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Status
Public on Nov 21, 2006
Title
small airways, smoker 001, RMA and MAS
Sample type
RNA
Source name
airway epithelial cells obtained by bronchoscopy and brushing
Organism
Homo sapiens Characteristics
age: 37
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 001, 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
GSE13931 Disparate Oxidant-related Gene Expression of Human Small Airway Epithelium Compared to Autologous Alveolar Macrophages
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
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
1992.7407
6746.148
P
2.19E-04
1053_at
83.198265
343.6239
P
0.003584867
117_at
33.190834
135.53818
P
0.00653198
121_at
135.45946
346.12042
P
0.039365407
1255_g_at
9.567991
2.9619122
A
0.8494729
1294_at
274.58716
702.00555
P
2.19E-04
1316_at
52.312813
186.35077
P
3.88E-04
1320_at
31.839949
81.30178
A
0.37818444
1405_i_at
608.7481
2691.3372
P
4.91E-04
1431_at
14.471274
99.315636
P
9.59E-04
1438_at
66.42434
177.2066
P
0.004862762
1487_at
124.31234
531.71606
P
0.035162866
1494_f_at
81.7993
289.93768
P
0.004180327
1552256_a_at
72.49782
197.34157
P
0.0239258
1552257_a_at
108.85947
340.4873
P
0.00585938
1552258_at
19.04306
56.71459
A
0.129639
1552261_at
194.79707
979.7232
P
7.32E-04
1552263_at
106.79003
486.7834
P
2.44E-04
1552264_a_at
248.50237
689.7266
P
2.44E-04
1552266_at
16.50913
64.12904
P
2.44E-04
54675 2210 Kbytes .Supplementary file Size Download File type/resource GSM101111.CEL.gz
8.3 Mb
(ftp) (http) CEL
GSM101111.CHP.gz
13.4 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
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