GSM5284455: IRF4-ChIP-seq from mouse cDC2; Mus musculus; ChIP-Seq
Cells were crosslinked with 1% formaldehyde, quenched with 1.25M Glycine, washed twice with PBS. The chromatin was sonicated to shear DNA size from 140 to 500 bp. Chromatin fragments were immunoprecipitated with anti-IRF4 antibodies (sc-6059x, Santa Cruz Biotechnology) and Dynabeads Protein G overnight at 4 °C. ChIPed DNA was eluted and reverse-crosslinked for 6 hr. DNA was purified with phenol:chloroform extraction followed by ethanol precipitation. Processes for DNA isolation, library construction, and sequencing are performed the same way with GSE66899 dataset. Detailed methods were described in Nature Immunology (2015)_Grajales-Reyes and Murphy (PMID: 26054719) Libraries for ChIP-seq were prepared using ThruPLEX-FD kit (Rubicon Genomics) and sequenced using Illumina HiSeq 2500 as single reads extending 50 bases.