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Sample GSM1127872 Query DataSets for GSM1127872
Status Public on Dec 09, 2013
Title eMCAo 0hrs
Sample type RNA
 
Source name eMCAo 0hrs
Organism Rattus norvegicus
Characteristics strain: Wistar
weight: 280-320g
gender: male
tissue: ischemic brain
Treatment protocol no treatment
Growth protocol All animals were handled according to the Council for International Organisation of Medical Sciences on Animal Experimentation (World Health Organisation, Geneva, Switzerland) and the National University of Singapore (IACUC/NUS) guidelines for laboratory animals. The protocol was approved by the Committee on the Ethics of Animal Experiments of the National University of Singapore (Protocol Number: 081/09 and 025/11). All surgery was performed using ketamine/xylazine as anesthesia, and all efforts were made to minimize suffering.
Extracted molecule total RNA
Extraction protocol Total RNA (+ miRNA) was extracted from brain tissues by a single-step method using Trizol reagent (Invitrogen, Life Technologies, USA) according to manufacturers’ protocol.
Label Hy3
Label protocol miRNA array was performed (PMID: 21829658) using total RNA (500 ng) which was 3′-end-labelled with Hy3 dye using the miRCURY LNA™ Power Labeling Kit (Exiqon, Denmark)
 
Hybridization protocol hybridization for 16-18hrs on miRCURY LNA™ Arrays, using MAUI® hybridization system according to manufacturer’s protocol (Exiqon, Denmark).
Scan protocol The microarray chips were then washed and scanned using InnoScan700, microarray scanner (Innopsys, Carbonne, France) and analysed on Mapix® Ver4.5 software.
Description around 3000 microRNAs capture probes cover human, mouse and rat microRNAs and present a global miRNA profiling for the specific species
Data processing Microarray analysis involved multiple sample analysis including background subtraction, t-Test/One-way ANOVA analysis, hierarchical clustering (PMID: 21829658). Normalization was performed using 5S rRNA. t-Test was performed between ‘‘control’’ and ‘‘test’’ sample groups and the t values were calculated for each mRNA. p-values were computed from the theoretical t-distribution. The clustering using hierarchical method was performed with average linkage and Euclidean distance metric. The clustering was generated using TIGR MeV (Multiple Experimental Viewer) software and statistical analysis was performed using Partek® Genomics Suite™ 6.6 (Partek Inc, USA). Only the microRNA presented in Rattus norvegicus (rno-miR-) were included for our analysis, while our raw data include the entire probe that was on the chip (hsa+mmu+rno).
 
Submission date Apr 22, 2013
Last update date Dec 09, 2013
Contact name Kandiah Jeyaseelan
E-mail(s) erijeya@nus.edu.sg
Organization name National University of Singapore
Department Biochemistry
Street address 8 Medical Drive
City Singapore
ZIP/Postal code 117597
Country Singapore
 
Platform ID GPL17042
Series (2)
GSE46266 microRNAs involved in regulating embolic stroke recovery following spontaneous reperfusion [miRNA]
GSE46269 miRNAs involved in regulating embolic stroke recovery following spontaneous reperfusion

Data table header descriptions
ID_REF
VALUE normalized signal intensity

Data table
ID_REF VALUE
hsa-let-7b*/mmu-let-7b*/rno-let-7b* 2543.89
hsa-let-7b/mmu-let-7b/rno-let-7b 70026.2
hsa-let-7c/mmu-let-7c/rno-let-7c 113408
hsa-let-7d*/mmu-let-7d*/rno-let-7d* 6825.33
hsa-let-7d/mmu-let-7d/rno-let-7d 32932.1
hsa-let-7e*/rno-let-7e* 1672.39
hsa-let-7e/mmu-let-7e/rno-let-7e 165893
hsa-let-7f/mmu-let-7f/rno-let-7f 251085
hsa-let-7i*/mmu-let-7i*/rno-let-7i* 21.7194
hsa-let-7i/mmu-let-7i/rno-let-7i 41956.5
hsa-miR-100/mmu-miR-100/rno-miR-100 36662.4
hsa-miR-101*/mmu-miR-101a*/rno-miR-101a* 21.7194
hsa-miR-101/mmu-miR-101a/rno-miR-101a 91976.3
hsa-miR-103/mmu-miR-103/rno-miR-103 74201.8
hsa-miR-106b*/mmu-miR-106b*/rno-miR-106b* 771.039
hsa-miR-106b/mmu-miR-106b/rno-miR-106b 27171
hsa-miR-10a*/mmu-miR-10a*/rno-miR-10a-3p 1645.25
hsa-miR-10a/mmu-miR-10a/rno-miR-10a-5p 781.899
hsa-miR-10b/mmu-miR-10b/rno-miR-10b 100.452
hsa-miR-122/mmu-miR-122/rno-miR-122 3019

Total number of rows: 346

Table truncated, full table size 13 Kbytes.




Supplementary file Size Download File type/resource
GSM1127872_KJLab_2012-07-11_15h34m16_14312456_fj0hRp.txt.gz 1.7 Mb (ftp)(http) TXT
Processed data included within Sample table

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