Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Ctcf

Cell type

Cell type Class
Blood
Cell type
CH12
Tissue
Blood
Lineage
cellLine
Description
B-cell lymphoma (GM12878 analog)

Attributes by original data submitter

Sample

source_name
CH12
biomaterial_provider
Weissman lab
lab
Stanford-m
lab description
Snyder - Stanford University
datatype
ChipSeq
datatype description
Chromatin IP Sequencing
cell
CH12
cell organism
mouse
cell description
B-cell lymphoma (GM12878 analog)
cell sex
F
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
None
treatment description
No special treatment or protocol applies
control
IgG-rab
control description
Input signal from Normal Rabbit IgG ChIP-seq.
age
immortalized
age description
Immortal cells
control
IgG-rab
control description
Input signal from Normal Rabbit IgG ChIP-seq.
controlid
CH12/None/Input/IgG-rab
replicate
1
strain
B10.H-2aH-4bp/Wts
strain description
Derived by inbreeding from selected F2 progeny of B10.A X B10.129

Sequenced DNA Library

library_name
GSM912909: Stanford_ChipSeq_CH12_CTCF_(SC-15914)_IgG-rab
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

mm10

Number of total reads
49138566
Reads aligned (%)
98.3
Duplicates removed (%)
24.9
Number of peaks
75793 (qval < 1E-05)

mm9

Number of total reads
49138566
Reads aligned (%)
98.1
Duplicates removed (%)
25.0
Number of peaks
75753 (qval < 1E-05)

Base call quality data from DBCLS SRA