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| Status |
Public on Oct 01, 2022 |
| Title |
Profiling the retinal microRNA (miRNA) transcriptomes in a rat model of oxygen-induced retinopathy (OIR) by next-generation sequencing |
| Organism |
Rattus norvegicus |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Purpose: The study aimed to determine the transcriptome profile of retinal miRNA in a Sprague Dawley (SD) rat model of oxygen-induced retinopathy
Methods: The newborn rats in OIR group were subjected to daily cycles of 80% oxygen for 21 hours and room air for 3 hours in a customised chamber for 14 days (postnatal day 14, P14), then return to room air for 15 days (postnatal day 29, P29). The newborn rats in sham group were housed in room air for 14 days. Retinal miRNA expression profiles of OIR or sham rats at P14 or OIR rats at P29 were generated by deep sequencing, in triplicate, using Illumina Hiseq-2500 RNA-seq platform. Briefly, the sequence reads from all samples were analysed for overall quality, screened for the presence of any contaminants and trimmed accordingly. The cleaned sequence reads were then processed through the quantification modules miRDEEP2 ver2.0.0.7 pipeline for known miRNA expression profiling. Rat miRNAs from miRBASE release21 were used for mapping and quantification. Differential miRNA expression analysis was undertaken using voom bioconductor package (https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf).
Results: A total of 465 miRNAs were identified in the rat retina. The miRNAs with significantly altered levels (P<0.05) were identified in OIR rats at P14 compared with the sham controls or OIR rats at P29. Among those altered miRNAs, seven miRNAs were down-regulated in OIR rats at P14 with Log2 (Fold Change) < -1 fold, and no miRNAs were up-regulated. Additionally, the expression of these down-regulated miRNAs in OIR rats at P14 was restored at P29 after they were exposed to room air.
Conclusion: Our study represents the first detailed analysis of retinal miRNA expression profile in rat model of OIR by miRNA-NGS technology.
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| Overall design |
The expression profiles of retinal miRNA from OIR or sham rats were generated by deep sequencing, in triplicate, using Illumina Hiseq-2500 RNA-seq platform.
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| Contributor(s) |
Wang J, Ling D, Tu L, Singh V, Riaz M, Liu G |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Oct 05, 2017 |
| Last update date |
Oct 01, 2022 |
| Contact name |
vikrant singh |
| E-mail(s) |
vikrantvicky.1987@gmail.com
|
| Organization name |
Royal college of Surgeons in Ireland
|
| Street address |
31 York Street
|
| City |
Dublin |
| State/province |
Ireland |
| ZIP/Postal code |
D02YN77 |
| Country |
Ireland |
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| Platforms (1) |
| GPL18694 |
Illumina HiSeq 2500 (Rattus norvegicus) |
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| Samples (9)
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| Relations |
| BioProject |
PRJNA413308 |
| SRA |
SRP119448 |
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