RNA-seq and ChIP-seq Characterization of Chromatin Remodelers

Cell lines over-expressing chromatin remodelers, including HDAC1 were characterized using RNA-sequencing (RNA-seq) and ChIP-sequencing (ChIP-seq). Data were generated and analyzed using established, published methods [28 (link), 29 (link)]. Briefly, RNA-sequencing libraries for MiaPaca-2 and Panc-1 cells were made using the Lexogen 3′ RNA-sequencing kit. They were pooled and sequenced on an Illumina NextSeq instrument with 75 bp single-end reads. Analysis used previously published methods including: Trimgalore for adapter trimming, fastqc for quality score assessment, STAR for alignment to hg38, HTSeq-gene to map reads to features, and DESeq2 for differential expression analysis. For ChIP-seq, HDAC1 over-expressing MiaPaca-2 cells were cross-linked, harvested, and DNA was precipitated using a commercial HDAC1 antibody (Invitrogen, PA1860). Libraries were constructed, pooled and sequenced using Illumina NovaSeq single end 75 bp reads. These data were generated and analyzed using published ENCODE protocols (https://www.encodeproject.org/documents/).