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Browse CottonPLEX Experiment Data

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Affymetrix Cotton Genome array expression data of root tissue of Gossypium herbaceum under drought stress and watered condition
Samir V Sawant, CSIR-NBRI, Department of Plant Molecular Biology, Lucknow, India (samirsawant@nbri.res.in)
Experiment design (12 hybridizations)
genotype
•sensitive •tolerant
stress condition
•water •drought

This experiment has been imported by PLEXdb from NCBI GEO (GSE36249)

Series_summary:
Genome-wide Transcriptional Analysis of Genes As...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Affymetrix Cotton Genome array expression data of root tissue of Gossypium herbaceum under drought stress and watered condition
Accession No: GO5
Microarray: Cotton
Visibility: public
Experiment Type:
Experiment Factor(s):
genotype
•sensitive   •tolerant
stress condition
•water   •drought
Quality Control: biological replicates
Treatment summary:
 genotype  stress condition  # replicates
 sensitive  water  3
 sensitive  drought  3
 tolerant  water  3
 tolerant  drought  3
Total hybridizations: 12
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE36249)

Series_summary:
Genome-wide Transcriptional Analysis of Genes Associated with Drought Stress in Gossypium herbaceum root
This experiment was designed to investigate the molecular mechanism associated with drought tolerance in root tissue of Gossypium herbaceum. The gene expression profiles of the root tissue using Affymetrix Cotton Genome Array were compared with drought tolerant and drought sensitive genotype of G.herbaceum under drought stress and watered condition. Many genes in various molecular function or biological processes were over- or under-represented between drought tolerant and sensitive genotype, suggesting various molecular mechanism and biochemical pathways are interlinked and tolerant genotype have developed multiple mechanisms as an adaptory behavior against drought stress.

Series_overall_design:
The transcriptional responses of root tissue in drought tolerant and sensitive genotype of Gossypium herbaceum under drought stress have been investigated. Physiological responses to drought stress, such as stomatal conductance, water use efficiency, root bending assay on different mannitiol concentration were also measured as indicators of imposed drought stress. Total RNA was isolated from root tissue from both genotype under drought stress and normal irrigated condition with three biological replicates


PLEXdb Curator's Comment:
After normalization we observed the distribution of data in the following treatment do not match with rest of the experiment:

GO5_H10 genotype=tolerant|stress condition=drought Rep-1
GO5_H11 genotype=tolerant|stress condition=drought Rep-2
GO5_H12 genotype=tolerant|stress condition=drought Rep-3

These observations are based on:
1. The boxplots of normalized data.
2. The correlation of replicates within this treatment, in the RMA/MAS scatter plots is very low, 0.4 to 0.6.
3. The RMA/MAS5.0 heatmaps
The data from this treatment should be treated with caution.
Publication: none
Created: 2012-05-01 13:41:00
Last Update: 2012-05-01 14:50:34
Released: 2012-05-02
GEO Accession GSE36249
Submitter: PLEXdb Curator
Name: Samir V Sawant
Institution: CSIR-NBRI, Department of Plant Molecular Biology, Lucknow, India
Head of Laboratory: Samir V Sawant
email(s):
Homepage:

 
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