Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
PBX3

Cell type

Cell type Class
Liver
Cell type
SMMC-7721
NA
NA

Attributes by original data submitter

Sample

source_name
SMMC-7721 overexpressing PBX3
cell type
liver cancer
cell line
SMMC-7721
chip antibody
PBX3 (Abcam ab109173, lot/batch number GR-46727-7)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cell lysates were clarified from sonicated nuclei and PBX3-DNA complexes were isolated with PBX3 antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). 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 15 cycles and library fragments of ~250 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 Genome Analyzer following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
30826910
Reads aligned (%)
170.7
Duplicates removed (%)
1.2
Number of peaks
19007 (qval < 1E-05)

hg38

Number of total reads
30826910
Reads aligned (%)
171.8
Duplicates removed (%)
1.0
Number of peaks
19463 (qval < 1E-05)

Base call quality data from DBCLS SRA