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
embryonic stem cells
cell line
R1 ESC
strain
129SV
genotype
wild-type

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Nuclei were extracted and chromatin sonicated to 250-500bp with a Covaris sonicator and IP was performed with antibody as indicated overnight. ChIP DNA, input DNA and cDNA were subject to end repair, A-tailing, adaptor ligation and cleavage with USER enzyme, followed by size selection of 250-500 bp and amplification with NEBNext sequencing primers

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
20691539
Reads aligned (%)
88.2
Duplicates removed (%)
13.0
Number of peaks
8822 (qval < 1E-05)

mm9

Number of total reads
20691539
Reads aligned (%)
87.9
Duplicates removed (%)
13.0
Number of peaks
8778 (qval < 1E-05)

Base call quality data from DBCLS SRA