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Sample GSM2865688 Query DataSets for GSM2865688
Status Public on Mar 17, 2018
Title Stretched_NRVMs_control_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: control
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 control, non-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)
GSE107378 Mechanical stretch induced transcriptomic profiles in cardiac myocytes [1-12 hours]
GSE107380 Mechanical stretch induced transcriptomic profiles in cardiac myocytes

Data table header descriptions
ID_REF
VALUE normalised Hy3/Hy5 ratios (log2 transformed) from all hybridizations were calculates, and in the data table are shown the median of replicated measurements of the same miRNA from each slide

Data table
ID_REF VALUE
13150 0.52199994
17752 1.364292213
10919 1.325980075
4610 2.151910115
42540 1.243577273
33596 1.211346959
10936 0.754837652
13148 1.483532994
42866 1.560662137
42471 1.405764491
42502 1.571202611
19596 1.387414843
11273 1.709510014
11182 1.13875585
42973 1.504305966
27217 1.482170244
19582 1.775359569
11074 0.668601359
29562 1.639717152
14313 1.616342964

Total number of rows: 390

Table truncated, full table size 5 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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