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Status
Public on Nov 21, 2006
Title
small airways, smoker 044, RMA and MAS
Sample type
RNA
Source name
airway epithelial cells obtained by bronchoscopy and brushing
Organism
Homo sapiens Characteristics
age: 50
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 044, 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 (14)
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
GSE13931 Disparate Oxidant-related Gene Expression of Human Small Airway Epithelium Compared to Autologous Alveolar Macrophages
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
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
2615.2297
8460.012
P
2.19E-04
1053_at
68.66434
231.68617
P
0.001353854
117_at
23.935286
56.453896
A
0.2674626
121_at
171.05447
516.232
P
0.004862762
1255_g_at
9.506586
36.310596
A
0.32083008
1294_at
269.56882
745.84814
P
2.66E-04
1316_at
43.89871
115.69267
P
0.007542912
1320_at
50.425243
185.0276
P
0.009985438
1405_i_at
328.26065
1358.4506
P
6.13E-04
1431_at
13.010557
68.63284
P
0.013091824
1438_at
130.53398
402.8098
P
4.68E-04
1487_at
143.81096
587.32056
P
0.007542912
1494_f_at
138.38365
449.41977
P
6.73E-04
1552256_a_at
87.29687
243.94061
P
0.0239258
1552257_a_at
153.88988
541.00793
P
2.44E-04
1552258_at
18.783115
78.87218
M
0.0561523
1552261_at
194.20638
665.0964
P
7.32E-04
1552263_at
66.82629
272.83325
P
2.44E-04
1552264_a_at
289.5189
842.2872
P
2.44E-04
1552266_at
22.307049
114.21966
P
2.44E-04
54675 2208 Kbytes .Supplementary file Size Download File type/resource GSM101115.CEL.gz
8.3 Mb
(ftp) (http) CEL
GSM101115.CHP.gz
13.5 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
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