SRX067396
GSM733645: Bernstein HepG2 CTCF

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
lab
Broad
lab description
Bernstein - Broad Institute
datatype
ChipSeq
datatype description
Chromatin IP Sequencing
cell organism
human
cell description
hepatocellular carcinoma
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
treatment
None
treatment description
No special treatment or protocol applies
control
std
control description
Standard input signal for most experiments.
controlid
wgEncodeEH000084
replicate
1,2
softwareversion
ScriptureVPaperR3

Sequenced DNA Library

library_name
GSM733645: Bernstein_HepG2_CTCF
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

Where can I get the processing logs?

Read processing pipeline log

hg38

Number of total reads
23569488
Reads aligned (%)
69.5
Duplicates removed (%)
7.2
Number of peaks
48413 (qval < 1E-05)

hg19

Number of total reads
23569488
Reads aligned (%)
68.9
Duplicates removed (%)
8.0
Number of peaks
48278 (qval < 1E-05)

Base call quality data from DBCLS SRA