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| Status |
Public on Apr 13, 2019 |
| Title |
CNV 3 |
| Sample type |
RNA |
| |
|
| Source name |
RPE-choroid-sclera complexes
|
| Organism |
Mus musculus |
| Characteristics |
tissue: RPE-choroid-sclera complexes from laser-induced CNV eye (7 days after the laser photocoagulation)
age: Seven to eight-week-old
Sex: male
|
| Treatment protocol |
The photocoagulation was applied in eyes of mice around the optic disc using a 532-nm diode laser (100 mW, 0.1 s duration, 50 μm). Twenty-five spots were burned on each eye, and the eyes were enucleated at 7 days after the laser photocoagulation. Age-matched mice without laser photocoagulation treatment were used as controls.
|
| Growth protocol |
The animals were maintained in cages in temperature-controlled rooms featuring a 12-h light/12-h dark cycle.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the RPE-choroid-sclera complexes using Trizol RNA extraction kit(Invitrogen life technologies). RPE-choroid-sclera complexes from 4 eyes were used as one sample.
|
| Label |
Cy3
|
| Label protocol |
Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random primers according to manufacturer’s protocol (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified using RNeasy Mini Kit (Qiagen,Genman). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured with NanoDrop ND-1000.
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| |
|
| Hybridization protocol |
1 μg of each labeled cRNA was fragmented by adding 5 μl of 10 × blocking agent and 1 μl of 25 × Fragmentation Buffer, then heating the mixture to 60 °C for 30 min, finally adding 25 μl of 2 × GE Hybridization buffer to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the lncRNA expression microarray slide. The slides were incubated in an Agilent Hybridization Oven for 17 hours at 65°C.
|
| Scan protocol |
The hybridized arrays were washed, fixed and scanned with the Agilent G2505C DNA Microarray Scanner.
|
| Description |
lncRNA and mRNA expression data from samples of laser-induced CNV mice.
|
| Data processing |
Acquired array images were analyzed by Feature Extraction software (Agilent Technologies,version 11.0.1.1).Quantile normalization and subsequent data processing were performed by using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs which at least 3 out of 6 samples signed with Present or Marginal flags(“All Targets Value”) were chosen for further data analysis.
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| |
|
| Submission date |
Apr 12, 2019 |
| Last update date |
May 20, 2019 |
| Contact name |
Yedi Zhou |
| E-mail(s) |
zhouyedi@csu.edu.cn
|
| Organization name |
The Second Xiangya Hospital, Central South University
|
| Department |
Department of Ophthalmology
|
| Street address |
No. 139, Middle Renmin Road
|
| City |
Changsha |
| State/province |
Hunan |
| ZIP/Postal code |
410011 |
| Country |
China |
| |
|
| Platform ID |
GPL19286 |
| Series (1) |
| GSE129743 |
Expression profiles of long non-coding RNAs and messenger RNAs in laser-induced choroidal neovascularization in mice. |
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