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
input DNA_noTam
strain
J1
genotype/variation
inducible SetDB1 KO
cell type
ES cells
treated with
none (noTam)
chip 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 histone-DNA complexes were isolated with antibody. For ChIP-seq libraries, 10 ng of input chromatin DNA or ChIP DNA were processed using the ChIP-seq sample prep kit (Illumina). Gel-purified ChIP-seq library DNA was further purified by phenol-chloroform extraction and ethanol precipitation, and processed for cluster generation, 15-cycle sequencing, and sequence analysis using Illumina Hiseq.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
35757912
Reads aligned (%)
98.9
Duplicates removed (%)
15.8
Number of peaks
253 (qval < 1E-05)

mm9

Number of total reads
35757912
Reads aligned (%)
98.8
Duplicates removed (%)
15.8
Number of peaks
223 (qval < 1E-05)

Base call quality data from DBCLS SRA