Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Breast
Cell type
T-47D
Primary Tissue
Breast
Tissue Diagnosis
Adenocarcinoma Ductal

Attributes by original data submitter

Sample

source_name
T-47D
biomaterial_provider
ATCC
datatype
ChipSeq
datatype description
Chromatin IP Sequencing
cell description
epithelial cell line derived from a mammary ductal carcinoma.
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 vendorname
Santa Cruz Biotechnology
antibody vendorid
sc-5916
treatment description
1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers)
controlid
SL1881
labexpid
SL2634,SL3014
replicate
1,2
softwareversion
MACS
antibody vendorname
Santa Cruz Biotech
antibody vendorid
sc-5916
treatment
DMSO_0.02pct
treatment description
1 h with 0.02% DMSO (Myers)
protocol
v041610.2
protocol description
2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers)
controlid
SL1881
labexpid
SL2634
replicate
1
replicate description
tier 1

Sequenced DNA Library

library_name
GSM803348: HudsonAlpha_ChipSeq_T-47D_CTCF_(SC-5916)_DMSO_0.02pct_v041610.2
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
69184006
Reads aligned (%)
69.4
Duplicates removed (%)
17.5
Number of peaks
29787 (qval < 1E-05)

hg38

Number of total reads
69184006
Reads aligned (%)
71.6
Duplicates removed (%)
15.7
Number of peaks
30019 (qval < 1E-05)

Base call quality data from DBCLS SRA