|
| Status |
Public on Jun 12, 2008 |
| Title |
Expression profiling of cotton (Gossypium hirsutum L. TM1) fiber transcriptome during the development |
| Platform organism |
Gossypium arboreum |
| Sample organism |
Gossypium hirsutum |
| Experiment type |
Expression profiling by array
|
| Summary |
In order to study gene expression at the genomic level during elongation and secondary cell wall synthesis of upland cotton fiber, oligonucleotide microarrays were employed. RNA was isolated from fibers in 7 different time points beginning prior to peak fiber expansion, continuing through termination of fiber expansion and ending at peak cellulose synthesis (5, 8, 10, 14, 17, 21, and 24dpa). The arrays contained ~25,000 oligonucleotides representing ~12,200 genes designed from a fiber EST database during peak cell expansion. Dynamic changes in gene expression were analyzed in a developmental context to identify stage-specific biological processes and pathways likely to be crucial to cell polar elongation or cellulose biosynthesis and secondary cell wall biogenesis. Genes with significant changes in expression relative to any preceding time point were identified (moderated t-statistics, adjusted p-value <0.05) for each developmental time point with an expected false discovery rate for multiple testing <5%
|
| |
|
| Overall design |
A bi-directional double-loop experimental design was adopted for the microarray analysis (Kerr and Churchill, 2001; Glonek, 2004) to analyze all possible significant changes in gene expression between any two developmental time points,. The double loop design guarantees that the two time points before and after each individual time point will have direct comparisons with multiple paths available to compare any two points. Self-hybridization control experiments between independent RNA isolations for each developmental stage demonstrated a high degree of reproducibility
|
| |
|
| Contributor(s) |
Sickler BA, Arpat BA, Wilkins TA |
| Citation(s) |
18570655 |
| |
| Submission date |
Jun 05, 2008 |
| Last update date |
Mar 19, 2012 |
| Contact name |
Thea A Wilkins |
| URL |
http://genomics.ttu.edu
|
| Organization name |
Texas Tech University
|
| Department |
Plant and Soil Sciences
|
| Lab |
Plant Functional Genomics Lab
|
| Street address |
2500 Broadway,Campus Box 42122
|
| City |
Lubbock |
| State/province |
TX |
| ZIP/Postal code |
TX 79409 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL6917 |
Cotton Fiber Oligonucleotide Microarray.V1 |
|
| Samples (6)
|
| GSM296894 |
Upland Cotton fiber Expression at 8dpa relative to 5dpa |
| GSM296895 |
Upland Cotton fiber Expression at 10dpa relative to 5dpa |
| GSM296896 |
Upland Cotton fiber Expression at 14dpa relative to 5dpa |
| GSM296897 |
Upland Cotton fiber Expression at 17dpa relative to 5dpa |
| GSM296898 |
Upland Cotton fiber Expression at 21 dpa relative to 5dpa |
| GSM296970 |
Upland Cotton fiber Expression at 24 dpa relative to 5dpa |
|
| Relations |
| BioProject |
PRJNA106099 |
Less...
More...