Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ARID2

Cell type

Cell type Class
Kidney
Cell type
786-O
Primary Tissue
Kidney
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
clear cell renal cell carcinoma cell line
cell line
clear cell renal cell carcinoma cell line 786-O
shRNA
PBRM1 shRNA #2
chip antibody
Santa Cruz ARID2 (E-3) sc-1666117 mouse monoclonal ab - 5 ug (lot# G2712)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Briefly, 15x10^6 786-O cells were cross-linked with 1% formaldehyde (Pierce, #28908) for 5 min at 4⁰C with gentle rocking. The fixed cells were sonicated using the TruChIP Chromatin Shearing Reagant Kit (Covaris, # PN 520154) following the manufacturer’s instructions. The IP step was carried out for 4 hr at 4⁰C with 5 μg of ARID2 (E-3) antibody (Santa Cruz), followed by a 2 hr incubation with Magna ChIP Protein A+G Magnetic Beads (Millipore, #16-663). After washing and chromatin elution, DNA was extracted via phenol/chloroform followed by DNA purification using Qiagen MiniElute PCR purification tubes. The amount and size of the precipitated DNA was evaluated using the Bioanalyzer. To generate enough DNA to make ChIP-seq libraries for sequencing, the entire process was repeated on a different batch of cells for each cell line. The precipitated DNA was then pooled for each cell line. ChIP-seq libraries were made following well-established protocols. Briefly, 2-10 ng of DNA was end-repaired, an A-overhang was added, Illumina Truseq adapters were ligated, DNA was run on an agarose gel and size-selected at 350-500 bp using the Qiagen Gel Extraction Kit, and finally libraries were PCR amplified for 10-14 cycles using KAPA Biosystems HiFi PCR Master Mix. Where not indicated, all library preparation steps involved New England Biolabs enzymes. The quality and concentration of the prepared libraries were assessed on the Bioanalyzer - the libraries produced U-shaped DNA profiles, with an average peak around 400bp. 75 bp single-end sequencing was performed on an Illumina NextSeq 500 machine.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
23164588
Reads aligned (%)
80.7
Duplicates removed (%)
16.3
Number of peaks
786 (qval < 1E-05)

hg38

Number of total reads
23164588
Reads aligned (%)
82.6
Duplicates removed (%)
14.9
Number of peaks
970 (qval < 1E-05)

Base call quality data from DBCLS SRA