Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0

Expression profiling of cotton (Gossypium hirsutum L. TM1) fiber transcriptome during the development


ABSTRACT: 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% 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

ORGANISM(S): Gossypium hirsutum

SUBMITTER: Brad Sickler 

PROVIDER: E-GEOD-11693 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

altmetric image

Publications

Double feature selection and cluster analyses in mining of microarray data from cotton.

Alabady Magdy S MS   Youn Eunseog E   Wilkins Thea A TA  

BMC genomics 20080620


<h4>Background</h4>Cotton fiber is a single-celled seed trichome of major biological and economic importance. In recent years, genomic approaches such as microarray-based expression profiling were used to study fiber growth and development to understand the developmental mechanisms of fiber at the molecular level. The vast volume of microarray expression data generated requires a sophisticated means of data mining in order to extract novel information that addresses fundamental questions of biol  ...[more]

Similar Datasets

2010-05-26 | E-GEOD-11689 | biostudies-arrayexpress
2010-05-16 | E-GEOD-13375 | biostudies-arrayexpress
2010-06-05 | E-GEOD-20996 | biostudies-arrayexpress
2010-10-12 | E-GEOD-24475 | biostudies-arrayexpress
2014-02-04 | E-GEOD-46940 | biostudies-arrayexpress
2010-05-25 | E-GEOD-10673 | biostudies-arrayexpress
2010-05-26 | E-GEOD-10717 | biostudies-arrayexpress
2010-05-25 | E-GEOD-10672 | biostudies-arrayexpress
2008-04-12 | E-GEOD-10679 | biostudies-arrayexpress
2010-05-18 | E-GEOD-11563 | biostudies-arrayexpress