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 fibroblast
strain
C57BL/6
cell type
MEF
genotype/variation
p53/Mdm2 double knock out
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immunoprecipitation (ChIP) was done according to the protocol published by Denissov and colleagues (Denissov et al., 2007). Briefly, cells were fixed in 1.1 % of PFA for 20 min, quenched with 0.125M glycine and lysed in 1% Triton X-100, 0,15 M NaCl, 1 mM EDTA, 0.3 % SDS and additional protease inhibitor. The cell lysate was sonicated as desired and used for antibody (2µg) and Protein A/G PLUS-Agarose incubation (Santa Cruz) over night. Bead interaction was released via 20 min rotation incubation in 1% SDS and 0.1 M NaHCO3 and DNA-protein crosslink was reversed via the addition of 0.2 M NaCl and shaking at 65 °C. DNA was purified by the MinElute PCR Purification Kit (Quiagen) and either used for targeted PCR (see primer table) or sequencing. For sequencing, DNA was sonicated again to reach fragment sizes less than 200 bp, and libraries were prepared with the NEBNext® Ultra™ DNA Library Prep Kit for Illumina (NEB). The size range of final libraries was determined with the Bioanalyzer 2100 from Agilent (290-310 bp). Libraries were amplified and sequenced by using cBot.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
22787512
Reads aligned (%)
89.3
Duplicates removed (%)
15.8
Number of peaks
451 (qval < 1E-05)

mm9

Number of total reads
22787512
Reads aligned (%)
89.1
Duplicates removed (%)
15.8
Number of peaks
471 (qval < 1E-05)

Base call quality data from DBCLS SRA