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 R1 ESCs
transcription factor
CTCF
mnase
25U
antibody
Anti CTCF

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
MNase digested chromatin was allowed to bind to antibodies for 2-4 hours. Paramagnetic protein G dynabeads were added for an additional hour and the beads were extensively washed. Bound chromatin was ligated to barcoded DNA adapters, and chromatin was reverse cross linked and pooled. Barcoded chromatin was amplified with Illumina NGS - compatible primers and DNA libraries were paired end sequenced by Illumina NextSeq 500.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
4842736
Reads aligned (%)
80.7
Duplicates removed (%)
9.5
Number of peaks
2033 (qval < 1E-05)

mm9

Number of total reads
4842736
Reads aligned (%)
80.6
Duplicates removed (%)
9.8
Number of peaks
2027 (qval < 1E-05)

Base call quality data from DBCLS SRA