LINE1 and PRC2 control nucleolar organization and repression of the 8C-state in human ESCs [H3K27me3 ChIP-seq,RSeT+DT_L1KD]

In this study, we performed H3K27me3 ChIP-seq to compare LINE1 knockdown naive hES cells with the control. RSeT media maintained naive H9 hES cells were transfected with non-specific targeting control anti-sense oligos (ASO-Ctr) and anti-sense oligos (ASO-L1), respectively. Transfected cells were maintained in the RSeT media added with 10 nM DZNep and 5nM TSA (RSeT+DT). 48 hours later, ASO transfected cells were collected and subjected to H3K27me3 ChIP-seq. ChIP steps were performed using the ChIP-lysates True MicroChIP-Seq kit (Diagenode # C01010132) following the instruction manuals. The rabbit antibody against H3K27me3 (Cell Signaling Technologies # 9733) was used for the pulldown. 5% of input from replicate sample 3 was saved before the pulldown, and used for input DNA extraction, as the instruction manuals indicated.