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Sample GSM3374643 Query DataSets for GSM3374643
Status Public on Aug 31, 2020
Title control rat collateral tissue replicate 1
Sample type RNA
 
Channel 1
Source name collateral blood vessel tissue control
Organism Rattus norvegicus
Characteristics gender: male
strain: Spraque-Dawley
tissue: collateral blood vessel tissue control
Treatment protocol Single femoral artery ligation and arteriovenous shunt to maximize fluid shear stress in collateral arteries. Contralateral leg was sham-operated and served as control
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Trizol following manufacturer's instructions
Label AF665
Label protocol The samples were directly labeled using Ncode Rapid labeling System (#MIRLSRPD-20) and arrayed on the multi-species miRNA Microarray V2 (#MIRA2-05)
 
Channel 2
Source name collateral blood vessel tissue control
Organism Rattus norvegicus
Characteristics gender: male
strain: Spraque-Dawley
tissue: collateral blood vessel tissue control
Treatment protocol Single femoral artery ligation and arteriovenous shunt to maximize fluid shear stress in collateral arteries. Contralateral leg was sham-operated and served as control
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Trizol following manufacturer's instructions
Label AF546
Label protocol The samples were directly labeled using Ncode Rapid labeling System (#MIRLSRPD-20) and arrayed on the multi-species miRNA Microarray V2 (#MIRA2-05)
 
 
Hybridization protocol Two differentially labelled reactions were combined into one tube and loaded onto the array
Scan protocol Arrays were scanned using a GenePix 400B microarray scanner (Molecular Devices)
Description Sample name: Psk 27 kk
Biological replicate 1 of 5. Collateral tissue Psk 27 kk (AF665) and collateral tissue Psk 28 kk (AF546)
Data processing The annotated data were normalized using a Latin Squares algorithm by the NCodeā„¢ Profiler data analysis software
The pairwise median fold-change, P-value, tissue rank, and test statistics for the miRNAs are listed in the Analyzed Data File. The values for each individual miRNA probe sequence printed in triplicate on the array are listed as separate rows in the analysis file. The miRNAs with p-values <0.05 for two out of the three spots on the array are considered statistically significant. A list of the statistically significant miRNAs for follow-up studies is provided on the second sheet in the Analyzed Data workbook. The replicate values for median fold-change, P-value, tissue rank, and test statistics for each of the miRNAs collapsed into one value are listed in the Collapsed Data File.
Data analysis used only the miRNA_IDs annotated in NCode Multi-Species miRNA Microarray V2.
 
Submission date Sep 04, 2018
Last update date Sep 01, 2020
Contact name Kerstin Troidl
E-mail(s) kerstin.troidl@mpi-bn.mpg.de
Organization name Max-Planck-Institute for Heart and Lung Research
Street address Ludwigstr. 43
City Bad Nauheim
ZIP/Postal code 61231
Country Germany
 
Platform ID GPL25527
Series (1)
GSE119434 Microarray-based miRNA expression in fluid shear stress-stimulated collateral blood vessels

Data table header descriptions
ID_REF
VALUE log2 (AF665/AF546) ratios

Data table
ID_REF VALUE
rno-let-7a_1 0.342526711
rno-let-7a_2 0.280666595
rno-let-7a_3 -0.147676642
rno-let-7b_1 -0.097419422
rno-let-7b_2 0.002921173
rno-let-7b_3 0.019849475
rno-let-7c_1 0.343612876
rno-let-7c_2 0.270234518
rno-let-7c_3 0.246386635
rno-let-7d_1 -0.119538912
rno-let-7d_2 -0.321347897
rno-let-7d_3 -0.02116189
rno-let-7d*_1 -0.283701549
rno-let-7d*_2 -0.202581281
rno-let-7d*_3 -0.082465956
rno-let-7e_1 0.193583028
rno-let-7e_2 0.069399732
rno-let-7e_3 0.011102529
rno-let-7f_1 0.077846034
rno-let-7f_2 -0.366626865

Total number of rows: 3321

Table truncated, full table size 83 Kbytes.




Supplementary file Size Download File type/resource
GSM3374643_Psk_27_kk_vs_Psk_28_kk.txt.gz 196.6 Kb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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