|
| Status |
Public on Oct 01, 2018 |
| Title |
ABTAA_Treated_1 |
| Sample type |
SRA |
| |
|
| Source name |
RPE-choroidal complex
|
| Organism |
Mus musculus |
| Characteristics |
Sex: male
age: 8-week-old
|
| Treatment protocol |
To administer indicated reagents intravitreally, 5 µg of reagent (5 mg/ml) was injected into the vitreal cavity using the micro-injector fitted with a glass capillary pipette.
|
| Growth protocol |
8-week-old male mice were used for generation of CNV. After dilation of the pupils with 5 mg/ml phenylephrine and 5 mg/ml tropicamide eye drops (Santen Pharmaceutical) and instillation of 0.5% proparacaine hydrochloride eye drops (Alcon) for topical anesthesia, laser photocoagulator (Lumenis Inc.) with a slit lamp delivery system was used with a glass coverslip as a contact lens to visualize the retina. Sufficient laser energy (532 nm wavelength, 250 mW power, 100 ms duration, 50 μm spot size) was delivered in 4 locations for each eye (the 3, 6, 9 and 12 o’clock positions of the posterior pole). Only burns that produced a bubble at the time of laser photocoagulation, indicating the rupture of the Bruch membrane, were included in this study. Spots containing hemorrhage at the laser site were excluded from the analysis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
collected using laser capture microdissection (PALM MicroBeam, Carl Zeiss)
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
To administer indicated reagents intravitreally, 5 µg of reagent (5 mg/ml) was injected into the vitreal cavity using the micro-injector fitted with a glass capillary pipette.
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample
|
| |
|
| Submission date |
Oct 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Hosung Bae |
| Organization name |
UC Irvine
|
| Street address |
839 Health Sciences Road Sprague Hall, Room 150
|
| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92697 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE88730 |
Therapeutic effects of Tie2 activation in treatment of neovascular age-related macular degeneration over conventional VEGF blockade. |
|
| Relations |
| BioSample |
SAMN05908302 |
| SRA |
SRX2245369 |
