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
mouse embryonic stem cells
cell type
mouse embryonic stem cells
cell number
5M per replicate
gender
female
chip antibody
IgG

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Nuclei were lysed and chromatin was resuspended in sonication buffer The chromatin was sonicated to average 220 bp and incubated with antibody overnight at 4'C. Antibody-bound chromatin was incubated with Protein G Dynabeads (Invitrogen, 10004D) for 4 hours at 4'C and eluted in Tris buffer (10mM Tris pH 8.0, 10mM EDTA, 1% SDS). Crosslinks were reversed by incubation overnight at 65'C followed by treatment with 0.2 mg/mL proteinase K (Life Technologies, AM2548) and 0.2 mg/mL RNAse A (Qiagen). DNA was purified using Qiagen Minelute Columns (Qiagen, 28006). Libraries were prepared by DNA tagmentation (Nextera) followed by PCR amplification.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

mm10

Number of total reads
20794763
Reads aligned (%)
73.3
Duplicates removed (%)
5.4
Number of peaks
283 (qval < 1E-05)

mm9

Number of total reads
20794763
Reads aligned (%)
73.2
Duplicates removed (%)
5.5
Number of peaks
257 (qval < 1E-05)

Base call quality data from DBCLS SRA