Expression profiling by high throughput sequencing
Summary
This dataset addresses two phenomena affected by reference strain bias in model organism research, specifically in the nematode C. elegans. I) C. elegans is the leading system for research into RNA interference (RNAi); this research has been conducted exclusively in the reference strain. However, sensitivity to RNAi is remarkably diverse across wild-type strains. Here, we used RNA sequencing to evaluate the transcriptional response of the reference strain and four other strains to RNAi by transcriptionally profiling these strains in three conditions: exogenous RNAi targeting germline-expressed genes 1) par-1 and 2) pos-1, and 3) the control condition. II) Gene expression quantification in non-reference strains relies on successful alignment of DNA reads to the reference genome, but high sequence divergence can lead to mapping failure. Here, we used this RNA-seq dataset to characterize the extent to which poor DNA genome assembly limits expression quantification inferences.
Overall design
RNA-seq profiles of day 1 early adult C. elegans whole nematodes: 5 wild isolates (strains: reference strain N2, QX1211, CB4856, EG4348, JU1088) x 3 conditions (control, RNAi against par-1, RNAi against pos-1) x 3 biological replicates per condition (45 samples total)
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