E(Pc) ChIP-seq experiment in fruitfly testis somatic gonadal cells and RNA-seq experiment in fruitfly testis

With the ChIP-seq experiment, we identified direct target genes of E(Pc) specifically in somatic gonadal cells. We found that the E(Pc)-binding genes are enriched with signaling pathway components, consistent with our functional data showing prevailing germline defects even when E(Pc) function is exclusively compromised in somatic gonadal cells. In addition, we also performed RNA-seq to compare transcriptomes between E(Pc) knockdown testes and control testes. Overall design: For ChIP-seq, we used fly testis expressing GFP-tagged E(Pc) specifically in somatic gonadal cells by Tj promoter driven GAL4>UAS system. ChIP-seq with GFP antibody was performed. For RNA-seq, RNA was purified from Tj-Gal4 or Tj-Gal4/+; UAS-E(Pc) shRNA/+ testes.