Duke University: Dataset Details, ID=E-GEOD-21372

Title: Gene expression throughout vertebrate embryogenesis

Accession Number: E-GEOD-21372

Repository: ArrayExpress

Data Type(s): Gene Expression

Experiment Type(s): Transcription profiling by array

Organism(s): Fundulus heteroclitus

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. 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.

Publication(s) associated with this dataset:

• Bozinovic G, Sit TL, Hinton DE, Oleksiak MF. 2011. Gene expression throughout a vertebrate's embryogenesis. BMC Genomics 12:132. doi:10.1186/1471-2164-12-132 PMID:21356103 PMCID:PMC3062618