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
Undifferentiated mouse embryonic stem cell line
cell type
undifferentiated embryonic stem cell line
cell line
d0
Sex
female
passage
passage 27
strain
F2: 129S1/CastEiJ x 129S1
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed as described in Lee et al. Nat Protoc. 2006;1(2):729-48. Paired-end Solexa ChIP libraries were prepared as described in Illumina ChIP sequencing manual with minor modifications and using NEB Next DNA sample prep reagent Set 1 (E6000S) (NEB). Input DNA was used as a control and for normalization. Modifications to the Illumina protocol were: 1- 30 ng of ChIP products were used as template, 2- paired-end adapters were ligated to end-repaired and A-tailed DNA using T4 DNA ligase (NEB) for 2 hours at 16°C, and 2- Phusion polymerase in GC buffer (Finzyme) was used instead of Phusion polymerase in HF buffer. DNA products were purified with QIAquick spin columns (Qiagen). Concentration, size distribution (400-500bp), and purity of libraries were assessed on DNA1000 Bioanalyzer chip (Agilent). Genome Analyzer II (Illumina) was used to perform 2x36 cycles of paired end sequencing.

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

mm10

Number of total reads
23018524
Reads aligned (%)
97.8
Duplicates removed (%)
46.2
Number of peaks
253 (qval < 1E-05)

mm9

Number of total reads
23018524
Reads aligned (%)
97.7
Duplicates removed (%)
46.7
Number of peaks
256 (qval < 1E-05)

Base call quality data from DBCLS SRA