Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Lung
Cell type
A549
Primary Tissue
Lung
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
A549
biomaterial_provider
ATCC
lab
Stanford
lab description
Snyder - Stanford University
datatype
ChipSeq
datatype description
Chromatin IP Sequencing
cell
A549
cell organism
human
cell description
epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis
cell karyotype
cancer
cell lineage
endoderm
cell sex
M
treatment
None
treatment description
No special treatment or protocol applies
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
control
IgG-rab
control description
Input signal from Normal Rabbit IgG ChIP-seq.
control
IgG-rab
control description
Input signal from Normal Rabbit IgG ChIP-seq.
controlid
wgEncodeEH002819

Sequenced DNA Library

library_name
GSM1003606: Stanford_ChipSeq_A549_CTCF_(SC-15914)_IgG-rab
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
61093175
Reads aligned (%)
82.8
Duplicates removed (%)
14.5
Number of peaks
45185 (qval < 1E-05)

hg38

Number of total reads
61093175
Reads aligned (%)
84.7
Duplicates removed (%)
13.2
Number of peaks
45423 (qval < 1E-05)

Base call quality data from DBCLS SRA