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
strain background
C57bl/6
cell type
Murine embryonic fibroblasts (MEFs)
passages
15-18
age
E12.5
genotype
wild type
treatment
none (untreated)
chip antibody
none (input)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with 1% formaldehyde for 10 min and nuclei were pelleted after sequential wash and resuspended in sonication buffer (0.1% SDS, 1mM EDTA, 10mM Tris (pH8.1)) and sonicated in a Covaris to shear the chromatin into 200-300 bp fragments and 10% Chromatin was decrosslinked and used as Input DNA. ChIP-seq libraries were constructed using a NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs). DNA sequence was performed by NextSeq system (Illumina).

Sequencing Platform

instrument_model
NextSeq 550

mm10

Number of total reads
11174572
Reads aligned (%)
88.1
Duplicates removed (%)
45.9
Number of peaks
86 (qval < 1E-05)

mm9

Number of total reads
11174572
Reads aligned (%)
87.9
Duplicates removed (%)
46.2
Number of peaks
210 (qval < 1E-05)

Base call quality data from DBCLS SRA