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
ChIP_addbackWt_CTCF-input
strain
129S6/SvEvTac
cell type
mouse embryonic stem cells
genotype/variation
Snf2h ko, Snf2h wiltype add-back
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was carried out as previously described (Weber et al., 2007) with slight modifications. Changes to the protocol were following; (1) chromatin was sonicated for ~50 cycles of 30 sec. using a Diagenode Bioruptor, with 45 sec. breaks in between cycles, (2) protein A/G magnetic Dynabeads Magnetic beads (Thermo Fisher Scientific) were used, (3) DNA was purified using on-column purification instead of chloroform/phenol extraction (Qiagen PCR Purification Kit). Immunoprecipitated DNA and input DNA were submitted to library preparation (NEBNext Ultra DNA Library Prep Kit, Illumina). In the library preparation protocol, input sample were amplified using 4 PCR cycles, IP sample using 12 cycles.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
31205439
Reads aligned (%)
97.5
Duplicates removed (%)
9.9
Number of peaks
485 (qval < 1E-05)

mm9

Number of total reads
31205439
Reads aligned (%)
97.3
Duplicates removed (%)
9.9
Number of peaks
521 (qval < 1E-05)

Base call quality data from DBCLS SRA