|
| Status |
Public on Mar 23, 2017 |
| Title |
AN11_Period1 |
| Sample type |
RNA |
| |
|
| Source name |
Whole-genome gene expression profiles of nasal scrapes
|
| Organism |
Homo sapiens |
| Characteristics |
subject: 11
period: 1
sample type: nasal scrape specimen
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted and purified from the clinical nasal scrapes specimens using the SV96 Total RNA Isolation System (Promega) according to a custom automated protocol. The extracted RNA was quantified using RiboGreen RNA Quantitation Reagent (Invitrogen) and its quality was assessed using Agilent RNA 6000 Pico Kit (Agilent, Santa Clara, CA) in an Agilent 2100 Bioanalyzer (Agilent).
|
| Label |
Biotin
|
| Label protocol |
Samples were amplified and labeled using the Ovation WB protocol (NuGEN Technologies, San Carlos, CA), according to the manufacturer’s instructions. In brief, 50 ng of total RNA was amplified using the Ribo-SPIA technology (NuGEN Technologies). After quantification, 4.4 ug cDNA was fragmented and labeled with biotin using the FL-Ovation cDNA Biotin Module V2 (NuGEN Technologies).
|
| |
|
| Hybridization protocol |
The amplified cDNAs were hybridized to Affymetrix gene expression chips (Human Rosetta Custom Affymetrix 2.0, Affymetrix, Santa Clara, CA) using standard Affymetrix protocols.
|
| Scan protocol |
Arrays were scanned using a GeneChip Scanner 3000 7G. The images were analyzed using the Affymetrix GeneChip Operating Software (GCOS).
|
| Data processing |
Expression values were extracted using the Robust Multichip Average method (Irizarry RA et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003;4:249-64) as implemented in the Affymetrix Power Tools software (available at: http://www.affymetrix.com/partners_programs/programs/developer/tools/powertools.affx).
|
| |
|
| Submission date |
Mar 24, 2015 |
| Last update date |
Mar 23, 2017 |
| Contact name |
Vladislav Malkov |
| E-mail(s) |
vladislav_malkov@merck.com
|
| Organization name |
Merck Sharp & Dohme Corp
|
| Department |
Human Genetics and Pharmacogenomics
|
| Street address |
33 Avenue Loius Pasteur
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL10379 |
| Series (1) |
| GSE67200 |
A Randomized Clinical Trial to Study the Effects of Single Doses of Corticosteroid on Response to Nasal Allergen Challenge in Patients |
|
