SRX199879
GSM1022651: UW ChipSeq HCT-116 CTCFRep2

Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Digestive tract
Cell type
HCT 116
Primary Tissue
Colon
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
HCT-116
biomaterial_provider
ATCC
lab
UW
lab description
Stamatoyannopoulous - University of Washington
datatype
ChipSeq
datatype description
Chromatin IP Sequencing
cell
HCT-116
cell organism
human
cell description
colorectal carcinoma (PMID: 7214343)
cell karyotype
cancer
cell lineage
endoderm
cell sex
M
antibody
CTCF
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
wgEncodeEH000950
labexpid
DS18568
labversion
Hotspot-v5.2,lmax-v1.0,WindowDensity-bin20-win+/-75
replicate
2

Sequenced DNA Library

library_name
GSM1022651: UW_ChipSeq_HCT-116_CTCFRep2
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP

Sequencing Platform

instrument_model
Illumina Genome Analyzer

Where can I get the processing logs?

Read processing pipeline log

hg19

Number of total reads
18502646
Reads aligned (%)
85.0
Duplicates removed (%)
6.7
Number of peaks
34195 (qval < 1E-05)

hg38

Number of total reads
18502646
Reads aligned (%)
85.7
Duplicates removed (%)
5.6
Number of peaks
34226 (qval < 1E-05)

Base call quality data from DBCLS SRA