GSE21372   Details

GSE Accession GSE21372
Title Gene expression throughout vertebrate embryogenesis
Submission Date 2010-04-16
Last Update Date 2013-06-05
Pubmed ID 21356103
Experiment Type Expression profiling by array
Contributor Marjorie,F,Oleksiak; Goran Bozinovic
Contact Name Marjorie,F.,Oleksiak
Contact E-mail moleksiak@rsmas.miami.edu
Organization Name University of Miami
Country USA
Organism Fundulus heteroclitus
Organism ID
Organism Synonym Atlantic killifish;killifish;mummichog
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.
Platform ID
Timepoint Count 40
Timepoints gse: [Timepoints, 40]
Disease hepatitis;
dementia;
impotence;
testicular cancer;
thrombocytopenia-absent radius syndrome;
congenital disorder;
thrombocytopenia
Disease ID 2237;
1307;
1875;
2998;
14699;
759;
1588