Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

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

Attributes by original data submitter

Sample

source_name
Mouse ES cells
cell line name
R1 clone Ch9
background strain
129X1 x 129S1
cell type
Mouse ES cells

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP, crosslinked chromatin was prepared using standard conditions or the SimpleChIP® Plus Enzymatic Chromatin IP Kit. For WGBS, genomic DNA was isolated by alkali lysis using classical methods. For ChIP libraries, the NEBNext ChIPSeq library kit or the SimpleChIP® Plus Enzymatic Chromatin IP Kit was used as per instructions. For WGBS libraries, DNA was bisulfite treated using the Zymo EZ DNA Methylation Lightning Kit followed by library preparation using the TruSeq DNA Methylation Kit (Illumina).

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
59060503
Reads aligned (%)
98.2
Duplicates removed (%)
17.6
Number of peaks
25008 (qval < 1E-05)

mm9

Number of total reads
59060503
Reads aligned (%)
98.0
Duplicates removed (%)
17.5
Number of peaks
25014 (qval < 1E-05)

Base call quality data from DBCLS SRA