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 fibroblasts (MEFs)
strain
C57BL/6
cell type
mouse embryonic fibroblasts (MEFs)
treatment
Untreated control on day 6
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed in 1% formaldehyde for 10 min, quenched with glycine and washed 2 times with PBS. Cells were then resuspended in lysis buffer and sonicated to shear the chromatin to an average length of 600 bp. Supernatants were precleared with Protein-A/G Dynabeads (Invitrogen) and 10% input was collected. Immunoprecipitations were performed with antibodies to H3K4me3 and H3K27me3 (Millipore). DNA-protein complexes were pulled down using Protein-A/G Dynabeads (Invitrogen) washed. DNA was recovered by overnight incubation at 65°C to reverse crosslinks and purified using QIAquick PCR purification columns (QIAGEN). Libraries were prepared from ChIP DNA experiments with the TruSeq® DNA LT/HT Sample Prep Kit (Illumina) following manufacturer’s instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
24915374
Reads aligned (%)
98.2
Duplicates removed (%)
20.3
Number of peaks
407 (qval < 1E-05)

mm9

Number of total reads
24915374
Reads aligned (%)
97.9
Duplicates removed (%)
20.3
Number of peaks
451 (qval < 1E-05)

Base call quality data from DBCLS SRA