|
| Status |
Public on Dec 09, 2013 |
| Title |
eMCAo 24hrs1 |
| Sample type |
RNA |
| |
|
| Source name |
eMCAo 24hrs
|
| 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 |
|
