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Browse CottonPLEX Experiment Data

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Identification of differentially expressed genes associated with semigamy in Pima cotton
Laura Rodriguez-Uribe, New Mexico State University, Department of Plant and environmental Sciences, Las Cruces, New Mexico (laurodri@nmsu.edu)
Experiment design (4 hybridizations)
genotype
•57-4 •PS-1
organism part name
•ovules •anthers

This experiment has been imported by PLEXdb from NCBI GEO (GSE27242)

Series_summary:
The comparative analysis between 57-4 and Pima S...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Identification of differentially expressed genes associated with semigamy in Pima cotton
Accession No: GO3
Microarray: Cotton
Visibility: public
Experiment Type:
Experiment Factor(s):
genotype
•57-4   •PS-1
organism part name
•ovules   •anthers
Quality Control: biological replicates
Treatment summary:
 genotype  organism part name  # replicates
 57-4  ovules  1
 57-4  anthers  1
 PS-1  ovules  1
 PS-1  anthers  1
Total hybridizations: 4
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE27242)

Series_summary:
The comparative analysis between 57-4 and Pima S-1 identified 284 genes in anthers and 1,864 genes in ovules as being differentially expressed in the semigametic genotype. Based on gene functions, 127 differentially expressed genes were common to both semigametic anthers and ovules, with 115 being consistently differentially expressed in both tissues. Nine of those genes were selected for qRT-PCR analysis, seven of which were confirmed. Furthermore, several well characterized metabolic pathways including glycolysis/gluconeogenesis, carbon fixation in photosynthetic organisms, sesquiterpenoid biosynthesis, and the biosynthesis of and response to plant hormones were shown to be affected by differentially expressed genes in the semigametic tissues.

Series_overall_design:
Anther and ovule tissues from 10 flowers of 57-4 and Pima S-1 was collected at zero days postanthesis (0 DPA) and placed in liquid nitrogen and stored at -80 °C. Total RNA was isolated using a hot borate method and cRNA was hybridized to the Affymetrix Cotton Genome GeneChips.
Publication: 'Identification of differentially expressed genes associated with semigamy in Pima cotton (Gossypium barbadense L.) through comparative microarray analysis.', Curtiss J, Rodriguez-Uribe L, Stewart JM, Zhang J.
BMC Plant Biol 2011 Mar 16;11:49.
pubmed: 21410961
Created: 2011-08-03 12:51:04
Last Update: 2011-08-05 12:12:46
Released: 2011-08-05
GEO Accession GSE27242
Submitter: PLEXdb Curator
Name: Laura Rodriguez-Uribe
Institution: New Mexico State University, Department of Plant and environmental Sciences, Las Cruces, New Mexico
Head of Laboratory: Jinfa Zhang
email(s):
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