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
Transformed mouse embryonic fibroblast line
cell type
transformed embryonic fibroblast cell line
cell line
MEF
Sex
female
passage
passage 14
strain
F1: 129S1 x CastEiJ
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed as described in Lee et al. Nat Protoc. 2006;1(2):729-48. Paired-end Solexa ChIP libraries were prepared as described in Illumina ChIP sequencing manual with minor modifications and using NEB Next DNA sample prep reagent Set 1 (E6000S) (NEB). Input DNA was used as a control and for normalization. Modifications to the Illumina protocol were: 1- 30 ng of ChIP products were used as template, 2- paired-end adapters were ligated to end-repaired and A-tailed DNA using T4 DNA ligase (NEB) for 2 hours at 16°C, and 2- Phusion polymerase in GC buffer (Finzyme) was used instead of Phusion polymerase in HF buffer. DNA products were purified with QIAquick spin columns (Qiagen). Concentration, size distribution (400-500bp), and purity of libraries were assessed on DNA1000 Bioanalyzer chip (Agilent). Genome Analyzer II (Illumina) was used to perform 2x36 cycles of paired end sequencing.

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

mm10

Number of total reads
28700110
Reads aligned (%)
96.8
Duplicates removed (%)
29.7
Number of peaks
299 (qval < 1E-05)

mm9

Number of total reads
28700110
Reads aligned (%)
96.6
Duplicates removed (%)
30.9
Number of peaks
309 (qval < 1E-05)

Base call quality data from DBCLS SRA