Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ARID2

Cell type

Cell type Class
Gonad
Cell type
Small cell ovary carcinoma
NA
NA

Attributes by original data submitter

Sample

source_name
BIN-67 (SCCOHT)
lentivirus
SMARCA4.T910M
cell line
BIN-67
chip antibody
ARID2 (CST, D8D8U)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
cells were fixed in 1% formaldehyde at 37 degrees Celsius for 10 minutes, quenched in 2.5 M glycine, and snap frozen. Cells were thawed and lysed and the prepared nuclei was placed in a Covaris miliTube and sonicated for 20 minutes on a Covaris AFA Sonicator at standard settings (140 PIP, 5 W, 10% duty factor). The equivalent of 10 million cells were used in each immunoprecpitation. Three micrograms of the following antibodies were used: anti-SMARCA4 (Abcam ab110641); anti-DPF2 (Abcam); anti-SMARCC1 (homemade rabbit antibody raised against amino acids 998-1073 of human protein); anti-SS18 (Cell Signaling Technologies D6I4Z); anti-ARID2 (Cell Signaling Technologies D8D8U); anti-H3K4me1 (Abcam); anti-H3K27ac (Abcam). IP's were washed in 150 and 500 mM salt solution as well as a LiCl wash. Protein-DNA fragments were eluted using an SDS/DTT buffer and reverse crosslinked overnight. DNA was captured with SPRI beads (Agilent). Size selection was used to eliminate DNA too large for library prep. Rubicon library prep was used to generate libraries, and libraries were sequenced on Illumina NextSeq 500. ChIP-sequencing libraries were prepared with the Rubicon Thruplex DNAseq prep kit using standard protocols.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
45817632
Reads aligned (%)
25.2
Duplicates removed (%)
71.9
Number of peaks
9792 (qval < 1E-05)

hg38

Number of total reads
45817632
Reads aligned (%)
26.5
Duplicates removed (%)
70.7
Number of peaks
9768 (qval < 1E-05)

Base call quality data from DBCLS SRA