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Sample GSM2865692 Query DataSets for GSM2865692
Status Public on Mar 17, 2018
Title Stretched_NRVMs_4h_rep_02
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: 4h 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)
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 -0.451819827
17752 -0.24170631
10919 -0.1635705
4610 0.2845982
42540 0.513498922
33596 -0.260700911
10936 -0.661315365
13148 0.108725204
42866 -0.048295125
42471 -0.056746509
42502 0.174975613
19596 -0.296764944
11273 0.136427409
11182 -0.611073
42973 0.308834411
27217 0.1258987
19582 0.527410646
11074 -0.726770697
29562 0.521166256
14313 0.037643053

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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