title: GSM4874330: H3K27ac_CTRL_rep1; Mus musculus; ChIP-Seq
library_construction_protocol: Cells were isolated from sorted CLL spenocytes (CD19+B220-) and fixed with 1% methanol-free 16% formaldehyde (Pierce Life Technologies) for 10 min at room temperature. Then 0.125M glycine was used to quench fixation, and incubated for 5 min at room temperature. Fixed cells were washed twice with 1x PBS (Gibco Life Technologies) with 1x EDTA-free protease inhibitor cocktail (Pierce Life Technologies). ChIP reaction was performed with Diagenode iDeal ChIP-seq kit for Transcription Factors (Diagenode) with modifications of the manual detailed below. Lysed samples were sonicated in 100 uL of complete Shearing buffer iS1b for 30 cycles 30sec ON/30sec OFF using Diagenode Bioruptor NextGen (Diagenode). Sheared chromatin was immunoprecipitated with 2ug anti-RBPJ antibody (ab25949, Abcam) or 1ug anti-H3K27ac (ab4729,  Abcam). One percent of total chromatin was set aside to be used as input control. Eluted and decross-linked DNA was purified with Diagenode MicroChIP DiaPure columns (Diagenode) and eluted in 30L of Nuclease-Free water. ChIP and input libraries for sequencing were prepared with Swift Biosciences Accel-NGS 2S Plus DNA Dual Indexing Library Kit (Swift Biosciences). Size selection steps were performed with Agencourt AMPure XP magnetic beads (Beckman Coulter). Library amplification was performed following DNA quantification with Invitrogen Qubit Fluorometer. Subsequently, ChIP-seq library was quantified with KAPA Library Quantification Kit (Roche) and Agilent Fragment Analyzer. Prepared libraries were sequenced using the sequencing platforms at GENEWIZ with Illumina HiSeq 4000 150 bp paired-end reads generating 65-90 million paired reads per library.
attributes.tag: GEO Accession
attributes.value: GSM4874330