Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Pluripotent stem cell
Cell type
ES cells
NA
NA

Attributes by original data submitter

Sample

source_name
embryonic stem cells
strain
159 (mixed 129-C57Bl/6)
genotype
WT
growth condition
serum
chip antibody
none (input)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immunoprecipitation (ChIP) was carried out essentially as previously described (Jermann et al. PNAS 2014). Library Construction Protocol: Libraries for ChIP-seq were prepared according to standard Illumina library preparation protocols. Twelve cycles of PCR (NEB Q5 Hot Start HiFi PCR) were performed on end-repaired, A-tailed and adapter-ligated DNA prior to gel size-selection. Quality of the libraries and size distribution was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies). Sequencing was performed on an Illumina HiSeq 2500 machine (50 bp read length, single end) according to Illumina standards.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
22773779
Reads aligned (%)
95.2
Duplicates removed (%)
5.5
Number of peaks
431 (qval < 1E-05)

mm9

Number of total reads
22773779
Reads aligned (%)
95.1
Duplicates removed (%)
5.6
Number of peaks
424 (qval < 1E-05)

Base call quality data from DBCLS SRA