Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SPI1

Cell type

Cell type Class
Liver
Cell type
Hep G2
Primary Tissue
Liver
Tissue Diagnosis
Carcinoma Hepatocellular

Attributes by original data submitter

Sample

source_name
HepG2_PU.1mRNA_FA_FLAG-ChIP
cell line
HEP-G2
cell type
hepatocellular carcinoma cell line
chip antibody
FLAG M2 (Sigma, #F3165)
transfected ivt mrna
PU.1
fixation method
FA
preperation batch
2

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were preparated from sonicated nuclei and protein/histone-DNA complexes were isolated with antibody. ChIP construction was essentially done as described (Pham et al. 2012) with slight modifications for BRG1, ETS1 and FLI1 samples, which were prepared using dual crosslinking with 2 mM DSG (Thermo Fisher Scientific) and 1% formaldehyde. Libraries for sequencing were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina according to manufacturer's instructions.

Sequencing Platform

instrument_model
NextSeq 550

hg38

Number of total reads
22197902
Reads aligned (%)
98.9
Duplicates removed (%)
4.7
Number of peaks
71165 (qval < 1E-05)

hg19

Number of total reads
22197902
Reads aligned (%)
98.3
Duplicates removed (%)
5.2
Number of peaks
71150 (qval < 1E-05)

Base call quality data from DBCLS SRA