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Status
Public on Nov 21, 2006
Title
small airways, smoker 027, RMA and MAS
Sample type
RNA
Source name
airway epithelial cells obtained by bronchoscopy and brushing
Organism
Homo sapiens Characteristics
Age: 44
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 027, 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 (7)
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
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
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
2097.944
7179.885
P
2.19E-04
1053_at
80.16585
302.37988
P
0.009985438
117_at
32.644653
91.43538
A
0.35869044
121_at
156.44774
575.47095
P
0.014936572
1255_g_at
10.015328
17.963823
A
0.45881578
1294_at
183.3602
436.6263
P
9.59E-04
1316_at
45.01219
115.875755
P
0.039365407
1320_at
31.868694
21.224434
A
0.6604422
1405_i_at
118.035355
488.7473
P
9.44E-04
1431_at
12.9482765
80.78897
P
0.031335693
1438_at
73.1572
138.6251
P
0.027859662
1487_at
187.67168
826.5751
P
0.024710983
1494_f_at
67.14083
282.56894
P
0.003066685
1552256_a_at
70.608
224.72742
A
0.0805664
1552257_a_at
179.0195
773.502
P
2.44E-04
1552258_at
18.587263
165.02667
A
0.129639
1552261_at
106.09736
482.24057
P
0.00195313
1552263_at
70.085495
357.8246
P
7.32E-04
1552264_a_at
161.43732
477.1187
P
0.00195313
1552266_at
17.383558
158.14503
P
0.0461426
54675 2209 Kbytes .Supplementary file Size Download File type/resource GSM101109.CEL.gz
8.5 Mb
(ftp) (http) CEL
GSM101109.CHP.gz
13.5 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
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