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
MEF, Input
cell type
mouse embryonic fibroblasts

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
PARP-1 ChIP-seq: Following mock ADP-ribosylation in intact nuclei from MEFs, the nuclei were crosslinked with 0.5% formaldehyde and clicked to biotin. Nuclei were sonicated in a water bath sonicator to a DNA fragment size distribution of 200 to 500 bp and chromatin was used for chromatin immunoprecipitation. Click-ChIP-seq: Following 8-Bu(3-yne)T-ADP-ribosylation in intact nuclei from MEFs, the nuclei were crosslinked with 0.5% formaldehyde and clicked to biotin. Nuclei were sonicated in a water bath sonicator to a DNA fragment size distribution of 200 to 500 bp and bound to streptavidin-conjugated magnetic beads. Following extensive washing, the beads were collected in a magnetic field and de-crosslinked overnight at 65°C. DNA was to be sequenced was recovered by magnetic separation from the beads and purified by PCIAA extraction and ethanol precipitation After purification, 50 ng of ChIP’d DNA for each condition was used to generate libraries for sequencing, as previously described {Robertson, 2007 #41}, with some modifications. Briefly, the DNA was end-repaired and a single “A”-base overhang was added using the Klenow fragment of E. coli DNA polymerase. The A-modified DNA was ligated with Ilumina sequencing adaptors using the Illumina TruSeq DNA Sample Prep Kit. The ligated DNA (250 ± 25 bp) was size-selected by agarose gel electrophoresis and extraction, amplified by PCR, and purified using AmPure beads (Beckman Coulter). The final libraries were subjected to QC (size, purity, adapter contamination) and sequenced using an Illumina HiSeq 2000 per the manufacturer’s instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
15035584
Reads aligned (%)
96.3
Duplicates removed (%)
29.4
Number of peaks
319 (qval < 1E-05)

mm9

Number of total reads
15035584
Reads aligned (%)
96.1
Duplicates removed (%)
29.5
Number of peaks
333 (qval < 1E-05)

Base call quality data from DBCLS SRA