Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

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

Attributes by original data submitter

Sample

source_name
Isogenic Hep3B cells
tissue
liver, hepatoma
passages
up to 10
chip-antibody
none
cell line
Hep3B
transfection
wildtype HIF-beta overexpression plasmid

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The cells were prepared in triplicate and pooled for ChIP. Cells were crosslinked with 1 % (v/v) formaldehyde (10 min. at 22 degrees Celsius) and washed twice with PBS, after which they were collected in a cold room in Farham Lysis Buffer. After centrifugation, the cell pellets were resuspended in RIPA buffer. Chromatin was sonicated to an average fragment size of 200-400 bp using Bioruptor UCD-300-TO (Diagenode). The chromatin was immunoprecipitated for ChIP-seq with V5-tag antibody (R960-25, Invitrogen). ChIP-seq samples were processed according to Illumina's instructions and DNA libraries were sequenced using Illumina HiSeq System (Illumina) in the EMBL Gene Core Facility (Heidelberg, Germany).

Sequencing Platform

instrument_model
Illumina HiSeq 1000

hg38

Number of total reads
127293455
Reads aligned (%)
74.6
Duplicates removed (%)
33.9
Number of peaks
3328 (qval < 1E-05)

hg19

Number of total reads
127293455
Reads aligned (%)
73.7
Duplicates removed (%)
35.5
Number of peaks
2411 (qval < 1E-05)

Base call quality data from DBCLS SRA