This data set accompanies the manuscript "Gene expression in rotifer diapausing eggs in response to divergent environmental predictability regimes". It consists of the fastq files from RNA sequencing of 12 samples of diapausing eggs from the rotifer Brachionus plicatilis. The reads have already been quality filtetered and trimmed. The 12 fastq files are gzipped and archived in trimmed.tar, where there is trimmed_md5sum.txt file to check for data integrity. There is also a "metadata.txt" describing the samples, and a short README.txt file.