Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Epidermis
Cell type
Dermal fibroblast
NA
NA

Attributes by original data submitter

Sample

source_name
foreskin
cell type
foreskin fibroblast
treatment
control
time
control
chip antibody
none (input)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Histones and DNA were cross-linked by 1% formaldehyde and extracted using a Magna ChIP G kit (Millipore). The chromatin was then sonicated to an average DNA fragment length of 200-300 bp. Illumina sequencing libraries were generated according to the manufacturer’s instructions. Briefly, 5-50 ng of ChIP product was end repaired, a-tailed and ligated to Illumina single end adapters by using an NEB Next kit (New England Biolabs). Adaptor-ligated DNA with a size of 200-300 bp was purified by running a gel and enriched via 19 cycles of PCR amplification with Phusion High-Fidelity DNA Polymerase, followed by sequencing on an Illumina HiSeq 2000 system.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
37633501
Reads aligned (%)
97.5
Duplicates removed (%)
11.3
Number of peaks
1064 (qval < 1E-05)

hg19

Number of total reads
37633501
Reads aligned (%)
96.4
Duplicates removed (%)
12.7
Number of peaks
1152 (qval < 1E-05)

Base call quality data from DBCLS SRA