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| Status |
Public on Jul 30, 2013 |
| Title |
Unprecedented alternative splicing and 3 Mb of novel transcribed sequence leads to significant transcript diversity in the transcriptome of the human retina |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
The mRNA repertoire is specific to a given tissue type. This specificity, whether it is in the levels of gene expression or the splicing pattern of the transcripts, is important to study to increase our general knowledge of transcription and alternative splicing, as well as to identify novel coding sequence that can be important for elucidating the mechanisms of disease. We have performed RNA-Seq on three normal human retinal samples and have found a profound level of novel alternative splicing including novel exons, exon skipping, and 3’ and 5’ alternate splice sites. Additionally, we have identified hundreds of novel genes. With so many novel splicing events identified in the retinal transcriptome, we set out to determine if these novel features were indeed real. We developed a high throughput capture set to target 14,696 of the novel features. We found that 99% of the novel features do validate, including those initially detected at a depth of coverage as low as one. These results confirm that the transcripts expressed in the retina are much more diverse than previously identified. The complete human retinal transcriptome described here will be useful for investigators studying multiple aspects of retinal biology and disease.
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| Overall design |
Characterization of alternative splicing in the normal human retinal transcriptome.
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| Contributor(s) |
Farkas MH, Grant GR, White JO, Sousa ME, Pierce EA |
| Citation(s) |
23865674 |
| Submission date |
Aug 31, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Eric Pierce |
| E-mail(s) |
eric_pierce@meei.harvard.edu
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| URL |
http://www.masseyeandear.org/research/ophthalmology/laboratories/oculargenomics/
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| Organization name |
Massachusetts Eye and Ear Infirmary
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| Department |
Ophthalmology
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| Lab |
Ocular Genomics Institute
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| Street address |
243 Charles Street
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (3) |
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| Relations |
| BioProject |
PRJNA174224 |
| SRA |
SRP015336 |
