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The epigenetic pattern and genome-wide CTCF occupancy in HL-60 cells treated with ATRA

ABSTRACT: 10^7 HL-60 cells were treated with 10 uM ATRA for two and five days. 10% whole cell lysates were saved as input after genomic DNA was broken into 200-500 bp by sonication. 1 μg IP grade antibodies of CTCF, H3K4me3 or H3K27me3 (CST, Boston, USA) were incubated with the rest of the lysate overnight, followed by 2 h protein-A beads incubation at 4 °C for target protein pull down. The CTCF enriched or H3K4/27me3 modified DNA or input DNA were repaired to 3’-dA overhang and added the ligated adapter. The DNA library was eliminated the unligated adapters and selected the appropriate size for sequence using an Illumina X Ten platform. The raw sequence reads of input and IP were trimmed adaptors and filter out low quality reads using Cutadapt (v1.9.1) and Trimmomatic (v0.35), and checked the quality of clean reads using Fastqc. Next, clean reads were mapped to the human genome (assembly hg38) using the Bowtie 2 (v2.2.6) algorithm. The process of peak calling (p<0.01) were performed by MACS 2 (v2.1.1) and analyzed the different binding domains based on FDR value less than 0.05 and annotated by DiffBind. De novo motif were analyzed using the R language and MEME. The peaks on certain genomic loci were visualized by Integrative Genomics Viewer (IGV). Gene ontology (GO) Analysis was used to interpret the biological function of the genes associated with differential peaks.

INSTRUMENT(S): HiSeq X Ten

ORGANISM(S): Homo sapiens

SUBMITTER: Yanping Hu

PROVIDER: E-MTAB-8558 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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