Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K9ac

Cell type

Cell type Class
Liver
Cell type
Hep 3B
Primary Tissue
Liver
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
Hep3B cells_ChIP
antibody
anti-H3K9ac, Active Motif, 39917
cell line
Hep3B
shRNA
Luc

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-IT High Sensitivity kit (Active motif) according to the manufacturer’s manual Prepared using DNA Library preparation kit (KAPA, KK8232), as per the manufacturer’s protocol. In brief, DNA was fragmented to a median size of 150bp by sonication. Fragmented DNA ends were polished and 5′-phosphorylated. After addition of 3′-A to the ends, indexed Y-adapters were ligated and the samples were PCR amplified.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
19733455
Reads aligned (%)
98.2
Duplicates removed (%)
7.8
Number of peaks
18932 (qval < 1E-05)

hg19

Number of total reads
19733455
Reads aligned (%)
97.9
Duplicates removed (%)
7.8
Number of peaks
18871 (qval < 1E-05)

Base call quality data from DBCLS SRA