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| Status |
Public on Nov 04, 2019 |
| Title |
Tissue- and Species-Specific Patterns of RNA metabolism in Post-Mortem Mammalian Retina and Retinal Pigment Epithelium |
| Organisms |
Papio anubis; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Accurate analysis of gene expression in human tissues using RNA Sequencing is often dependent on the quality of source material. One major source of variation in mRNA quality is post-mortem time. While it is known that individual transcripts show differential post-mortem stability, few studies have directly and comprehensively analyzed mRNA stability following death, and in particular, the extent to which tissue- and species-specific factors influence post-mortem mRNA stability are poorly understood. This knowledge is particularly important for ocular tissues studies, where tissues obtained post-mortem are frequently used for research or therapeutic applications. To directly investigate this question, we profiled mRNA levels in both neuroretina and retinal pigment epithelium (RPE) from mouse and baboon over a series of post-mortem intervals. We found substantial changes in gene expression as early as 15 minutes in the mouse and as early as three hours in the baboon eye tissues. Importantly, our findings demonstrate both tissue- and species- specific patterns of RNA metabolism, by identifying a set of genes that are either rapidly degraded or very stable in both species and/or tissues. Taken together, the data from this study lays the foundation for understanding RNA regulation post-mortem, and provide novel insights into RNA metabolism in the tissues of the mammalian eye.
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| Overall design |
Mice at different post-mortem intervals were used to collect retina and RPE/choroid tissues.
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| Contributor(s) |
Kallestad L |
| Citation(s) |
31616038 |
| Submission date |
Aug 05, 2019 |
| Last update date |
Nov 04, 2019 |
| Contact name |
Les Kallestad |
| Organization name |
University of California Irvine
|
| Department |
Ophthalmology
|
| Lab |
Krzysztof Palczewski
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| Street address |
829 Health Sciences Rd
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| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92617 |
| Country |
USA |
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| Platforms (2) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL27009 |
Illumina NextSeq 500 (Papio anubis) |
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| Samples (106)
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| Relations |
| BioProject |
PRJNA558787 |
| SRA |
SRP217513 |
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