RNA-seq and ChIP-seq samples were sequenced with the Illumina NextSeq technology, and output data were processed with the bcl2fastq software tool. Sequence quality was assessed using FastQC v0.11.2 (43), and quality trimming was done using the FASTX toolkit. RNA-seq and ChIP-seq reads were aligned to the hg19 genome using TopHat v2.0.9 (44) and Bowtie v0.12.9 (45), and only uniquely mapped reads with a two-mismatch threshold were considered for downstream analysis. Gene annotations from Ensembl 72 were used. Output BAM files were converted into bigwig track files to display coverage throughout the genome (in reads per million) using the GenomicRanges package (46) and other standard Bioconductor R packages.

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