Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Pml

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, wild-type
strain
C57BL/6
cell type
MEF
genotype/variation
wild-type
passages
Passage 10-15
state/treatment
Proliferating, untreated
chip antibody
anti-PML (Millipore, catalog# 05-718, lot# 2684855)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq: Cells (10e7 cells/ChIP) were harvested and fixed with 1% formaldehyde for 10 min before quenching with 125 mM glycine. Cells were lysed for 30 min at 4C on a rotator in RIPA buffer (140 mM NaCl, 10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% deoxycholate, 1 mM PMSF, protease inhibitor cocktail) adjusted to 1% SDS, and sonicated 3 times 15 min in a Bioruptor® (Diagenode). After sedimentation at 10,000 g for 10 min, the supernatant was collected and diluted 10x in RIPA buffer without SDS to constitute input chromatin. Chromatin was incubated overnight at 4oC on a rotator with antibodies coupled to magnetic Dynabeads Protein G. ChIP samples were washed 3 times in ice-cold RIPA buffer. Crosslinks were reversed and DNA eluted for 6 h at 37C in 50 mM NaCl, 20 mM Tris-HCl pH 7.5, 5 mM EDTA, 1% SDS, 0.5 µg/ml RNase A, and 2 µg/ml Proteinase K added twice. DNA was purified and dissolved in H2O.For RNA-seq: 10e6 cells were cultured. For RNA-seq: Total RNA was isolated using the Ambion TRIzol® Reagent RNA extraction kit (Life Technologies), quality checked using a BioAnalyzer 2100 and processed for library preparation. Sequencing library was prepared according to the Illumina protocol, and sequenced on an Illumina HiSeq2500 at the Norwegian Sequencing Center.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
49895811
Reads aligned (%)
97.5
Duplicates removed (%)
24.5
Number of peaks
527 (qval < 1E-05)

mm9

Number of total reads
49895811
Reads aligned (%)
97.2
Duplicates removed (%)
24.5
Number of peaks
589 (qval < 1E-05)

Base call quality data from DBCLS SRA