Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
PCGF2

Cell type

Cell type Class
Others
Cell type
Fibroblasts
NA
NA

Attributes by original data submitter

Sample

source_name
Cultured fibroblasts
genotype
normal foreskin
chip antibody
MEL18 (Santa Cruz sc-10744)
treatment
300 nM solvent (methanol) for 4 h

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
DNA samples were end repaired, poly-A tailed and Illumina single end adapters were ligated following the standard Illumina protocol with minor adjustments. Agencourt AMPure XP beads at 0.8x ratio were used to size select out adapter dimers after adapter ligation. The Illumina kit Phusion enzyme was replaced by Kapa HiFi HotStart ready mix. Post PCR, AMPure XP beads were used at a 1:1 ratio to maintain size integrity and to allow use of the Invitrogen SizeSelect E-gel system. Samples were finally purified with QAIquick gel extraction kit and quality controlled on the DNA 1000 BioAnalyser 2100 chip before clustering and subsequent 50-51bp single end sequencing on the Illumina HiSeq 2500.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
68775793
Reads aligned (%)
72.6
Duplicates removed (%)
20.0
Number of peaks
4539 (qval < 1E-05)

hg38

Number of total reads
68775793
Reads aligned (%)
73.5
Duplicates removed (%)
19.3
Number of peaks
5019 (qval < 1E-05)

Base call quality data from DBCLS SRA