RNA-seq on Zfp961 GFP flox/flox mESCs to verify ERVKs repression by Zfp961.

To investigate the functional consequences in the absence of ZFP961 in mESCs, we treated the Zfp961-GFPflox/flox cells with 4-OHT to deplete the ZFP961 alleles, and then performed RNA-seq on three independent Zfp961-GFPflox/flox ESC lines before and after Cre mediated excision. Considerate that stable DNA methylation may remain upon Zfp961 absent, therefore ERVKs could still be repressed, we then treated Zfp961-GFPflox/flox cells with 5aza, which a inhibitor of DNA methylation, 24h before Zfp961 deletion with 4-OHT addition. After 4-OHT treatment,we performed RNAseq again, and this time we observed a ETnERV2-int, with belongs to ERVK elements, was upregulated after Zfp961 deletion. Overall design: Basically, three Zfp961-GFP floxed mESCs cell lines treated with 4-OHT or EtOH as control and two cell lines treated with 5AZA for 24h and then treated with 4-OHT or EtOH. RNA of these cell lines was isolated and sequenced.