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Alkaline-stress response in Glycine soja leaf identifies specific transcription factors and ABA-mediated signaling factors
Yanming Zhu, Northeast Agriculture University, Department of Life sciences, Harbin, China (ymzhu2001@neau.edu.cn)
Experiment design (14 hybridizations)
time
•0(control) hrs •0.5 hrs •1 hrs •3 hrs •6 hrs •12 hrs •24 hrs

This experiment has been imported by PLEXdb from NCBI GEO (GSE20323) Series_summary: Transcriptome of Glycine soja leaf tissue during a detail...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Alkaline-stress response in Glycine soja leaf identifies specific transcription factors and ABA-mediated signaling factors
Accession No: GM32
Microarray: Soybean
Visibility: public
Experiment Type:
Experiment Factor(s):
time
•0(control) hrs  •0.5 hrs  •1 hrs  •3 hrs  •6 hrs  •12 hrs  •24 hrs
Quality Control: biological replicates
Treatment summary:
 time  # replicates
 0(control) hrs  2
 0.5 hrs  2
 1 hrs  2
 3 hrs  2
 6 hrs  2
 12 hrs  2
 24 hrs  2
Total hybridizations: 14
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE20323)

Series_summary:
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 (Pā€‰<ā€‰0.001). 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.

Series_overall_design:
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.
Publication: 'Alkaline-stress response in Glycine soja leaf identifies specific transcription factors and ABA-mediated signaling factors.', Ge Y, Li Y, Lv DK, Bai X, Ji W, Cai H, Wang AX, Zhu YM.
Funct Integr Genomics 2010 Oct 12.
pubmed: 20938706
Created: 2011-04-26 13:07:59
Last Update: 2011-06-06 14:25:47
Released: 2011-06-06
GEO Accession GSE20323
Submitter: PLEXdb Curator
Name: Yanming Zhu
Institution: Northeast Agriculture University, Department of Life sciences, Harbin, China
Head of Laboratory: Yanming Zhu
email(s):
Homepage:

 
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