Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Hdac3

Cell type

Cell type Class
Blood
Cell type
Pro-B cells
NA
NA

Attributes by original data submitter

Sample

source_name
pro-B Ba/F3_ChIP_HDAC3minus
cell line
pro-B Ba/F3 cell line
condition
IL3 deprivation for 6h
chip antibody
HDAC3 (Santa Cruz, sc11417X)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were cross-linked with 1% formaldehyde for 15 minutes, lysates were clarified from sonicated nuclei, and protein-DNA complexes were isolated with antibodies. Library construction was performed as described in Ford et al, 2014. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 5-15 cycles and library fragments of ~250-450 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2000 Sequencing System.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
9409599
Reads aligned (%)
84.4
Duplicates removed (%)
49.6
Number of peaks
314 (qval < 1E-05)

mm9

Number of total reads
9409599
Reads aligned (%)
84.1
Duplicates removed (%)
49.9
Number of peaks
305 (qval < 1E-05)

Base call quality data from DBCLS SRA