Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Srf

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
Cultured MEFs (Mouse Embryonic fibroblasts)
cell type
Cultured MEFs (Mouse Embryonic fibroblasts
genotype
wildtype
chip antibody
SRF (sc-335) (Lot: D3013)
scaling factor used
(total mapped reads normalised to 30MM reads)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chip-Seq: DNA samples were end repaired, poly-A tailed and Illumina single end adapters were ligated following the standard Illumina protocol with minor adjustments. Agencourt AMPure XP beads at 0.8x ratio were used to size select out adapter dimers after adapter ligation. The Illumina kit Phusion enzyme was replaced by Kapa HiFi HotStart ready mix. Post PCR, AMPure XP beads were used at a 1:1 ratio to maintain size integrity and to allow size select on 2%Agarose gel. Samples were finally purified with QAIquick gel extraction kit and quality controlled on the DNA 1000 BioAnalyser 2100 chip. Samples have been multiplexed and run on Hi-seq 2000/1000 (6 samples per multiplexed lane).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
79905233
Reads aligned (%)
71.5
Duplicates removed (%)
51.4
Number of peaks
1943 (qval < 1E-05)

mm9

Number of total reads
79905233
Reads aligned (%)
71.3
Duplicates removed (%)
51.4
Number of peaks
2083 (qval < 1E-05)

Base call quality data from DBCLS SRA