Myc-tagged Protein ChIP-seq Protocol

ChIP assay was performed using 1 Day ChIP kit and Shearing ChIP kit (Diagenode, Denville, USA) according to the manufacturer’s protocol. After lentiviral transduction and cross-linking, mouse kidney fibroblasts were fixed with formaldehyde and the DNA was sheared into small fragments. After incubation with a Myc-tag antibody (Cell signaling, Beverly, USA), the pulled-down complexes were de-crosslinked and treated with proteinase K. The purified DNA samples were proceeded further for library preparation by TruSeq RNA Library Prep Kit v2 (Illumina, USA) and quality control and library validation were performed by Fragment Analyzer and Kapa PCR (Illumina, USA), respectively. The fragments were sequenced by an Illumina HiSeq4000 instrument. For data analysis, a previous established protocol^{48 (link)} was followed. Briefly, the raw reads from two independent biological replicates were first concatenated and then peak calling was performed with MACSII in order to obtain the count numbers. We used settings for narrow peaks (200 bp window size, 200 bp gap size, and false discovery rate of 0.01) in all cases.