Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
PBX3

Cell type

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

Attributes by original data submitter

Sample

GEO Accession
GSM1010755
antibody antibodydescription
Rabbit Polyclonal IgG. Antibody Target: PBX3
antibody targetdescription
Pbx 3 (D-17)
antibody vendorid
sc-891
antibody vendorname
Santa Cruz Biotechnology
antibody
Pbx3
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
SL13321
datatype description
Chromatin IP Sequencing
datatype
ChipSeq
lab description
Myers - Hudson Alpha Institute for Biotechnology
lab
HudsonAlpha
labexpid
SL16043,SL13476
protocol description
Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)
protocol
v042211.1
replicate
1,2
softwareversion
MACS
treatment description
No special treatment or protocol applies
treatment
None

Sequenced DNA Library

library_name
GSM1010755: HudsonAlpha_ChipSeq_A549_Pbx3_v042211.1
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
75783948
Reads aligned (%)
82.6
Duplicates removed (%)
8.5
Number of peaks
9862 (qval < 1E-05)

hg38

Number of total reads
75783948
Reads aligned (%)
84.3
Duplicates removed (%)
7.3
Number of peaks
10318 (qval < 1E-05)

Base call quality data from DBCLS SRA