|
| Status |
Public on Mar 03, 2020 |
| Title |
6h: laser4 |
| Sample type |
RNA |
| |
|
| Source name |
calvaria, laser ablated
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: bone
age: 10 weeks old
|
| Treatment protocol |
Rectangular bone defect (8 × 3 mm area) was prepared by a few strokes of bur drilling (mean feed speed: approximately 0.75 mm/s) or 3 strokes (chisel contact tip, panel setting: 220 mJ/pulse and 20 Hz, output energy: 127 mJ/pulse, energy density at tip end: 20.2 J/cm2/pulse, feed speed: approximately 2 mm/s, pulse duration: 200 µs). In controls, periosteum was removed without bone ablation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, California, USA) with NucleoSpin RNA (TaKaRa Bio, Shiga, Japan). cDNA was synthesized using a PrimeScript RT Master Mix (TaKaRa Bio) according to the manufacturer’s instructions.
|
| Label |
Cy3
|
| Label protocol |
The Agilent Low Input Quick Amp Labeling kit (Agilent Technologies, Santa Clara, California, USA) was used to generate cRNA with a sample input of 200 ng total RNA for single-color microarray (Cy3) analysis according to the manufacturer’s instructions.
|
| |
|
| Hybridization protocol |
cRNAs were analyzed by hybridization onto an Agilent SurePrint G3 Unrestricted Gene Expression 8 × 60 K Microarray (Agilent Technologies) according to the manufacturer’s instructions.
|
| Scan protocol |
Fluorescence signals from the hybridized microarrays were detected using the Agilent Microarray Scanner System (Agilent Technologies) according to the manufacturer’s instructions.
|
| Description |
Gene expression after 6hr in laser ablated bone in calvaria
|
| Data processing |
Raw microarray data were extracted using Feature Extraction Software (ver. 11.0.1.1; Agilent Technologies).
Microarray data were quantile normalized and log2-transformed (Shippy et al., 2006) using R (ver. 3.6.0).
|
| |
|
| Submission date |
Mar 02, 2020 |
| Last update date |
Mar 03, 2020 |
| Contact name |
Sayaka Katagiri |
| E-mail(s) |
[email protected]
|
| Phone |
+819015353994
|
| Organization name |
Tokyo Medical and Dental University
|
| Street address |
1-5-45
|
| City |
Tokyo |
| ZIP/Postal code |
113-8549 |
| Country |
Japan |
| |
|
| Platform ID |
GPL22740 |
| Series (2) |
| GSE146180 |
Er:YAG laser irradiation decreases Sost expressions in bone and osteogenic cell (6h after surgery) |
| GSE146183 |
Er:YAG laser irradiation decreases Sost expressions in bone and osteogenic cell |
|
