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
Input_PD8_MEFs
strain
C57BL/6
cell type
mouse embryonic fibroblasts (MEFs)
passages
PD8

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
MEFs were cross-linked with 1% formaldehyde solution (Sigma, F8775) for 10 min at room temperature. Fixation was quenched by glycin at a final concentration of 0.125 M for 5 min. Next, chromatin was sheared using a Bioruptor sonicator until DNA was fragmented to 300-500 bp. The supernatant was pre-cleared with 20 μL salmon sperm DNA/Protein A sepharose beads (Sigma, GE17-5280). Subsequently, 250 μg fraction and 3 μg histone modification antibody were combined and agitated overnight at 4 °C. Antibody-protein-DNA complexes were pull-down by 30 μL Protein A sepharose beads slurry and washed. The eluted complexes were subsequently decross-linked at at 65 °C for 5 h. After phenol chloroform extraction step, ChIP DNA were provided for establishing sequencing libraries which followed illumina manufacturer's protocol and the libraries were sequenced on illumina Hiseq platform (Genewiz, Corp). Libraries were prepared for sequencing using standard Illumina protocols

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
100662665
Reads aligned (%)
92.3
Duplicates removed (%)
21.6
Number of peaks
1261 (qval < 1E-05)

mm9

Number of total reads
100662665
Reads aligned (%)
92.2
Duplicates removed (%)
21.7
Number of peaks
1160 (qval < 1E-05)

Base call quality data from DBCLS SRA