Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

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 cells
cell line
HepG2
chip ab
None

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
HepG2 and S2 cells were fixed in 1% methanol-free formaldehyde (Thermo Scientific, 28906) in D-MEM (for HepG2 cells) or Express Five SFM (for S2 cells) for 15 min at room temperature under gentle shaking. Formaldehyde was quenched for 5 min by adding 125 mM glycine final concentration. Cells were rinsed twice with ice-cold PBS, harvested by scraping (HepG2) and pelleted (300 g, 10 min, 4 °C). Cells were processed according to RELACS / AutoRELACS protocols Libraries were prepared according to Illumina's instructions using NebNext Ultra II kit. After Illumina adapter ligation, library was PCR amplified. Fragments were size-selected to eliminate adapter dimers contamination using AMPure XP beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on NovaSeq 6000 machine, following manufacturer's protocol. High-throughput RELACS ChIP-seq and automated high-throughput AutoRELACS ChIP-seq

Sequencing Platform

instrument_model
Illumina NovaSeq 6000

hg38

Number of total reads
31519857
Reads aligned (%)
96.8
Duplicates removed (%)
40.6
Number of peaks
0 (qval < 1E-05)

hg19

Number of total reads
31519857
Reads aligned (%)
96.4
Duplicates removed (%)
40.8
Number of peaks
1 (qval < 1E-05)

Base call quality data from DBCLS SRA