|
| Status |
Public on Sep 03, 2015 |
| Title |
Standard |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
callus in standard fracture healing model
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
gender: male
tissue: callus in standard fracture healing model
|
| Extracted molecule |
total RNA |
| Extraction protocol |
On post-fracture day 14, the newly generated specific tissues, that is, the fracture callus for the standard healing fracture and the fibrous tissue surrounding the fracture site for the nonunions, were harvested. All harvested tissues were stored in RNAlater (Ambion, Austin, TX) at 4℃ until used. The tissue specimens from 5 different animals in each group on post-fracture day 14 were pooled, and were submitted to Cosmo Bio (Tokyo, Japan) for RNA isolation and microarray analysis. Total cellular RNA including miRNA was extracted from the tissue specimens, using miRCURY RNA Isolation Kit (Exiqon, Vedbaek, Denmark) according to manufacture's protocol.
|
| Label |
Hy3
|
| Label protocol |
1000 ng of total RNA was labeled with miRCURY LNA microRNA Power Labeling kit (Exiqon) according to manufacture's protocol.
|
| |
|
| Channel 2 |
| Source name |
Universal Reference
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
gender: male
sample type: Universal Reference
|
| Extracted molecule |
total RNA |
| Extraction protocol |
On post-fracture day 14, the newly generated specific tissues, that is, the fracture callus for the standard healing fracture and the fibrous tissue surrounding the fracture site for the nonunions, were harvested. All harvested tissues were stored in RNAlater (Ambion, Austin, TX) at 4℃ until used. The tissue specimens from 5 different animals in each group on post-fracture day 14 were pooled, and were submitted to Cosmo Bio (Tokyo, Japan) for RNA isolation and microarray analysis. Total cellular RNA including miRNA was extracted from the tissue specimens, using miRCURY RNA Isolation Kit (Exiqon, Vedbaek, Denmark) according to manufacture's protocol.
|
| Label |
Hy5
|
| Label protocol |
1000 ng of total RNA was labeled with miRCURY LNA microRNA Power Labeling kit (Exiqon) according to manufacture's protocol.
|
| |
|
| |
| Hybridization protocol |
Labeled RNA was hybridized to the microarray slide for 16-20 hr at 56 degrees C and washed with miRCURY LNA microRNA Power Labeling kit (Exiqon) according to manufacture's protocol.
|
| Scan protocol |
Hybridization signals were detected by DNA microarray scanner G2505C (Agilent Technologies) with resolution of 10 micrometres .
The scanned images were analyzed using Agilent Feature Extraction ver.10.7.3.1
|
| Description |
Universal Reference means that the sample was mixed with a equal volumes of each samples.
|
| Data processing |
At first Hy3 (samples) signal was normalized with division used Hy5 (Universal reference) signal. Then each signal value of unique probe ID was calculated from average of Hy3/Hy5 normalized signal intensities of replicated probes.
|
| |
|
| Submission date |
Feb 18, 2014 |
| Last update date |
Sep 03, 2015 |
| Contact name |
Takahiro Waki |
| E-mail(s) |
orutop@yahoo.co.jp
|
| Phone |
81-78-382-5985
|
| Organization name |
Kobe University Graduate School of Medicine
|
| Department |
Orthopaedic Surgery
|
| Street address |
7-5-1, Kusunoki-cho, Chu0-ku
|
| City |
Kobe |
| State/province |
Hyogo |
| ZIP/Postal code |
650-0017 |
| Country |
Japan |
| |
|
| Platform ID |
GPL11434 |
| Series (1) |
| GSE55088 |
miRNA expression data from callus in standard fracture healing models and from fibrous tissues in nonunion models in rats on post-fracture day 14 |
|
