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Sample GSM2865691 Query DataSets for GSM2865691
Status Public on Mar 17, 2018
Title Stretched_NRVMs_4h_rep_01
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 -0.301247184
17752 0.197633669
10919 0.169756638
4610 0.972289014
42540 0.711680721
33596 0.216704351
10936 -0.252068627
13148 0.560714133
42866 0.58970413
42471 0.422475921
42502 0.830420529
19596 0.274518464
11273 0.692437177
11182 0.107276402
42973 0.603194078
27217 0.721980709
19582 1.022172452
11074 -0.092188967
29562 0.863590005
14313 0.565182118

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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