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Sample GSM227868 Query DataSets for GSM227868
Status Public on Jul 03, 2008
Title Nose10 (Never Smoker)
Sample type RNA
 
Source name Nasal epithelial samples from Never Smoker
Organism Homo sapiens
Characteristics Never Smoker
Treatment protocol Buccal mucosa samples collected from cheek scrapings, stored in RNA later; Nasal epithelial samples collected by brushing inferior nasal turbinate, brushes stored in RNA later.
Growth protocol Cells collected from human samples.
Extracted molecule total RNA
Extraction protocol Trizol extraction of buccal mucosa samples performed based on manufacturer's protocol, with RNA from serial collections from same patient pooled to obtain minimum of 8ug for hybridization to HG-U133A_2 arrays; Nasal epithelial RNA isolated via Qiagen RNeasy Mini Kits per manufacturer’s protocol, with enough RNA from one collection to hybridize to HG-U133A_2 arrays.
Label biotin
Label protocol Eight micrograms of total RNA from bronchial epithelial cells were converted into double-stranded cDNA with the SuperScript II reverse transcriptase (Invitrogen) with an oligo-dT primer containing a T7 RNA polymerase promoter (Genset, Boulder, CO). The ENZO Bioarray RNA transcript labeling kit (Affymetrix) was used for in vitro transcription of the purified double-stranded cDNA.
 
Hybridization protocol The biotin-labeled cRNA was purified by using the RNeasy kit (Qiagen, Valencia, CA) and fragmented into ~ 200 base pairs by alkaline treatment (200 mM Tris-acetate, pH 8.2/500 mM potassium acetate/150 mM magnesium acetate). Each verified cRNA sample was then hybridized overnight onto the Affymetrix HG-U133A_2 array.
Scan protocol Confocal laser scanning (Agilent) performed to detect the streptavidin-labeled fluor.
Description Gene expression data from never smoker nasal epithelial sample
Data processing A single weighted mean expression level for each gene was derived using MICROARRAY SUITE 5.0 (MAS 5.0) software . The MAS 5.0 software also generated a detection P value [P(detection)] using a one-sided Wilcoxon sign-ranked test, which indicated whether the transcript was reliably detected. The trimmed mean target intensity of each array was arbitrarily set to 100.
 
Submission date Sep 07, 2007
Last update date Aug 14, 2011
Contact name Sriram Sridhar
E-mail(s) sridhars@medimmune.com
Phone 6178771485
Organization name MedImmune
Department Translational Medicine
Street address 1 MedImmune Way
City Gaithersburg
State/province MD
ZIP/Postal code 20878
Country USA
 
Platform ID GPL571
Series (1)
GSE8987 Expression data from buccal and nasal epithelium of current and never smokers

Data table header descriptions
ID_REF
VALUE Signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 215.736 P 0.0020226
AFFX-BioB-M_at 287.941 P 0.00556451
AFFX-BioB-3_at 183.782 P 0.0166701
AFFX-BioC-5_at 596.38 P 0.000389797
AFFX-BioC-3_at 530.864 P 4.42873e-05
AFFX-BioDn-5_at 729.481 P 7.00668e-05
AFFX-BioDn-3_at 3662.02 P 0.000389797
AFFX-CreX-5_at 6766.09 P 4.42873e-05
AFFX-CreX-3_at 8904.07 P 4.42873e-05
AFFX-DapX-5_at 4.63923 A 0.794268
AFFX-DapX-M_at 31.1069 A 0.51489
AFFX-DapX-3_at 16.1472 A 0.659339
AFFX-LysX-5_at 5.09043 A 0.760937
AFFX-LysX-M_at 17.561 A 0.672921
AFFX-LysX-3_at 36.788 P 0.0336773
AFFX-PheX-5_at 2.73616 A 0.991564
AFFX-PheX-M_at 2.25342 A 0.966323
AFFX-PheX-3_at 54.4807 A 0.48511
AFFX-ThrX-5_at 11.7763 A 0.891021
AFFX-ThrX-M_at 4.66954 A 0.921998

Total number of rows: 22277

Table truncated, full table size 670 Kbytes.




Supplementary file Size Download File type/resource
GSM227868.CEL.gz 3.3 Mb (ftp)(http) CEL
GSM227868.CHP.gz 5.6 Mb (ftp)(http) CHP
GSM227868.EXP.gz 353 b (ftp)(http) EXP
Processed data included within Sample table
Processed data provided as supplementary file

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