Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K9ac

Cell type

Cell type Class
Liver
Cell type
Huh-7.5
Tissue
liver
Lineage
endoderm
Description
hepatocellular carcinoma, hepatocytes selected for high levels of hepatitis C replication

Attributes by original data submitter

Sample

source_name
liver
tissue
liver
cell type
Huh-7.5
chip antibody
ChIPAb Acetyl-Histone H3 (Lys-9) Purified 17-658 (Millipore)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP assays were performed using the Magna Chip G kit (Milipore) as described by the manufacturer instructions. In brief, HCV infected and non-infected Huh7/FT3-7 cells were fixed with 1% formaldehyde to cross-link proteins to DNA. After crosslinking, cells were then lysed, nuclei were purified, and chromatin was fragmented by sonication (Covaris S220) to generate DNA fragments of 200-1000 bp. Chromatin was incubated overnight with 5 µg of either specific antibodies against H3K9Ac ,H3K43Me, H3K93Me and H3K273Me Abs (Milipore) or a normal Rabbit IgG Ab/ beads only (Milipore) as a negative control for the immunoprecipitation experiments. Immunoprecipitated chromatin was then washed and eluted. After reversal of the crosslinks the DNA was purified. The purified DNA was then used for qPCR and next generation sequencing (NGS) Libraries were prepared by using NEBNext® Ultra TM DNA Library Prep Kit for Illumina® (NEB #E7370S/L)

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
11543824
Reads aligned (%)
77.2
Duplicates removed (%)
14.4
Number of peaks
16093 (qval < 1E-05)

hg19

Number of total reads
11543824
Reads aligned (%)
76.9
Duplicates removed (%)
14.7
Number of peaks
16100 (qval < 1E-05)

Base call quality data from DBCLS SRA