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
embryonic fibroblast chromatin
strain
C57BL/6
passage
Proliferating passage 4
cell type
E13.5 MEFs
antibody
none
genotype/variation
wild type

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was conducted according to protocols adapted from Cecchini et al., 2014. Briefly, asynchronously cycling cells were fixed in either 1% formaldehyde in 1X PBS or in 2mM ethylene glycol bis(succinimidyl succinate (EGS) in 1X PBS followed by 1% formaldehyde. Both fixing reactions were neutralized with 0.125M glycine. Cross-linked chromatin was sonicated so most chromatin was ≤400 bp. Sheared chromatin was then normalized between experimental groups and pre-cleared with protein G Dynabeads and IgG. Pre-cleared chromatin was then incubated with protein G Dynabeads and ChIP antibodies to immunoprecipitate proteins. Libraries were constructed according to the NEBNext Ultra II DNA library prep kit.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
112463362
Reads aligned (%)
95.7
Duplicates removed (%)
28.2
Number of peaks
518 (qval < 1E-05)

mm9

Number of total reads
112463362
Reads aligned (%)
95.4
Duplicates removed (%)
28.0
Number of peaks
612 (qval < 1E-05)

Base call quality data from DBCLS SRA