|
| Status |
Public on Mar 17, 2018 |
| Title |
Stretched_NRVMs_24h_rep_03 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Neonatal rat ventricular myocytes
|
| Organism |
Rattus norvegicus |
| Characteristics |
age: 2-4 days old
cell type: ventricular myocytes
strain: Sprague-Dawley
treatment: 24h stretch
|
| Treatment protocol |
Stretch was introduced to cells by applying a cyclic vacuum suction under the flexible bottomed plates by computer-controlled equipment (Flexercell Strain Unit FX-3000, Flexcell).
|
| Growth protocol |
Neonatal rat ventricular myocytes were prepared from 2-4 days old Sprague-Dawley rats as previously described (Pikkarainen et al.J. Biol. Chem. 278, 23807–23816 (2003).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Tisolated with TRIzol Reagent (Sigma Aldrich) according to the manufacturer’s protocol (Invitrogen) by using the Phase Lock Gel system (Eppendorf).
|
| Label |
Cy5
|
| Label protocol |
Labeling was performed by Exiqon, according to manufacturer protocol; in brief 2 ug of total RNA was labeled using the miRCURY Hy3/Hy5 labeling kit according to Exiqon protocol (Vedbaek, Denmark).
|
| |
|
| Channel 2 |
| Source name |
common reference pool
|
| Organism |
Rattus norvegicus |
| Characteristics |
source: common reference pool
|
| Treatment protocol |
Stretch was introduced to cells by applying a cyclic vacuum suction under the flexible bottomed plates by computer-controlled equipment (Flexercell Strain Unit FX-3000, Flexcell).
|
| Growth protocol |
Neonatal rat ventricular myocytes were prepared from 2-4 days old Sprague-Dawley rats as previously described (Pikkarainen et al.J. Biol. Chem. 278, 23807–23816 (2003).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Tisolated with TRIzol Reagent (Sigma Aldrich) according to the manufacturer’s protocol (Invitrogen) by using the Phase Lock Gel system (Eppendorf).
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by Exiqon, according to manufacturer protocol; in brief 2 ug of total RNA was labeled using the miRCURY Hy3/Hy5 labeling kit according to Exiqon protocol (Vedbaek, Denmark).
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed by Exiqon according to manufacturer protocol.
|
| Scan protocol |
Scanning was performed by Exiqon according to manufacturer protocol.
|
| Description |
MicroRNA expression data from stretched neonatal rat ventricular myocytes
|
| Data processing |
Data processing was performed by Exiqon according to manufacturer protocol; in brief normalization included background subtraction and normalization with global Lowess (Locally Weighter Scatterplot Smoothing) regression algorithm. This within-slide normalization was performed to minimize differences between the colors in an intensity-dependent manner. The criterion for deciding that a miRNA had failed on a particular array was the observation that 2 or more of the 4 replicated measures of this miRNA had a signal that was below background. In addition, Hy3 and Hy5 signals lower than 1.5x of the median signal intensity of the given slide were excluded. Replicated measurements of the same miRNA from each slide were averaged to per-chip median values and then used to obtain geometric means and standard deviations for each miRNA.
|
| |
|
| Submission date |
Nov 27, 2017 |
| Last update date |
Mar 17, 2018 |
| Contact name |
Jaana Rysae |
| E-mail(s) |
jaana.rysa@gmail.com
|
| Organization name |
University of Eastern Finland
|
| Department |
School of Pharmacy
|
| Street address |
Yliopistonranta 1C
|
| City |
Kuopio |
| ZIP/Postal code |
70211 |
| Country |
Finland |
| |
|
| Platform ID |
GPL7722 |
| Series (2) |
| GSE107379 |
Mechanical stretch induced transcriptomic profiles in cardiac myocytes [24-48 hours] |
| GSE107380 |
Mechanical stretch induced transcriptomic profiles in cardiac myocytes |
|
