Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Breast
Cell type
HMEC
Primary Tissue
Breast
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
HMEC
biomaterial_provider
Lonza
lab
Broad
lab description
Bernstein - Broad Institute
datatype
ChipSeq
datatype description
Chromatin IP Sequencing
cell organism
human
cell description
mammary epithelial cells
cell karyotype
normal
cell lineage
ectoderm
cell sex
U
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
wgEncodeEH000093
replicate
1,2
softwareversion
ScriptureVPaperR3

Sequenced DNA Library

library_name
GSM733724: Bernstein_HMEC_CTCF
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg19

Number of total reads
29706628
Reads aligned (%)
61.2
Duplicates removed (%)
14.9
Number of peaks
36749 (qval < 1E-05)

hg38

Number of total reads
29706628
Reads aligned (%)
62.6
Duplicates removed (%)
13.9
Number of peaks
36341 (qval < 1E-05)

Base call quality data from DBCLS SRA