Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Prdm5

Cell type

Cell type Class
Bone
Cell type
MC3T3
NA
NA

Attributes by original data submitter

Sample

source_name
MC3T3 mouse cell line
chip antibody
Prdm5
cell strain
MC3T3

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
40291630
Reads aligned (%)
97.3
Duplicates removed (%)
11.4
Number of peaks
711 (qval < 1E-05)

mm9

Number of total reads
40291630
Reads aligned (%)
97.1
Duplicates removed (%)
11.4
Number of peaks
802 (qval < 1E-05)

Base call quality data from DBCLS SRA