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Series GSE21372 Query DataSets for GSE21372
Status Public on Apr 19, 2011
Title Gene expression throughout vertebrate embryogenesis
Organism Fundulus heteroclitus
Experiment type Expression profiling by array
Summary This study presents statistical analyses of gene expression during all 40 developmental stages in the teleost Fundulus heteroclitus using four biological replicates per stage. Patterns of gene expression for 7,000 genes appear to be important as they recapitulate developmental timing. Among the 45% of genes with significant expression differences between pairs of temporally adjacent stages, significant differences in gene expression vary from as few as five to more than 660. Five adjacent stages have disproportionately more significant changes in gene expression (>200 genes) relative to other stages: four to eight and eight to sixteen cell stages, onset of circulation, pre- and post-hatch, and during complete yolk absorption. The fewest differences among adjacent stages occur during gastrulation. Yet, at stage 16 (pre-mid-gastrulation), the largest number of genes has peak expression. This stage has an over-representation of genes in oxidative respiration and protein expression (ribosomes, translational genes and proteases). Unexpectedly, among all ribosomal genes, both strong positive and negative correlations occur. Similar correlated patterns of expression occur among all significant genes. These data provide statistical support for the temporal dynamics of developmental gene expression during all stages of vertebrate development.
 
Overall design A double-loop design was used for the microarray hybridizations, where each sample is hybridized to 2 arrays using both Cy3- and Cy5-labelled fluorophores (Kerr and Churchill 2001a; Kerr and Churchill 2001b). The loop consisted of Cy3- and Cy5-labelled embryo aRNAs from 4 biological pools for each of 40 stages (S). In total, 160 biological pools were hybridized to 80 microarrays. Each array had different combinations of biological pools (Altman and Hua 2006). The double loop formed was S1→ S2 → S3→ … S40→ S1 and S40→ S39→ S38→ … S2→ S1 → S40, where each arrow represents a separate hybridization (array) with the biological pool at the base of the arrow labeled with Cy3 and the biological pool at the head of the arrow labelled with Cy5.
 
Contributor(s) Oleksiak MF, Bozinovic G
Citation(s) 21356103
Submission date Apr 16, 2010
Last update date Jun 05, 2013
Contact name Marjorie F. Oleksiak
E-mail moleksiak@rsmas.miami.edu
Organization name University of Miami
Department Marine Biology and Fisheries
Street address 4600 Rickenbacker Causeway
City Miami
State/province FL
ZIP/Postal code 33149
Country USA
 
Platforms (1)
GPL10430 Rosenstiel Fundulus heteroclitus 7K array
Samples (160)
GSM544538 stage_01_Unf_Cy3_1
GSM544539 stage_02_Cy3_159
GSM544540 stage_02_Cy3_3
Relations
BioProject PRJNA126081

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
GSE21372_RAW.tar 41.9 Mb (http)(custom) TAR (of TXT)
Raw data provided as supplementary file
Processed data included within Sample table

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