We found that the CSR-1 endoRNAi pathway functions in preventing a premature activation of embryonic transcription in developing Caenorhabditis elegans oocytes. An important component of this pathway is the dicer-related helicase DRH-3. To examine embryonic transcripts in the drh-3(rrr2) mutant on a global scale, we performed RNA sequencing on drh-3(rrr2) mutants and wild type animals. The RNA sequencing data of the wild type animals has been uploaded already under the accession number GSE62858, samples: GSM1534604 RNASeq_N2_1 and GSM1534605 RNASeq_N2_2. Overall design: Total RNA sequencing was performed on RNA extracted from drh-3(rrr2) mutant animals in duplicates. Two samples in total.