ChIP and input DNA libraries were performed as previously
described63 (link). Briefly,
cells were cross-linked with 1% formaldehyde for 10min at room temperature and
formaldehyde was then inactivated by the addition of 125mM glycine for 5min.
Sonicated DNA fragments with 100–300bp were pre-cleared and
immunoprecipitated with Protein A+G Magnetic beads coupled with Anti-H3K27Ac
antibody (ab4729, Abcam) or Anti-YY1 antibody (#61779, active motif). 5μg
antibody per 1ml volume reaction was added for both antibodies. After reverse
crosslinking, immunoprecipitated DNAs and input DNAs were end-repaired and
ligated adapters to the DNA fragments using NEBNext Ultra End-Repair/dA-Tailing
Module (E7442, NEB) and NEBNext Ultra Ligation Module (E7445, NEB).
High-throughput sequencing of the ChIP fragments was performed using Illumina
NextSeq 500 following the manufacturer’s protocols.
Analysis was carried out with ChIP-seq analysis pipeline on St. Jude
Cloud (https://platform.stjude.cloud/tools/chip-seq ). Briefly, the reads
were aligned to the human genome (GRCh37-lite) with bwa55 (link) (v0.7.12), then ambiguously-mapped and
duplicate reads were removed. Fragment length was estimated based on a
cross-correlation plot generated by SPP64 (link) (v1.10.1). MACS65 (link) (v2.1.1) was used to call the peaks. The results were
filtered against known false positive peaks using the ENCODE black
list66 (link).
described63 (link). Briefly,
cells were cross-linked with 1% formaldehyde for 10min at room temperature and
formaldehyde was then inactivated by the addition of 125mM glycine for 5min.
Sonicated DNA fragments with 100–300bp were pre-cleared and
immunoprecipitated with Protein A+G Magnetic beads coupled with Anti-H3K27Ac
antibody (ab4729, Abcam) or Anti-YY1 antibody (#61779, active motif). 5μg
antibody per 1ml volume reaction was added for both antibodies. After reverse
crosslinking, immunoprecipitated DNAs and input DNAs were end-repaired and
ligated adapters to the DNA fragments using NEBNext Ultra End-Repair/dA-Tailing
Module (E7442, NEB) and NEBNext Ultra Ligation Module (E7445, NEB).
High-throughput sequencing of the ChIP fragments was performed using Illumina
NextSeq 500 following the manufacturer’s protocols.
Analysis was carried out with ChIP-seq analysis pipeline on St. Jude
Cloud (
were aligned to the human genome (GRCh37-lite) with bwa55 (link) (v0.7.12), then ambiguously-mapped and
duplicate reads were removed. Fragment length was estimated based on a
cross-correlation plot generated by SPP64 (link) (v1.10.1). MACS65 (link) (v2.1.1) was used to call the peaks. The results were
filtered against known false positive peaks using the ENCODE black
list66 (link).
