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| Status |
Public on Jan 04, 2017 |
| Title |
Evolution of A-to-I RNA Editing in Drosophila |
| Organisms |
Drosophila ananassae; Drosophila melanogaster; Drosophila pseudoobscura; Drosophila simulans; Drosophila virilis; Drosophila yakuba |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
We applied microfluidic multiplex PCR and deep sequencing (mmPCR-seq) and targeted RNA sequencing to quantify RNA editing levels at targeted sites in 6 Drosophila species and 8 strains of D. melanogaster.
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| Overall design |
We performed two rounds of targeted RNA sequencing. In the first round, we used mmPCR-seq to amplify and sequence all selected editing loci for all samples from six species. For D. ana, D. pse, and D. vir, we designed additional multiplex primers for ~210 loci that could be amplified in D.mel, D.sim and D.yak but not in D.ana, D.pse and D.vir. We used these primers for the second round of targeted RNA sequencing. We amplified these loci using a regular PCR machine. All samples were then barcoded, pooled and sequenced in one Illumina MiSeq run with 150 bp paired-end reads.
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| Contributor(s) |
Zhang R, Deng P, Jacobson D, Li J |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Aug 25, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jin Billy Li |
| E-mail(s) |
jin.billy.li@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
Genetics
|
| Street address |
300 Pasteur Drive. Alway M303
|
| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platforms (9)
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| GPL13304 |
Illumina HiSeq 2000 (Drosophila melanogaster) |
| GPL13306 |
Illumina HiSeq 2000 (Drosophila simulans) |
| GPL13307 |
Illumina HiSeq 2000 (Drosophila yakuba) |
| GPL13309 |
Illumina HiSeq 2000 (Drosophila ananassae) |
| GPL13310 |
Illumina HiSeq 2000 (Drosophila pseudoobscura) |
| GPL13313 |
Illumina HiSeq 2000 (Drosophila virilis) |
| GPL22419 |
Illumina MiSeq (Drosophila ananassae) |
| GPL22420 |
Illumina MiSeq (Drosophila pseudoobscura) |
| GPL22421 |
Illumina MiSeq (Drosophila virilis) |
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| Samples (52)
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| This SubSeries is part of SuperSeries: |
| GSE86056 |
A-to-I RNA Editing in Drosophila |
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| Relations |
| BioProject |
PRJNA340151 |
| SRA |
SRP082966 |
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