RNA-Sequencing data from PofD119, Zhr1, PoX2Df1.688 and Oregon-R adult Drosophila melanogaster (Females and Males, separately).

The prominent role of pericentromeric Mbp block of 1.688 satellites in hybrid incompatibility, facilitating role of distributed X-linked 1.688 satellites in dosage compensation in males and being as a necessary element for POF recruitment to chromosome X in females led us to further investigate the role of 1.688 satellites and POF in chromosome-wide gene regulation by comparing RNA-seq data from the relevant mutants in comparison to wildtype. Overall design: Four biological replicates were isolated for each of the four genotypes and two sexes, in total 32 samples based on 10 individual adult flies (6-24 h after hatching the pupa) per sample.