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
strain
C57BL/6
genotype/variation
Eed-/-
dox treatment
yes
cell passage
5
antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and JARID2-DNA complexes were isolated with JARID2 antibody (Li et al., 2010) ChIP-seq libraries were prepared according to Illumina protocol and sequenced using a HiSeq machine. Single-end sequencing was carried out to obtain about 50 million (M), 100bp long reads per sample. Read alignment with Bowtie2-2.1.0 (Langmead and Salzberg, 2012; Langmead et al., 2009) with standard parameters and one mismatch in the seed sequence and consecutive duplicate filtering resulted in at least 35M reads per sample. Only reads with mapping quality Qphred20 were kept for the enrichment analysis.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
55065547
Reads aligned (%)
98.8
Duplicates removed (%)
12.3
Number of peaks
443 (qval < 1E-05)

mm9

Number of total reads
55065547
Reads aligned (%)
98.7
Duplicates removed (%)
12.3
Number of peaks
458 (qval < 1E-05)

Base call quality data from DBCLS SRA