|
| 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 |
| 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 |
GPL96 |
| Series (1) |
| GSE8987 |
Expression data from buccal and nasal epithelium of current and never smokers |
|
