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Sample GSM4367846 Query DataSets for GSM4367846
Status Public on Mar 03, 2020
Title 6h: laser1
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) kataperi@tmd.ac.jp
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

Supplementary file Size Download File type/resource
GSM4367846_6h_laser1.txt.gz 12.1 Mb (ftp)(http) TXT
Processed data are available on Series record

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