Comparison of transcriptomes of N2 and fog-2(q71) mutant Caenorhabditis elegans

In this experiment, steady-state mRNA levels were determined for replicated samples of N2 (wild-type reference) and fog-2(q71) homozygous mutant C. elegans. All samples were adult XX animals, which for N2 are self-fertile hermaphrodites and for fog-2(q71) spermless hermaphrodites, i.e. true females. For the fog-2 mutant animals, only those that had mated with males, and were thus gravid, were picked for RNA isolation. This ensures that all comparisons are between similar, embryo-containing animals. The experiment was motivated by the role of FOG-2 in post-transcriptional control of gene expression in germ cells, inferred from its the germline-specific phenotype of its loss and from its physical associated with the GLD-1 RNA-binding protein. Specifically, a possible role for FOG-2 in influencing mRNA stability was addressed. Overall design: Three biological replicate samples of mRNA were prepared for both N2 and fog-2(q71). Each sample was then used to prepare both oligo-dT-primed and random hexamer-primed Illumina short-read sequencing libraries. Oligo-dT and random-primed results were compared to assess possible impacts of fog-2 activity on polyadenylation.

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