|
| Status |
Public on Jan 30, 2013 |
| Title |
NRVM_0h_04 |
| Sample type |
RNA |
| |
|
| Source name |
NRVMs on iso FN for 1h
|
| Organism |
Rattus norvegicus |
| Characteristics |
background strain: Sprague-Dawley
tissue: engineered neonatal rat ventricular tissues
|
| Treatment protocol |
Tissues were rinsed with PBS and RNA was extracted using Stratagene Absolutely RNA Miniprep Kit (Agilent Technologies).
|
| Growth protocol |
NRVMs were seeded on iso and aniso silicone substrates and cultured in supplemented M199 with 10% FBS for the first 48 hours in culture and then supplemented M199 with 2% FBS for the remainder of time in culture.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
cDNA was labelled with Affymetrix DNA Labeleing Reagent according to the manufacturer's instructions from 1 ug total RNA.
|
| |
|
| Hybridization protocol |
Following fragmentation, 2.5 ug of cRNA were hybridized for 17 hours at 45C on Affymetrix GeneChip Rat Gene 1.0 ST Arrays in Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using Affymetrix GeneChip Scanner 3000 7G.
|
| Description |
NRVM, iso FN, 0h, no stretch, harvest4, for harvest normalization
|
| Data processing |
Probe cell intensity data files were loaded into Affymetrix Expression Console Software and normalized using the robust multichip average (RMA) method. Signal values were log2-transformed and analyzed with Bioconductor open source software and the limma package in R. Expression values for each condition were averaged, fit to a linear model, and compared using Bayes statistics.
|
| |
|
| Submission date |
Jan 29, 2013 |
| Last update date |
Jan 30, 2013 |
| Contact name |
Megan Laura McCain |
| E-mail(s) |
megan.mccain@gmail.com
|
| Organization name |
Harvard University
|
| Department |
Engineering and Applied Sciences
|
| Lab |
Disease Biophysics Group
|
| Street address |
60 Oxford St Room 332
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02144 |
| Country |
USA |
| |
|
| Platform ID |
GPL6247 |
| Series (1) |
| GSE43846 |
Expression data from cyclically stretched engineered neonatal rat ventricuar myocyte (NRVM) tissues |
|
