Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Ctcf

Cell type

Cell type Class
Blood
Cell type
Pro-B cells
NA
NA

Attributes by original data submitter

Sample

source_name
Pro-B cell
strain
C57BL/6
genotype
Rag2-/-
cell type
in vitro cultured Pro-B cells (4d)
antibody
Rabbit anti-Ctcf antibody (07-729, Millipore, unpurified)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
About 5x107 pro-B cells were used for chromatin precipitation by streptavidin pulldown (Bio-ChIP) Ebert et al., 2011 The precipitated genomic DNA was quantified by real-time PCR, and at least 5 ng of ChIP-precipitated DNA were used as starting material for the generation of paired-end sequencing libraries as described by Illumina’s ChIP Sequencing sample preparation protocol followed by size selection of DNA fragments of 200–350 bp. Completed libraries were quantified with the Agilent Bioanalyzer dsDNA 1000 assay kit and Agilent QPCR NGS library quantification kit.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
53440570
Reads aligned (%)
97.8
Duplicates removed (%)
14.6
Number of peaks
70888 (qval < 1E-05)

mm9

Number of total reads
53440570
Reads aligned (%)
97.7
Duplicates removed (%)
14.8
Number of peaks
70754 (qval < 1E-05)

Base call quality data from DBCLS SRA