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
MEF
antibodies
none
genotype/variation
WT

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were harvested, washed with PBS 1X, fixed in 2mL per 1x107 cells (10 min in 1% formaldehyde), quenched with 250mM Tris HCL pH 8 in 10mL (at 125 mM final), washed three times with PBS 1X, and pelleted. Each pellet containing 1x107 cells was lysed, resuspended in 1 mL of sonication buffer on ice (10 mM Tris at pH 8, 1 mM EDTA, 0.2% SDS, and protease inhibitors), transferred to TC 12x12 tubes (Covaris), and sonicated (Covaris settings: 20 min, 5% duty cycle, 140W, 200 cycles). Sonication was assessed by reverse cross-linking (65oC, RNAse A at 1µg/µL, overnight), followed by DNA extraction. Fragment size (between 200-400bp) was checked on a Bioanalyzer (Agilent 2100). Immunoprecipitations were performed with chromatin from 4x107, with Dynabeads (Protein G, ThermoFisher) in IP buffer (10 mM Tris at pH 8, 1 mM EDTA, 0.1% SDS, 150 mM NaCl, 10% Triton X-100, and protease inhibitors) overnight. Chromatin was reversed cross-linked (65oC, Proteinase K at 400ng/µL, overnight) and DNA was extracted. Illuminal ChIP-seq protocol

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
38309674
Reads aligned (%)
97.9
Duplicates removed (%)
18.1
Number of peaks
315 (qval < 1E-05)

mm9

Number of total reads
38309674
Reads aligned (%)
97.7
Duplicates removed (%)
18.1
Number of peaks
305 (qval < 1E-05)

Base call quality data from DBCLS SRA