title: GSM4774112: LVshARID1A_H3K4me1_rep1; Homo sapiens; ChIP-Seq
library_construction_protocol: 72 hours following lentiviral transduction, cells were treated with 1% formaldehyde in cell culture media for 15 min at room temp. Formaldehyde was quenched by the addition of 0.125 M Glycine, and cells were washed with PBS. 1x10^7 crosslinked cells were used per IP. Chromatin from crosslinked cells was fractionated by digestion with micrococcal nuclease using the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling) per the manufacturers' instructions. IPs were performed using the SimpleChIP Enzymatic Chromatin IP Kit per the manufacturers' instructions. 4 ug H3K4me1 (abcam, ab8895) antibody was used per IP sample. DNA was purified using the ChIP DNA Clean & Concentrator Kit (Zymo). Libraries for Input and IP samples were prepared by the Van Andel Genomics Core from 10 ng of input and IP material when available, and all material when less than 10ng available, using the KAPA Hyper Prep Kit (v5.16) (Kapa Biosystems, Wilmington, MA USA). Prior to PCR amplification, end-repaired and A-tailed DNA fragments were ligated to IDT for Illumina unique dual adapters (IDT DNA Inc, Coralville, IA, USA) at a concentration of 3uM. Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems). Individually indexed libraries were pooled and 50 bp, paired end sequencing was performed on an Illumina NovaSeq6000 sequencer using an SP, 100 cycle sequencing kit (Illumina Inc., San Diego, CA, USA). Each library was sequenced to minimum read depth of 100M reads per input, 50M reads per IP. Base calling was done by Illumina RTA3 and output was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.