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| Status |
Public on Nov 18, 2021 |
| Title |
Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling (Nanopore) |
| Organisms |
Saccharomyces cerevisiae; Caenorhabditis elegans; Drosophila melanogaster; Homo sapiens; human feces metagenome |
| Experiment type |
Other
|
| Summary |
Pseudouridine (Ψ) is an abundant mRNA modification in the mammalian transcriptome, but its function has remained elusive due to the difficulty of transcriptome-wide mapping. We develop nanopore native RNA sequencing for quantitative Ψ analysis that utilizes native content training, machine learning model prediction, and single read coordination. We find interferon inducible Ψ modifications in the interferon stimulated gene transcripts, consistent with a role of Ψ in the efficacy of mRNA vaccines.
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| Overall design |
Nanopore seq of two biological replicates of untreated, IFN gamma treated and IFN beta treated HeLa cells. Nanopore seq of rRNA mixture from human, yeast, C.elegans, Drosophila and stool microbiome
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| Contributor(s) |
Huang S, Katanski CD, Dersh D, Zhang W, Dai Q, Yewdell J, Eren AM, Pan T |
| Citation(s) |
34872593 |
| |
| Submission date |
Jul 22, 2021 |
| Last update date |
Feb 15, 2022 |
| Contact name |
Tao Pan |
| E-mail(s) |
taopan@uchicago.edu
|
| Phone |
(773) 702-4179
|
| Organization name |
University of Chicago
|
| Department |
Biochemistry and Molecular Biology
|
| Street address |
929 E. 57th Street
|
| City |
Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60637 |
| Country |
USA |
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| Platforms (2) |
| GPL24106 |
MinION (Homo sapiens) |
| GPL30425 |
MinION (Caenorhabditis elegans; Drosophila melanogaster; Homo sapiens; human feces metagenome; Saccharomyces cerevisiae) |
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| Samples (7)
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| This SubSeries is part of SuperSeries: |
| GSE180656 |
Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling |
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| Relations |
| BioProject |
PRJNA749032 |
| SRA |
SRP329477 |
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