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
in vitro transformed human skin fibroblasts
cell type
in vitro transformed human skin fibroblasts
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were harvested with trypsin and ChIP was performed as previously described (Sailaja et al., Methods in molecular biology, 2012). Library construction was carried out as published (Blecher-Gonen et al., 2013, Nat Prot). Paired end libraries were constructed using standard Illumina protocols, with some modifications. Agencourt AMPure XP (Beckman Coulter) at 0.8x ratio were used to size select out adapter dimers. The Illumina Phusion enzyme was replaced by Kapa HiFi HotStart ready mix (Kapa Biosystems). An Invitrogen SizeSelect R-gel system (Life Technologies) was used to size select following PCR amplification.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
29454881
Reads aligned (%)
96.8
Duplicates removed (%)
1.4
Number of peaks
1133 (qval < 1E-05)

hg19

Number of total reads
29454881
Reads aligned (%)
96.0
Duplicates removed (%)
1.7
Number of peaks
611 (qval < 1E-05)

Base call quality data from DBCLS SRA