Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Glycine soja cultivar:N24852

ABSTRACT: Identification and Analysis of NaHCO3 Stress Responsive Genes in Wild Soybean (Glycine soja) Roots by RNA-seq

PROVIDER: PRJNA354842 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR5053010_1.fastq.gz	Fastqsanger.gz
	SRR5053010_2.fastq.gz	Fastqsanger.gz
	SRR5053001_1.fastq.gz	Fastqsanger.gz
	SRR5053001_2.fastq.gz	Fastqsanger.gz
	SRR5053011_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 24

Similar Datasets

Glycine soja cultivar:N24852

Project description:Identification and Analysis of NaHCO3 Stress Responsive Genes in Wild Soybean (Glycine soja) Roots by RNA-seq

| PRJNA354715 | ENA

Global transcriptome profiling of wild soybean (Glycine soja) roots under NaHCO3 treatment

Project description:Plant roots are the primary site of perception and injury for saline-alkaline stress. The current knowledge of the saline-alkaline stress transcriptome is most focused on salt (NaCl) stress. Only a little alkaline (NaHCO3) stress transcriptome is limited to one time point after stress. Time-course analysis and comparative investigation on roots in the alkaline stress condition are needed to understand the gene response networks that are subject to alkaline tolerance. We used microarrays to detail the global programme of gene expression underlying NaHCO3 treatment and identified distinct classes of regulated genes during this process. Three week old Glycine soja seedling roots from 3cm root apex were harvested in two independent biological replicates after 0, 0.5, 1, 3, 6, 12 and 24h treatment with 50mmol/L NaHCO3 stress for RNA extraction and hybridization on Affymetrix microarrays. To minimize biological variance, roots from three plants originating from the same experiment, condition and cultivar was pooled.

2010-08-14 | E-GEOD-17883 | biostudies-arrayexpress

Glycine soja

Project description:Transcriptome Analysis of Wild Soybean (Glycine soja) Infected by Soybean Cyst Nematode

| PRJNA369554 | ENA

Glycine soja

Project description:Glycine soja overview

| PRJNA135335 | ENA

Alkaline-stress response in Glycine soja leaf identifies specific transcription factors and ABA-mediated signaling factors

Project description:Transcriptome of Glycine soja leaf tissue during a detailed time course formed a foundation for examining transcriptional processes during NaHCO(3) stress treatment. Of a total of 2,310 detected differentially expressed genes, 1,664 genes were upregulated and 1,704 genes were downregulated at various time points. The number of stress-regulated genes increased dramatically after a 6-h stress treatment. GO category gene enrichment analysis revealed that most of the differentially expressed genes were involved in cell structure, protein synthesis, energy, and secondary metabolism. Another enrichment test revealed that the response of G. soja to NaHCO(3) highlights specific transcription factors, such as the C2C2-CO-like, MYB-related, WRKY, GARP-G2-like, and ZIM families. Co-expressed genes were clustered into ten classes (Pâ<â0.001). Intriguingly, one cluster of 188 genes displayed a unique expression pattern that increases at an early stage (0.5 and 3 h), followed by a decrease from 6 to 12 h. This group was enriched in regulation of transcription components, including AP2-EREBP, bHLH, MYB/MYB-related, C2C2-CO-like, C2C2-DOF, C2C2, C3H, and GARP-G2-like transcription factors. Analysis of the 1-kb upstream regions of transcripts displaying similar changes in abundance identified 19 conserved motifs, potential binding sites for transcription factors. The appearance of ABA-responsive elements in the upstream of co-expression genes reveals that ABA-mediated signaling participates in the signal transduction in alkaline response. Young leaves of three-week-old Glycine soja were harvested in two independent biological replicates after 0, 0.5, 1, 3, 6, 12 and 24h treatment with 50mmol/L NaHCO3 stress for RNA extraction and hybridization on Affymetrix microarrays. To minimize biological variance, leaves from three plants originating from the same experiment, condition and cultivar was pooled.

2010-10-13 | E-GEOD-20323 | biostudies-arrayexpress

Glycine soja

Project description:Glycine soja Genome sequencing

| PRJNA195632 | ENA

Identification of wild soybean miRNAs and their target genes responsive to aluminum stress

Project description:In this study, two small RNA libraries and two degradome libraries were constructed from roots of Al-treated and Al-free Glycine soja seedlings. For miRNA, a total of 7,287,655 and 7,035,914 clean reads in Al-treated and Al-free small RNAs libraries were generated, and 105 known miRNAs ,51 p3/p5 strands of known miRNA and 80 novel miRNAs were identified. Among them, expression of 34 miRNAs was responsive to Al stress. Through degradome sequencing, 82 and 11 genes were identified as tagerts of known and novel miRNAs obtained from this study, respectively. Gene Ontology (GO) annotations of target transcripts indicated that 52 out of 66 targets cleaved by conserved miRNA families may play role in regulation of transcription. sample 1: Examination of small RNA in Al-free wild soybean roots; sampple 2: Examination of small RNA in Al-treated wild soybena roots; sample 3: identification of miRNA targets in Al-free wild soybean roots; sample 4: identification of miRNA targerts in Al-treated wild soybean roots

2012-05-25 | E-GEOD-38065 | biostudies-arrayexpress

Glycine soja

Project description:Glycine soja Raw sequence reads

| PRJNA716521 | ENA

Glycine soja

Project description:Glycine soja Raw sequence reads

| PRJNA493962 | ENA

Glycine soja

Project description:Glycine soja Transcriptome or Gene expression

| PRJNA120063 | ENA