Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Epitope tags

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
Murine embryonic fibroblasts (MEFs)
genotype/variation
WT
antibody
Anti-HA tag antibody - ChIP Grade (ab9110)
strain
C57BL/6
time point
16h
agent
IFN-Beta

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. 50ug of chromatin was immunoprecipitated using anti-H3K36me3 antibody (Abcam), anti-HA antibody (Abcam) and anti-ZMYND11 antibody (Millipore). Immunoprecipitated chromatin was de-crosslinked and DNA purified. 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
21085025
Reads aligned (%)
97.5
Duplicates removed (%)
10.4
Number of peaks
755 (qval < 1E-05)

mm9

Number of total reads
21085025
Reads aligned (%)
97.5
Duplicates removed (%)
10.7
Number of peaks
733 (qval < 1E-05)

Base call quality data from DBCLS SRA