Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Embryonic fibroblast
Cell type
MEF
Tissue
Embryonic Fibroblast
Lineage
primaryCells
Description
Mouse Embryonic Fibroblast

Attributes by original data submitter

Sample

source_name
Mouse Embryonic Fibroblasts
genotype
Firre KO
cell type
Mouse Embryonic Fibroblasts
Sex
female
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The ChIP assay was performed as previously described (Lee et al, Nature Protocols, 2006). . The chromatin was sheared by using a Covaris S220 instrument. The pull-down was performed using a CTCF antibody (Millipore Sigma #07-729).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
5781743
Reads aligned (%)
93.4
Duplicates removed (%)
13.9
Number of peaks
190 (qval < 1E-05)

mm9

Number of total reads
5781743
Reads aligned (%)
93.0
Duplicates removed (%)
14.2
Number of peaks
204 (qval < 1E-05)

Base call quality data from DBCLS SRA