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
embryonic fibroblasts, E13.5
strain
mixed
cell type
3T9 fibroblasts
genotype
c-mycflox/flox
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 250 bp were immunoprecipitated using different antibodies. Libraries were prepared for Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection on gel and PCR with index primers.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
61243650
Reads aligned (%)
94.6
Duplicates removed (%)
15.5
Number of peaks
625 (qval < 1E-05)

mm9

Number of total reads
61243650
Reads aligned (%)
94.3
Duplicates removed (%)
15.4
Number of peaks
725 (qval < 1E-05)

Base call quality data from DBCLS SRA