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
Conditional Jmjd2c knockout ESCs
cell type
Conditional Jmjd2c knockout ESCs
treatment
-
chip antibody
IgG
strain
C57BL/6

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immunoprecipitation (ChIP) was performed using formaldehyde crosslinked chromatin sonicated to an average size of 200-600 bp and the indicated antibodies. 5-10 ng of DNA was processed using NEBNext and Illumina ChIP seq kits according to the manufacturer's instructions. In brief, DNA was adaptor-ligated, subjected to gel size selection, amplified and analyzed by Solexa/Illumina high-throughput sequencing.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
40141469
Reads aligned (%)
89.2
Duplicates removed (%)
20.4
Number of peaks
728 (qval < 1E-05)

mm9

Number of total reads
40141469
Reads aligned (%)
89.0
Duplicates removed (%)
20.5
Number of peaks
773 (qval < 1E-05)

Base call quality data from DBCLS SRA