Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BRCA2

Cell type

Cell type Class
Kidney
Cell type
hTERT-HME1
Primary Tissue
Breast
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
hTert-HME1
cell type
hTert-HME1 cell line
index for hiseq
CGATGT
cell line
hTert-HME1
antibody
BRCA2

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Log-phase growth cells were crosslinked in 1% formaldehyde at a density of 5x105 cells per milliliter for 10 minutes at room temperature, then quenched with 125 mM glycine for 5 minutes, washed in PBS and snap frozen. Cells were then thawed and nuclei isolated by triton-X permeabilization followed by washing in a low detergent buffer. Then RIPA was added and sonication was performed by Branson (3 pulses of 30 seconds each with power output 4 W), followed by 14 cycles of sonication on the Bioruptor Pico. Chromatin extracts were then cleared by centrifugation and immunoprecipitation was performed with antibodies and protein A/G agarose beads overnight. The next day the beads were extensively washed with RIPA, then PBS, then resuspended in TE with 1% SDS and crosslinks were reversed overnight at 65 degrees Celcius. The next day RNase A treatment and proteinase K treatment were performed, followed by recovery of DNA with the Qiaquick spin columns. High throughput sequencing libraries were then constructed by A tailing, adapter ligation and 10-15 cycles of PCR followed by library purification, removal of PCR primer-dimers and high-throughput sequencing by HiSeq 4000.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg19

Number of total reads
69101115
Reads aligned (%)
176.8
Duplicates removed (%)
7.8
Number of peaks
5447 (qval < 1E-05)

hg38

Number of total reads
69101115
Reads aligned (%)
178.7
Duplicates removed (%)
7.4
Number of peaks
6713 (qval < 1E-05)

Base call quality data from DBCLS SRA