Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ERCC6

Cell type

Cell type Class
Others
Cell type
Fibroblasts
NA
NA

Attributes by original data submitter

Sample

source_name
CSB∆N1 CHIP
cell type
fibroblast

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were collected in Buffer B (150 mM NaCl, 0.5 mM MgCl2, 20 mM HEPES pH7.8, 10% Glycerol, 0.5% Triton X-100) and soluble CSB was removed from nuclei by centrifugation at 1500 RPM for 5 min at 4°C. The resulting cell pellets were subsequently fixed with 1% formaldehyde for 10 min at room temperature. Crossed-linked cells were sonicated at 40% amplitude (30 sec on, 90sec off, for 24 min total) using The Branson 101-135-126 Sonifier. Chromatin IP (ChIP) was performed using monoclonal anti-CSB antibody against the N-terminal 507 amino acids (1B1), To generate the library from ChIP experiments, ChIP-Seq Library Protocol with multiplexing was used. This protocol was developed before Illumina released its multiplex truSeq ChIP-seq kit, and the details can be found on http://ngsc.med.upenn.edu/. According to the protocol, 10 ng of ChIP DNA product was used to start the library construction.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
26707065
Reads aligned (%)
67.6
Duplicates removed (%)
28.8
Number of peaks
1513 (qval < 1E-05)

hg38

Number of total reads
26707065
Reads aligned (%)
70.3
Duplicates removed (%)
26.8
Number of peaks
1585 (qval < 1E-05)

Base call quality data from DBCLS SRA