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
fibroblast_menadione_CSB-ChIP
cell type
fibroblast
treated with
menadione
chip antibody
Mouse monoclonal anti-CSB N Terminus (1B1)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
CHIP protocol: Cells were 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) [Dr. Hua-Ying Fan, Univ. of Pennsylvania, PMID 23028371]. To generate the library from ChIP experiment, 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
37217254
Reads aligned (%)
68.9
Duplicates removed (%)
27.9
Number of peaks
1508 (qval < 1E-05)

hg38

Number of total reads
37217254
Reads aligned (%)
70.8
Duplicates removed (%)
26.4
Number of peaks
1456 (qval < 1E-05)

Base call quality data from DBCLS SRA