Genome-wide expression analysis of Caenorhabditis briggsae SPR-4/IVP-1 and HTZ-1/IVP-2 mutants

The goal of this study is to identify differentially expressed genes in Cbr-spr-4(gu163)/Cbr-ivp-1(gu163) and Cbr-htz-1(gu167)/Cbr-ivp-2(gu167) mutant compare to AF16 wild-type (WT). Our study represents the first analysis of Cbr-spr-4/Cbr-ivp-1 and Cbr-htz-1/Cbr-ivp-2 transcriptomes in C. briggsae and facilitates investigations of Cbr-spr-4/Cbr-ivp-1 and Cbr-htz-1/Cbr-ivp-2 mediated processes Total RNA was extracted from synchronized L3 animals (representing AF16 wild-type isolate, Cbr-spr-4(gu163)/Cbr-ivp-1(gu163) and Cbr-htz-1(gu167)/Cbr-ivp-2(gu167)), using standard TRIZOL methods. Animals were synchronized and staged by mounting the samples on slides and observing them under the Nomarski microscope. RNA was extracted just prior to the stage when vulval precursors (Pn.p cells) initiate division. At this stage, vulval cells are most responsive to Cbr-lin-3 levels. Three independent biological replicates were prepared from AF16, Cbr-spr-4(gu163) and Cbr-htz-1(gu167) strains for RNAseq, and the samples were processed, depleted for rRNA and sequenced using Illumina HiSeq platform by Genome Quebec. Differentially-expressed genes were called at a false discovery rate (FDR) of 0.05% using the DESeq package in R