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Series GSE27506 Query DataSets for GSE27506
Status Public on May 06, 2011
Title Transcriptome analyses using the Chen Lab Cotton 25k oligo microarray
Organism Gossypium hirsutum
Experiment type Expression profiling by array
Summary The chip of cotton oligonucleotide microarrrays, which contain ~23,000 UniGenes from our own ESTs sequence project (Gossypium hirsutum L. TM-1 immature ovules (GH_TMO) ) and open resources, was developed. Transcriptome analyses were performed to compare gene expression changes in laser capture microdissected (LCM) fiber cell initials (or epidermis) and inner ovules. The gene expression profiles of the fiber cell initials were compared with those of the inner ovules in each developmental stage prior to (-2DPA), right at (0DPA), and shortly after the initiation of fiber cells (2DAP and 7DPA). Many genes in various molecular functions or biological processes were over- or under-represented between fibers and non-fiber tissues in each developmental stage, suggesting temporal regulation of gene expression during early stages of fiber development.
 
Overall design For gene expression studies using a large set cotton oligo-microarray, 4 developmental stages were chosen. To study differential expression during fiber initiation, ovules at -2 DPA, 0 DPA, and 2 DPA were used. One of the fiber elongation stage tissues (7 DPA) was included. In each developmental stage, epidermis was separated from inner ovules and subjected to the hybridization. In addition, epidermis and ovule comparisons were performed individually with 0 DPA as a control point for comparison.
 
Contributor(s) Lee JJ, Cheung F, Town C, Chen J
Citation(s) 21779324
Submission date Feb 24, 2011
Last update date Mar 23, 2012
Contact name Z Jeffrey Jeffrey Chen
E-mail(s) zjchen@austin.utexas.edu
Phone 512-475-9327
Organization name The University of Texas at Austin
Department Molecular Biosciences
Lab Polyploidy, Hybrid Vigor, and Epigenetics
Street address 2506 Speedway NMS 3.122 Stop A500
City Austin
State/province TX
ZIP/Postal code 78712
Country USA
 
Platforms (1)
GPL6937 Chen Lab Cotton 25k oligo array
Samples (40)
GSM678872 1.1 -2DPA (inner ovule cells) vs. -2DPA (ovule epidermal cells)
GSM678893 1.2 -2DPA (inner ovule cells) vs. -2DPA (ovule epidermal cells)
GSM678894 1.3 -2DPA (inner ovule cells) vs. -2DPA (ovule epidermal cells)
Relations
BioProject PRJNA138571

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE27506_RAW.tar 106.8 Mb (http)(custom) TAR (of GPR)
SRA Run SelectorHelp
Raw data provided as supplementary file
Processed data included within Sample table

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