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
mESCs
strain
R1 129/Sv
chip antibody
none
genotype
Tet1-/- Tet2-/-

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with 1% formaldehyde for 10 min at 37◦C; then, crude nuclei were purified. Chromatin was fragmented by sonication to obtain fragments 200–2000 bp in length. Then chromatin was reverse-crosslinked and DNA was purifiied and quantified with a Qubit fluorometer using the Quant-iT dsDNA HS assay kit DNA was end-repaired, adenylated, and ligated to TruSeq sequencing adaptors. DNA was purified by AMPure beads or DNA purification kit according to the DNA amount. Library DNA was amplified by Phusion HF (NEB, Cat. M0530L). The amplified DNA was size selected using 2% agarose gel for 200-500bp DNA fragments.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
16125731
Reads aligned (%)
97.2
Duplicates removed (%)
12.7
Number of peaks
357 (qval < 1E-05)

mm9

Number of total reads
16125731
Reads aligned (%)
96.9
Duplicates removed (%)
12.7
Number of peaks
368 (qval < 1E-05)

Base call quality data from DBCLS SRA