaves (PSL) and Pi-deficient leaves (PDL), and therefore a total of four libraries were constructed. Using a 2-fold change and a P-value ≤0.05 as the cut-off for selecting the differentially expressed transcripts, we globally identified short-term Pi-stress responsive genes. more...

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15008

4 Samples

Download data: XLSX

(Submitter supplied) The diurnal transcriptome of field-grown Glycine max was investigated in relation to diurnal physiological processes in the field and compared to diurnal transcription data from growth chamber studies

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15008

16 Samples

Download data: XLS

(Submitter supplied) In this study, we examined the genome-wide deposition of two opposing histone modifications H3K4me3 and H3K27me3, in mid-maturation (stage B1) soybean embryos.

Organism:

Glycine max

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL15008

30 Samples

Download data: BED

(Submitter supplied) Transcriptome analysis of cold-treated leaves (unifoliates) of soybean seedlings were performed. RNAseq analysis was performed using two lanes on a Illumina HiSeq2000 and sequenced on a 100bp, paired-end run.

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15008

9 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15008

139 Samples

Download data: TXT

(Submitter supplied) Cytosine methylation is a base modification that is often used by genomes to store information that is stably inherited through mitotic cell divisions. Most cytosine DNA methylation is stable throughout different cell types or by exposure to different environmental conditions in plant genomes. Here, we profile the epigenomes of ~100 Glycine max lines to explore the extent of natural epigenomic variation. more...

Organism:

Glycine max

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15008

304 Samples

Download data: TSV, TXT