Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
FOXA1

Cell type

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

Attributes by original data submitter

Sample

GEO Accession
GSM1010725
antibody antibodydescription
Mouse monoclonal IgG, raised against recombinant HNF-3a of human origin. Antibody Target: FOXA1
antibody targetdescription
This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver. (provided by RefSeq)
antibody vendorid
sc-101058
antibody vendorname
Santa Cruz Biotechnology
antibody
FOXA1_(SC-101058)
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
SL3251,SL2665
datatype description
Chromatin IP Sequencing
datatype
ChipSeq
lab description
Myers - Hudson Alpha Institute for Biotechnology
lab
HudsonAlpha
labexpid
SL3251,SL2665
protocol description
2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers)
protocol
v041610.2
replicate
1,2
treatment description
1 h with 0.02% Ethanol (Myers)
treatment
EtOH_0.02pct

Sequenced DNA Library

library_name
GSM1010725: HudsonAlpha_ChipSeq_A549_FOXA1_(SC-101058)_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
54141733
Reads aligned (%)
71.3
Duplicates removed (%)
20.8
Number of peaks
38808 (qval < 1E-05)

hg38

Number of total reads
54141733
Reads aligned (%)
73.2
Duplicates removed (%)
19.3
Number of peaks
38782 (qval < 1E-05)

Base call quality data from DBCLS SRA