SRX199893
GSM1022665: UW ChipSeq HRPEpiC CTCFRep2

Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Neural
Cell type
HRPEpiC
Tissue
epithelium
Lineage
ectoderm
Description
retinal pigment epithelial cells

Attributes by original data submitter

Sample

source_name
HRPEpiC
biomaterial_provider
ScienCell
lab
UW
lab description
Stamatoyannopoulous - University of Washington
datatype
ChipSeq
datatype description
Chromatin IP Sequencing
cell
HRPEpiC
cell organism
human
cell description
retinal pigment epithelial cells
cell karyotype
normal
cell lineage
ectoderm
cell sex
U
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
wgEncodeEH000962
labexpid
DS18570
labversion
Hotspot-v5.2,lmax-v1.0,WindowDensity-bin20-win+/-75
replicate
2

Sequenced DNA Library

library_name
GSM1022665: UW_ChipSeq_HRPEpiC_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

hg38

Number of total reads
19765003
Reads aligned (%)
89.7
Duplicates removed (%)
8.7
Number of peaks
40011 (qval < 1E-05)

hg19

Number of total reads
19765003
Reads aligned (%)
89.1
Duplicates removed (%)
9.7
Number of peaks
39937 (qval < 1E-05)

Base call quality data from DBCLS SRA