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 line
SSEA1+ CSCs
treatment
Input
antibody
none
genotype/variation
wildtype

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed as detailed by Sailaja et al PNAS 109:E3687-3695 2012 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. Sequenced was performed on an Illumina HiSeq 2500 at The Crick Institute, London.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
37194269
Reads aligned (%)
95.1
Duplicates removed (%)
2.5
Number of peaks
35247 (qval < 1E-05)

hg19

Number of total reads
37194269
Reads aligned (%)
94.8
Duplicates removed (%)
2.5
Number of peaks
34936 (qval < 1E-05)

Base call quality data from DBCLS SRA