Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
FOXA2

Cell type

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

Attributes by original data submitter

Sample

GEO Accession
GSM1010724
antibody antibodydescription
Goat polyclonal IgG, epitope mapping at the N-terminus of FOXA2 of human origin. Antibody Target: FOXA2
antibody targetdescription
The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II. (provided by RefSeq)
antibody vendorid
sc-6554
antibody vendorname
Santa Cruz Biotechnology
antibody
FOXA2_(SC-6554)
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 organism
human
cell sex
M
cell
A549
controlid
SL3077,SL3253,SL3978
datatype description
Chromatin IP Sequencing
datatype
ChipSeq
lab description
Myers - Hudson Alpha Institute for Biotechnology
lab
HudsonAlpha
labexpid
SL3077,SL3253
protocol description
2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers)
protocol
v041610.2
replicate
1,2
softwareversion
MACS
treatment description
1 h with 0.02% Ethanol (Myers)
treatment
EtOH_0.02pct

Sequenced DNA Library

library_name
GSM1010724: HudsonAlpha_ChipSeq_A549_FOXA2_(SC-6554)_EtOH_0.02pct_v041610.2
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeHaibTfbs

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
76714945
Reads aligned (%)
35.6
Duplicates removed (%)
48.0
Number of peaks
46895 (qval < 1E-05)

hg38

Number of total reads
76714945
Reads aligned (%)
36.2
Duplicates removed (%)
47.3
Number of peaks
45064 (qval < 1E-05)

Base call quality data from DBCLS SRA