Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

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

Attributes by original data submitter

Sample

source_name
pre-B cell line
chip antibody catalog/vendor
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3" to 5" exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were size selected and purified by Agencourt Ampure XP beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
25257231
Reads aligned (%)
98.7
Duplicates removed (%)
5.7
Number of peaks
1040 (qval < 1E-05)

hg19

Number of total reads
25257231
Reads aligned (%)
97.7
Duplicates removed (%)
7.3
Number of peaks
1124 (qval < 1E-05)

Base call quality data from DBCLS SRA