Genome binding/occupancy profiling by high throughput sequencing
Summary
The objectives of this study are to understand the regulatory roles of MAZ in biological processes using the NGS-deriveed ChIP-seq, DNA-MEDIP-seq and RNA-seq data in HAP1 control cells and MAZ knockout cells. Our comparative analysis of these data generated from the HAP1 control and MAZ KO cells shows that MAZ is required for recruiting STAT1 to its target sites by reshaping epigenetic landscape in the human genome, thereby mediating antiviral response cells. Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for STAT1 and H3K4me3, H3K27Ac in HAP1 cells.
Overall design
ChIP-Seq of HAP1/K562 control cells and MAZ knockdown/kockout cells were generated by deep sequencing in duplicate using Illumina GAIIx. The ChIP-seq sequence reads were aligned with Bowtie2 followed by calling peaks with MACS2 software. Distribution of STAT1, H3K4me3, H3K27Ac and DNA methylation was analyzed using Deeptools and other software.
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