Transcriptomics,Genomics

Dataset Information

35

Variation in embryonic mortality and maternal transcript expression among Atlantic cod (Gadus morhua) females: a functional genomics study


ABSTRACT: Early life stage mortality is an important issue for Atlantic cod aquaculture. The impact of the cod maternal (egg) transcriptome on egg quality and mortality during embryonic development is poorly understood. In the present work we studied embryonic mortality and maternal transcript expression using 15 females within an Atlantic cod broodstock development program. Cumulative mortality at 7 days post-fertilization (segmentation stage) and percent hatch were used to assess embryonic survival as an indicator of egg quality. A 20,000 probe (20K) microarray experiment compared the 7 hour post-fertilization (7 hpf, ~ 2-cell stage) egg transcriptome of the two lowest quality females (both with less than 1 percent hatch) to that of the highest quality female (greater than 50 percent hatch). Overall design: At 7 hours post-fertilization, 3 batches of 0.25 ml eggs were collected from each of the two lowest quality females (females 12 and 13) and the highest quality female (female 2). For each female, total RNA was isolated from each of the three batches separately, and pooled before microarray analysis. Two 4-array direct comparison experiments were performed. For each 4-array experiment, one of the ‘low quality’ females was compared to the ‘high quality’ female, and each RNA was labeled in 4 labeling reactions: two with AlexaFluor 647 and two with AlexaFluor 555. Each 4-array experiment consisted of four technical replicates: two duplicates and two dye-swaps. Females 12 and 13 are two biological replicates.

INSTRUMENT(S): CGP Atlantic cod 20K oligo array v1.0

SUBMITTER: Matthew Rise  

PROVIDER: GSE54233 | GEO | 2014-12-31

SECONDARY ACCESSION(S): PRJNA236004

REPOSITORIES: GEO

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