Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Ctcf

Cell type

Cell type Class
Blood
Cell type
MEL
Tissue
Blood
Lineage
cellLine
Description
Leukemia (K562 analog)

Attributes by original data submitter

Sample

source_name
MEL
biomaterial_provider
Weissman lab
lab
Stanford-m
lab description
Snyder - Stanford University
datatype
ChipSeq
datatype description
Chromatin IP Sequencing
cell
MEL
cell organism
mouse
cell description
Leukemia (K562 analog)
cell sex
M
antibody
CTCF_(SC-15914)
antibody antibodydescription
Goat polyclonal, epitope mapping near the C-terminus of CTCF of human origin. Antibody Target: CTCF
antibody targetdescription
Transcriptional regulator with 11 highly conserved zinc finger domains. Depending on context, can bind a histone acetyltransferase (HAT)-containing complex and function as transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as transcriptional repressor. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation. Can dimerize, mediating long-range chromatin looping. When bound to chromatin, provides an anchor point for nucleosomes positioning. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites.
antibody vendorname
Santa Cruz Biotech
antibody vendorid
sc-15914
treatment
DMSO_2.0pct
treatment description
5 d with 2% Dimethyl sufloxide (DMSO) (Weissman)
control
std
control description
Standard input signal for most experiments.
age
immortalized
age description
Immortal cells
control
std
control description
Standard input signal for most experiments.
controlid
wgEncodeEM002791
labversion
PeakSeq1.0
strain
Unknown
strain description
Unknown strain origin

Sequenced DNA Library

library_name
GSM1003784: Stanford_ChipSeq_MEL_CTCF_(SC-15914)_DMSO_2.0pct_std
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP

Sequencing Platform

instrument_model
Illumina Genome Analyzer

mm10

Number of total reads
52789682
Reads aligned (%)
96.6
Duplicates removed (%)
28.3
Number of peaks
58438 (qval < 1E-05)

mm9

Number of total reads
52789682
Reads aligned (%)
96.4
Duplicates removed (%)
28.3
Number of peaks
58394 (qval < 1E-05)

Base call quality data from DBCLS SRA