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
mESCs
cell type
strain 129 mESCs
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq samples were prepared as described in Morey et al, 2015. Briefly, 5 million mESCs were removed from the dish using accutase and resuspended in 2i media. mESCs were then fixed in 1 % formaldehyde for 10 min before adding 0.0125 M glycine for 5 min to quench the reaction. Chromatin was then immunoprecipitated with 5 ug of antibody Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
128760828
Reads aligned (%)
97.9
Duplicates removed (%)
13.6
Number of peaks
1356 (qval < 1E-05)

mm9

Number of total reads
128760828
Reads aligned (%)
97.6
Duplicates removed (%)
13.5
Number of peaks
1530 (qval < 1E-05)

Base call quality data from DBCLS SRA