Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Breast
Cell type
MCF-7
Primary Tissue
Breast
Site of Extraction
Pleura
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
MCF-7
biomaterial_provider
ATCC
datatype
ChipSeq
datatype description
Chromatin IP Sequencing
cell description
mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis
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
wgEncodeEH000589
labversion
baseAlignCounts.pl v 1,fseq v 1.84, iff_MCF7,p-value cutoff: 0.05
replicate
1,2
treatment
estrogen
treatment description
45 min with 100 nM Estradiol (Crawford)
antibody
CTCF
antibody antibodydescription
rabbit polyclonal
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
MCF-7/Input
labversion
align_on_cluster_bwa.pl v 1
replicate
1
replicate description
tier 1

Sequenced DNA Library

library_name
GSM822309: UT-A_ChipSeq_MCF-7_estrogen_CTCF
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
120472384
Reads aligned (%)
80.8
Duplicates removed (%)
17.7
Number of peaks
86016 (qval < 1E-05)

hg38

Number of total reads
120472384
Reads aligned (%)
82.6
Duplicates removed (%)
16.5
Number of peaks
84533 (qval < 1E-05)

Base call quality data from DBCLS SRA