We performed RNA-seq experiment to identify A/B-compartments on the Hi-C map and correlate it with gene expression. Here we share RNA-seq raw reads for 5 Anopheles mosquito species (Anopheles albimanus, Anopheles Atroparvus, Anopheles gambiae M, Anopheles merus, Anopheles stephensi) at 15-18h embryonic stage of development.