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 cell
cell line
R1
cell type
Embryonic stem cell
genotype
Dendra2-RPB1, Halo-MED19
state
EpiLC
chip antibody
none
young_id
20180126_6668

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked on plates with 1% formaldehyde in media for 15 minutes at room temperature. 50 million cells were used per ChIP reaction. Whole cell extracts were sonicated on a QSonica Q700 tip sonicator to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Library construction was performed by the Whitehead Institute Genome Technology Core using the Swift Biosciences Accel-NGS 2S Plus DNA Library Kit according to manufacturer's protocol.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
55266734
Reads aligned (%)
93.5
Duplicates removed (%)
30.5
Number of peaks
4927 (qval < 1E-05)

mm9

Number of total reads
55266734
Reads aligned (%)
93.1
Duplicates removed (%)
30.4
Number of peaks
1350 (qval < 1E-05)

Base call quality data from DBCLS SRA