|
| Status |
Public on Jun 19, 2018 |
| Title |
DGM-01753_M6_sm (demographics_pollution) |
| Sample type |
RNA |
| |
|
| Source name |
small airway epithelium brushing
|
| Organism |
Homo sapiens |
| Characteristics |
smoking status: COPD smoker
30-day mean pm2.5 exposure level: 16.8652
time of serial bronchoscopy (month): M6
cell type: small airway epithelium brushing
|
| 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 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 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 |
DGM-01753
307SAE-S_PM2.5_resid.csv
|
| Data processing |
Gene expression was normalized using the Single-channel array normalization (SCAN)/Universal exPression Codes (UPC) method and University of Michigan HG-U133 Plus 2.0 microarray probeset definitions (version 21) . Genes with a UPC value of <0.2 in all samples were excluded. SAE gene expression was modeled as a linear function of 30-day mean PM2.5 level. P values were calculated by two-sided Wald test, reflecting the probability that the regression coefficient for the pollution variable is non-zero.
|
| |
|
| Submission date |
Dec 15, 2017 |
| Last update date |
Jun 19, 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 (1) |
| GSE108134 |
Ambient Pollution Related Reprogramming of the Human Small Airway Epithelial Transcriptome |
|
