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Status
Public on Nov 21, 2006
Title
small airways, smoker 049, RMA and MAS
Sample type
RNA
Source name
airway epithelial cells obtained by bronchoscopy and brushing
Organism
Homo sapiens Characteristics
age: 46
Extracted molecule
total RNA
Extraction protocol
Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.
Label
biotin
Label protocol
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).
Hybridization protocol
Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol
GeneChips were scanned using the GeneChip Scanner 3000 7G.
Description
small airways, smoker 049, RMA and MAS
Data processing
The CEL files were generated using Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings
Submission date
Mar 20, 2006
Last update date
Aug 28, 2018
Contact name
Yael Strulovici-Barel
E-mail(s)
yas2003@med.cornell.edu Organization name
Weill Cornell Medical College
Department
Department of Genetic Medicine
Lab
Crystal
Street address
1300 York Avenue
City
New York
State/province
NY
ZIP/Postal code
10021
Country
USA
Platform ID
GPL570 Series (15)
GSE4498 Expression data of small airway epithelium from phenotypically normal smokers and non-smokers
GSE5058 Airway epithelium, small airways, normal non-smokers, phenotypic normal smokers, smokers with COPD and early COPD
GSE5060 Airway epithelium, large and small airways, phenotypically normal smokers, non-smokers, early COPD and COPD
GSE8545 Variability in Small Airway Epithelial Gene Expression Among Normal Smokers
GSE11784 Biologic Phenotyping of the Human Small Airway Epithelial Response to Cigarette Smoking
GSE11906 Quality Control in Microarray Assessment of Gene Expression in Human Airway Epithelium
GSE11952 Coordinate Control of Nrf2 Mediated Genes in the Human Small Airway Epithelium Highly Responsive to Smoking
GSE13932 Genetic Variability Modulation of SPOCK3 Gene Expression in the Human Small Airway Epithelium
GSE17905 Smoking-mediated Up-regulation of GAD67 Expression in the Human Airway Epithelium
GSE18385 Smoking-induced Up-regulation of AKR1B10 Expression in the Airway Epithelium of Healthy Individuals
GSE19407 Smoking-induced Wnt pathway downregulation
GSE19667 Threshold of Biologic Response of the Small Airway Epithelium to Low Levels of Tobacco Smoke
GSE20250 CNV Polymorphisms Modulate the Expression of GST Subtypes in the Human Small Airway Epithelium and Alveolar Macrophages
GSE20257 Smoking-induced Disarray of the Apical Junctional Complex Gene Expression Architecture in the Human Airway Epithelium
GSE21359 Association of CXCL14 in the Human Airway Epithelium with Chronic Obstructive Lung Disease and Lung Cancer
Relations Reanalyzed by
GSE60486 Reanalyzed by
GSE119087
Data table header descriptions ID_REF Probe set ID
VALUE Signal intensity derived from the CEL files, using RMA method
VALUE_MAS MAS5-calculated Signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call
Data table ID_REF VALUE VALUE_MAS ABS_CALL DETECTION P-VALUE 1007_s_at
2130.1326
7420.707
P
2.19E-04
1053_at
60.52254
236.26408
P
0.013091824
117_at
27.868433
61.376503
A
0.12764525
121_at
129.48018
414.2146
P
0.039365407
1255_g_at
9.235668
4.3978214
A
0.9686643
1294_at
197.72386
451.9632
P
3.88E-04
1316_at
48.81215
135.15686
P
0.001353854
1320_at
33.590454
14.729601
A
0.62181556
1405_i_at
55.789753
226.53183
P
9.44E-04
1431_at
10.242283
38.505222
A
0.107300945
1438_at
69.98383
166.14879
P
0.001353854
1487_at
106.82869
477.84012
P
0.031335693
1494_f_at
557.01263
2742.149
P
2.19E-04
1552256_a_at
56.341785
139.5018
P
0.0302734
1552257_a_at
146.60612
572.38184
P
0.00292969
1552258_at
15.181738
45.05166
A
0.334473
1552261_at
163.72269
725.3947
P
2.44E-04
1552263_at
78.92961
381.7365
P
2.44E-04
1552264_a_at
254.72876
726.25323
P
2.44E-04
1552266_at
16.287727
75.81754
P
0.00415039
54675 2209 Kbytes .Supplementary file Size Download File type/resource GSM101116.CEL.gz
8.0 Mb
(ftp) (http) CEL
GSM101116.CHP.gz
13.2 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
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