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
embryonic stem cells, input
cell type
embryonic stem (ES) cells
genetic background
hybrid 129-C57BL/6
genotype/variation
wt
treatment
none
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
10^7 mES cells were crosslinked, chromatin was extracted and fragmented with micrococcal nuclease to mostly mono nucleosomes. 1% of chromatin was set aside as Input control. The chromatin was incubated with antibody over night, Protein A coupled Dynabeads were added for 2 hours and thereafter immunoprecipitated DNA was washed and de-crosslinked. Purified DNA was subsequently used for library preparation. For a detailed protocol, see Ostapcuk et al, 2017. Libraries were prepared using the NEB Next DNA library prep kit according to manufacturer's instructions. For barcodes, see sample characteristics.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
49648909
Reads aligned (%)
97.0
Duplicates removed (%)
8.1
Number of peaks
300 (qval < 1E-05)

mm9

Number of total reads
49648909
Reads aligned (%)
96.9
Duplicates removed (%)
8.1
Number of peaks
326 (qval < 1E-05)

Base call quality data from DBCLS SRA