Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

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 embryo fibroblasts (MEF)
cell type
mouse embryonic fibroblast
strain
C57BL/6
genotype/variation
Prdm5 ab1 lacz/lacz

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed in 1% formaldehyde for 10 min and cross-linking was quenched by addition of 0.125 M glycine. Cells were then harvested in ChIP buffer and sonicated with a Bioruptor UCD-300 to obtain fragments around 250 bp in size. Plolyclonal custom-made PRDM5 antibodies were used for Immunoprecipitation. Precipitated DNA was recovered by purification with a QIAquick PCR purification kit (Qiagen) Libraries for sequencing were obtained using a ChIP-Seq DNA sample prep kit (Illumina) according to the manufacturer's reccomendations

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

mm10

Number of total reads
38507199
Reads aligned (%)
97.8
Duplicates removed (%)
36.9
Number of peaks
716 (qval < 1E-05)

mm9

Number of total reads
38507199
Reads aligned (%)
97.6
Duplicates removed (%)
36.9
Number of peaks
768 (qval < 1E-05)

Base call quality data from DBCLS SRA