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
biomaterial_provider
ATCC
datatype
ChipSeq
datatype description
Chromatin IP Sequencing
cell description
hepatocellular carcinoma
treatment
None
treatment description
No special treatment or protocol applies
antibody antibodydescription
Rabbit polyclonal. Antibody Target: CTCF
antibody targetdescription
CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
antibody vendorname
Millipore
antibody vendorid
07-729
controlid
wgEncodeEH000538
labversion
baseAlignCounts.pl v 1,fseq v 1.84, iff_HepG2,p-value cutoff: 0.05,1% ENCODE array platform validation tests
replicate
1,2
antibody targetdescription
CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
antibody vendorname
Millipore
antibody vendorid
07-729
controlid
HepG2/Input
labversion
align_on_cluster_bwa.pl v 1
replicate
1
replicate description
tier 1

Sequenced DNA Library

library_name
GSM822287: UT-A_ChipSeq_HepG2_CTCF
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
14659217
Reads aligned (%)
80.8
Duplicates removed (%)
12.2
Number of peaks
55019 (qval < 1E-05)

hg38

Number of total reads
14659217
Reads aligned (%)
82.2
Duplicates removed (%)
11.4
Number of peaks
55082 (qval < 1E-05)

Base call quality data from DBCLS SRA