ChIP-Seq with Tagmentation Library Prep

Cells were cultured to 80% confluency and were cross-linked using 1% formaldehyde by rocking for 10 min at room temperature and then quenched with 0.125 M glycine. Cross-linked cells were washed in PBS and collected using a scrapper. Libraries were obtained following chromatin immunoprecipitation (ChIP)-tagmentation protocol described elsewhere.^{15 (link)} Briefly, a standard ChIP protocol was followed using the ChIP-IT Express Chromatin Immunoprecipitation Kit (Active Motif, 53008) that included cell lysis, sonication of chromatin (Covaris S220 ultrasonicator), and immunoprecipitation using antibodies bound to beads. At this step, the sequencing adapters were introduced in a single step by tagmentation (Nextera Tag DNA Enzyme) of bead-bound chromatin. Following tagmentation, the kit protocol was resumed with additional bead washes, tagmented ChIP-DNA elution, reverse cross-linking at 65°C overnight, and DNA purification (ChIP DNA Clean & Concentrator, Zymo Research). Library preparation was performed using custom Nextera primers as described for ATAC-seq. Library cluster generation and single-end sequencing was performed on the Illumina platform. Reads were aligned with BWA version 0.7.12^{16 (link)} to human genome reference of build Hg19, and duplicates were marked with Picard version 1.92 (http://broadinstitute.github.io/picard).