Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Ctcf

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
cell line
F123 ESC
strain
F1 hybrid (castaneus x S129/SvJae)
chip antibody
ab70303
genotype
nbd_Syn-6_insertion

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Crosslinked cells were processed by Covaris truChIP Chromatin Shearing kit and chromatin were sonicated to 300-500bp by Covaris M220. ChIP DNA and Input DNA were constucted into illumina Tru-seq libraries as previously described (Jian Yan et al., 2013), followed by size selection for 300-500bp.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
26179203
Reads aligned (%)
96.6
Duplicates removed (%)
16.5
Number of peaks
58573 (qval < 1E-05)

mm9

Number of total reads
26179203
Reads aligned (%)
96.5
Duplicates removed (%)
16.6
Number of peaks
60240 (qval < 1E-05)

Base call quality data from DBCLS SRA