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
mouse embryonic stem cell
cell type
cell line
strain
C57BL/6
chip antibody
CTCF (Cell Signaling, 2899)
treatment
siNC (negative control siRNA)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were first crosslinked by formaldehyde, then digested with Mnase, then sonicated in N-lauroyl-sarcosine containing buffer to dissolve the chromatin. The clarified chromatin were immunoprecipitated with agarose conjucated with antibodies. Libraries were prepared according to NEBNext Ultra DNA Library Prep Kit for Illumina (E7370L) and were sequenced using HiSeq2000 or Nova-seq.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
33333751
Reads aligned (%)
97.8
Duplicates removed (%)
13.3
Number of peaks
10911 (qval < 1E-05)

mm9

Number of total reads
33333751
Reads aligned (%)
97.5
Duplicates removed (%)
13.3
Number of peaks
11800 (qval < 1E-05)

Base call quality data from DBCLS SRA