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
cell type
Mouse embryonic fibroblasts
transgenes
flagMyod1 + rtTA
days post transgene induction
2 days
chip antibody
input

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Approximately 30 million cells were used for each experiment. Chromatin was sheared using the Covaris sonicator until DNA was fragmented to 200-500bp. For each reaction 1% of sonicated chromatin was kept as input DNA. 5ug of H3K27ac (Abcam ab4729) antibody was added to remaining chromatin and incubated overnight at 4°C. 100uL of protein G Dynabeads (Thermo Fisher; 10003D) were added to each ChIP reaction and incubated for at least 4h at 4°C. Beads were then washed, eluted and reverse cross-linked overnight. After reverse cross-linking, isolated DNA was RNase treated for 30min at 37°C, purified using QIAquick PCR purification columns (Qiagen) and eluted in DEPC water. ChIP-seq libraries were prepared using the NEBNext library prep kit (NEB; E6240) following the supplier's protocols with slight modifications. Adaptor ligation was performed using regular T4 ligase and ligase buffer. Size selection (200-500bp) was performing after adaptor ligation and PCR enrichment using 2% low-melt agarose gel (Lonza; 50080), and DNA was purified using the QiaQuick gel extraction columns from Qiagen.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
10664200
Reads aligned (%)
97.3
Duplicates removed (%)
63.5
Number of peaks
343 (qval < 1E-05)

mm9

Number of total reads
10664200
Reads aligned (%)
97.2
Duplicates removed (%)
63.8
Number of peaks
335 (qval < 1E-05)

Base call quality data from DBCLS SRA