Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

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
cell type
liver hepatocellular carcinoma
provider/strain
ATCC, HB-8065
chip antibody
CTCF (Abcam, ab70303)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
RELACS: nuclei have been extracted, permeabilized and barcoded following RELACS protocol. Nuclei labeled with distinct barcodes have been pooled and lysed to complete chromatin preparation. Traditional ChIP-seq: after nuclei extraction chromatin has been fragmented by sonication. Immunoprecipitation has been performed using the antibody of interest. RELACS libraries: as described in the paper, using A-tailing strategy and ligation of adapters containing nuclear barcodes. After ChIP and DNA purification library preparation has been completed by PCR amplification using NEB workflow (NEBNext Ultra II DNA library preparation kit (E7645L, NEB)). Traditional ChIP-seq libraries: NEBNext Ultra II DNA library preparation kit (E7645L, NEB)

Sequencing Platform

instrument_model
Illumina HiSeq 3000

hg19

Number of total reads
31022170
Reads aligned (%)
69.2
Duplicates removed (%)
50.3
Number of peaks
6533 (qval < 1E-05)

hg38

Number of total reads
31022170
Reads aligned (%)
70.2
Duplicates removed (%)
50.1
Number of peaks
6661 (qval < 1E-05)

Base call quality data from DBCLS SRA