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
datatype
ChipSeq
datatype description
Chromatin IP Sequencing
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
antibody antibodydescription
Goat polyclonal IgG, epitope mapping at the N-terminus of CTCF of human origin. Antibody Target: CTCF
antibody targetdescription
This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq)
antibody vendorname
Santa Cruz Biotechnology
antibody vendorid
sc-5916
treatment description
1 h with 100 nM Dexamethasone (Myers)
protocol description
one 15-cycle round of PCR (Myers)
controlid
SL474
labexpid
SL1204,SL1077
replicate
1,2
antibody targetdescription
This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq)
antibody vendorname
Santa Cruz Biotech
antibody vendorid
sc-5916
treatment
DEX_100nM
treatment description
1 h with 100 nM DEX (Myers)
protocol
PCR1x
protocol description
1-cycle of PCR (Myers)
controlid
SL474
labexpid
SL1204
replicate
1
replicate description
tier 1

Sequenced DNA Library

library_name
GSM803453: HudsonAlpha_ChipSeq_A549_CTCF_(SC-5916)_DEX_100nM_PCR1x
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
64960688
Reads aligned (%)
41.8
Duplicates removed (%)
37.2
Number of peaks
41043 (qval < 1E-05)

hg38

Number of total reads
64960688
Reads aligned (%)
42.6
Duplicates removed (%)
36.5
Number of peaks
39467 (qval < 1E-05)

Base call quality data from DBCLS SRA