|
| Status |
Public on Mar 01, 2010 |
| Title |
Buccal Cell Smoker 26 replicate A |
| Sample type |
RNA |
| |
|
| Source name |
buccal mucosa cells from swab, from both cheeks of smokers or nonsmokers
|
| Organism |
Homo sapiens |
| Characteristics |
smoking status: smoker
cell type: buccal mucosa cells
|
| Treatment protocol |
Buccal samples were taken using a sterile cytobrush plus with a 30 second brushing. Immediately after sampling, each cytobrush was placed in a 2 ml micro-centrifuge containing 1 ml RNAlater.
|
| Growth protocol |
NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from buccal samples using the Rneasy Micro Kit with modification as given in Spivack et al. Cancer Res. 2004, 64:6805 and in Kupfer et al submitted.
|
| Label |
biotin
|
| Label protocol |
20 ng total RNA was both reverse transcribed and amplified using the Ovation RNA amplificztion System V2 (Nugen Technologies). This template material was fragmented and biotin labeled using the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, Inc.).
|
| |
|
| Hybridization protocol |
Arrays were hybridized for 18 hours at 45 deg C at 60 rpm in a GeneChip Hybridization Oven model 640 (Affymetric, Inc.). Fluidics protocol FS450_0004 was used with the GeneChip Fluidics Station model 450 to wash the arrays.
|
| Scan protocol |
Scanning was done on a GeneChip Laser Scanner model 3000 with system running GCOS version 1.4.
|
| Description |
n/a
|
| Data processing |
GCOS (ver 1.4) report derived with TGT Value set at 100. Bioconductor package AffyQCReport and ProbeLevelModeling was used for quality assessment. Summarized and quantile normalized data was generated using the application at the Automated Microarray Pipeline (http://compbio.dfci.harvard.edu/amp/). Relative differential gene expression analysis comparing smokers to nonsmokers was performed with SAM, Rank Product Analysis, unsupervised hierarchiacal clustering and T-test using the packages available on the MultiExperiment Viewer, ver 4.3.01 with default settings.
|
| |
|
| Submission date |
May 19, 2009 |
| Last update date |
Apr 29, 2015 |
| Contact name |
Dennis M Burian |
| E-mail(s) |
[email protected]
|
| Phone |
405-954-6087
|
| Organization name |
Federal Aviation Administration
|
| Department |
Aviation Medicine
|
| Lab |
Bioaeronautical Sciences Research Lab
|
| Street address |
6500 S. MacArthur Blvd., AAM610
|
| City |
Oklahoma City |
| State/province |
OK |
| ZIP/Postal code |
73169 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE16149 |
Examining smoking-induced differential gene expression changes in buccal mucosa |
|
