 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 23, 2019 |
| Title |
Control 1 |
| Sample type |
SRA |
| |
|
| Source name |
RPE-choroid-sclera complexes
|
| Organism |
Mus musculus |
| Characteristics |
tissue: RPE-choroid-sclera complexes
disease state: normal eye
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 |
RNA was isolated from the RPE-choroid-sclera complexes following instructions of the manufacturer using Trizol RNA extraction kit (Invitrogen,Carlsbad,CA,USA). RPE-choroid-sclera complexes from 4 eyes were pooled as one sample.
For each sample, the total RNA was sequentially ligated to 3’ and 5’ small RNA adapters.cDNA synthesis and library PCR amplification were then performed by Illumina’s proprietary RT primers and amplification primers. Subsequently, ~134-160 bp PCR amplified fragments (corresponding to 14∼40nt small RNA size range) were extracted and purified from the PAGE gel.
The prepared tsRNAs-seq libraries are finally quantified by Agilent BioAnalyzer 2100 (Agilent Technologies,Santa Clara,CA,USA).The diluted libraries were loaded onto reagent cartridge and forwarded to the sequencing run by using Illumina NextSeq 500 system (Illumina, San Diego, CA,USA) with NextSeq 500/550 V2 kit (Illumina).
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
miRNAs and tsRNAs expression data from samples of normal mice
|
| Data processing |
Raw sequencing data generated form Illumina NextSeq 500 system that pass the Illumina chastity filter are used for the following sequence analysis.
Trimmed reads (trimmed 5’, 3’-adaptor bases) are aligned allowing for 1 mismatch only to the mature tRNA sequences, then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software.
The remaining reads are aligned allowing for 1 mismatch only to miRNA reference sequences with miRDeep2.
Based on alignment statistical analysis (mapping ratio,read length,fragment sequence bias),we determine whether the results can be used for subsequent data analysis. If so, the expression profiling and differentially expressed tRFs & tiRNAs and miRNAs are calculated.
Principal Component Analysis (PCA), Correlation Analysis, Pie plots, Vennplots, Hierarchical clustering, Scatter plots and Volcano plots are performed for the expressed tRF & tiRNA in R or perl environment for statistical computing and graphics.
Genome_build: The mature tRNA libraries and precursor tRNA libraries： tRNA sequences of cytoplasmic were downloaded from GtRNAdb.tRNA sequences of mitochondrial were predicted with tRNAscan-SE software. miRNA:miRbase
Supplementary_files_format_and_content: txt file includes CPM
|
| |
|
| Submission date |
May 22, 2019 |
| Last update date |
May 23, 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 |
GPL19057 |
| Series (1) |
| GSE131646 |
Expression profiles of microRNAs and transfer RNA-derived small RNAs in laser-induced choroidal neovascularization in mice. |
|
| Relations |
| BioSample |
SAMN11831214 |
| SRA |
SRX5883485 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3791655_control1.txt.gz |
14.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
