|
| Status |
Public on Feb 03, 2015 |
| Title |
P2 postnatal biological rep. 1 |
| Sample type |
RNA |
| |
|
| Source name |
Rat postnatal day 2 (parotid acini total RNA)
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprauge Dawley
age: P2
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
PICO Pure RNA isolation kit from Life Technologies was used per the manufacturers instructions
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard protocol for NuGEN Ovation Pico WTA System V2 reagent Kit from 1.5ng and 4.5ng total RNA
|
| |
|
| Hybridization protocol |
Following fragmentation, cRNA were hybridized for 16 hr at 45C to Affymetrix Rat 230 2.0 Arrays according to the Nugene FL-Ovation cDNA Biotin Module V2 Labeling and Hybridization User Manual from Affymetrix
|
| Scan protocol |
GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix) and the GeneChip Command Console 1.0 (Affymetrix)
|
| Description |
mRNA expression during parotid acini terminal differentiation
|
| Data processing |
The data were normalized using the 'rma' function in the Bioconductor package 'affy', with the default settings. Prior to analysis data were filtered according to the following: 1. Remove any probe not mapping to an Entrez ID 2. For two or more probes mapping to the SAME Entrez ID, keep only the one with the largest variability across the samples 3. Remove all probes with have variability across the samples below the 50th percentile (essentially filters out the probes whose variability is in the bottom half).
|
| |
|
| Submission date |
Feb 03, 2015 |
| Last update date |
Feb 03, 2015 |
| Contact name |
Douglas Darling |
| E-mail(s) |
douglas.darling@louisville.edu
|
| Organization name |
University of Louisville
|
| Department |
Oral Immunology and Infectious Diseases
|
| Street address |
501 S. Preston St.
|
| City |
Louisville |
| State/province |
KY |
| ZIP/Postal code |
40202 |
| Country |
USA |
| |
|
| Platform ID |
GPL1355 |
| Series (2) |
| GSE65586 |
mRNA expression in parotid acinar cells during terminal differentiation |
| GSE65587 |
Expression in parotid acinar cells during terminal differentiation |
|
