Chromatin IP (ChIP), RNA expression (RNA-seq and qPCR), and small RNA-seq

ChIP and RNA-seq were performed as previously described (Zeller et al. 2016). Libraries were prepared from chromatin IP and genomic DNA samples as described previously (Zeller et al. 2016). Read density along the genome was calculated by tiling the genome into 500-bp windows (nonoverlapping) and counting the number of sequence fragments within each window, using the qCount function of the QuasR package. To compensate for differences in the read depths, libraries were normalized to the total number of reads per library. ChIP-seq signals are displayed as average enrichment of IP – input (log2). For RNA-seq, total RNA was isolated and expression levels determined as previously described (Zeller et al. 2016). For small RNA-seq total small RNA was isolated using the Norgen single-cell RNA purification kit (51800). Purified small RNA was treated with 1 mlTAP (Lucigen) for 1 h at 37°C and libraries were prepared using QiaSeq miRNA library kit. See Supplemental Material for detailed description.