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

GEO Accession
GSM1010903
antibody antibodydescription
Goat polyclonal IgG, epitope mapping at the N-terminus of CTCF of human origin. Antibody Target: CTCF
antibody targetdescription
This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq)
antibody vendorid
sc-5916
antibody vendorname
Santa Cruz Biotechnology
antibody
CTCF_(SC-5916)
cell description
colorectal carcinoma (PMID: 7214343)
cell karyotype
cancer
cell lineage
endoderm
cell organism
human
cell sex
M
cell
HCT-116
controlid
SL12247,SL12246
datatype description
Chromatin IP Sequencing
datatype
ChipSeq
lab description
Myers - Hudson Alpha Institute for Biotechnology
lab
HudsonAlpha
labexpid
SL13074,SL12242
protocol description
Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)
protocol
v042211.1
replicate
1,2
softwareversion
MACS
treatment description
No special treatment or protocol applies
treatment
None

Sequenced DNA Library

library_name
GSM1010903: HudsonAlpha_ChipSeq_HCT-116_CTCF_(SC-5916)_v042211.1
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeHaibTfbs

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
45909877
Reads aligned (%)
46.7
Duplicates removed (%)
23.4
Number of peaks
41906 (qval < 1E-05)

hg38

Number of total reads
45909877
Reads aligned (%)
47.2
Duplicates removed (%)
22.8
Number of peaks
42031 (qval < 1E-05)

Base call quality data from DBCLS SRA