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Sample GSM227865 Query DataSets for GSM227865
Status Public on Jul 03, 2008
Title Mouth_14 (Current Smoker)
Sample type RNA
Source name Buccal mucosa sample from Current Smoker
Organism Homo sapiens
Characteristics Current 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 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 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 array.
Scan protocol Confocal laser scanning (Agilent) performed to detect the streptavidin-labeled fluor.
Description Gene expression data from current smoker buccal mucosa 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
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 GPL96
Series (1)
GSE8987 Expression data from buccal and nasal epithelium of current and never smokers

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

Data table
AFFX-BioB-5_at 743.69 P 0.000340305
AFFX-BioB-M_at 1347.19 P 4.42873e-05
AFFX-BioB-3_at 759.351 P 6.02111e-05
AFFX-BioC-5_at 2217.96 P 5.16732e-05
AFFX-BioC-3_at 2329.52 P 4.42873e-05
AFFX-BioDn-5_at 3724.37 P 4.42873e-05
AFFX-BioDn-3_at 11695.7 P 6.02111e-05
AFFX-CreX-5_at 26231 P 4.42873e-05
AFFX-CreX-3_at 33828.7 P 4.42873e-05
AFFX-DapX-5_at 65.1768 A 0.116113
AFFX-DapX-M_at 64.3425 A 0.139482
AFFX-DapX-3_at 21.7854 A 0.631562
AFFX-LysX-5_at 19.2541 A 0.529762
AFFX-LysX-M_at 7.21129 A 0.97611
AFFX-LysX-3_at 10.8339 A 0.631562
AFFX-PheX-5_at 8.14823 A 0.897835
AFFX-PheX-M_at 2.19789 A 0.971554
AFFX-PheX-3_at 66.7834 A 0.58862
AFFX-ThrX-5_at 73.005 A 0.41138
AFFX-ThrX-M_at 36.253 A 0.5

Total number of rows: 22283

Table truncated, full table size 649 Kbytes.

Supplementary file Size Download File type/resource
GSM227865.CEL.gz 3.1 Mb (ftp)(http) CEL
GSM227865.CHP.gz 5.4 Mb (ftp)(http) CHP
GSM227865.EXP.gz 503 b (ftp)(http) EXP
Processed data included within Sample table
Processed data provided as supplementary file

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