Minati et al. 2021 (PRJNA705358)
General Details
| Title | One-shot analysis of translated mammalian lncRNAs with AHARIBO |
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| Organism | |
| Number of Samples | 5 |
| Release Date | 2021/02/27 00:00 |
| Sequencing Types | |
| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
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Repository Details
| SRA | SRP308484 |
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| ENA | SRP308484 |
| GEO | GSE167865 |
| BioProject | PRJNA705358 |
Publication
| Title | |
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| Authors | Minati L,Firrito C,Del Piano A,Peretti A,Sidoli S,Peroni D,Belli R,Gandolfi F,Romanel A,Bernabo P,Zasso J,Quattrone A,Guella G,Lauria F,Viero G,Clamer M |
| Journal | eLife |
| Publication Date | 2021 Feb 17 |
| Abstract | A vast portion of the mammalian genome is transcribed as long non-coding RNAs (lncRNAs) acting in the cytoplasm with largely unknown functions. Surprisingly, lncRNAs have been shown to interact with ribosomes, encode peptides, or act as ribosome sponges. These functions still remain mostly undetected and understudied owing to the lack of efficient tools for genome-wide simultaneous identification of ribosome-associated and peptide-producing lncRNAs. Here, we present AHA-mediated RIBOsome isolation (AHARIBO), a method for the detection of lncRNAs either untranslated, but associated with ribosomes, or encoding small peptides. Using AHARIBO in mouse embryonic stem cells during neuronal differentiation, we isolated ribosome-protected RNA fragments, translated RNAs, and corresponding de novo synthesized peptides. Besides identifying mRNAs under active translation and associated ribosomes, we found and distinguished lncRNAs acting as ribosome sponges or encoding micropeptides, laying the ground for a better functional understanding of hundreds of lncRNAs. © 2021, Minati et al. |
| PMC | PMC7932693 |
| PMID | 33594971 |
| DOI |
| Run Accession | Study Accession | Scientific Name | Cell Line | Library Type | Treatment | GWIPS-viz | Trips-Viz | Reads | BAM | BigWig (F) | BigWig (R) | ||
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| SRR13800639 | PRJNA705358 | Mus musculus | mESC | Ribo-Seq | untreated |  |
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| SRR13800640 | PRJNA705358 | Mus musculus | mESC | Ribo-Seq | untreated | |
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| SRR13800641 | PRJNA705358 | Mus musculus | mESC | Ribo-Seq | untreated | |
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| SRR13800642 | PRJNA705358 | Mus musculus | mESC | Ribo-Seq | untreated | |
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| SRR13800643 | PRJNA705358 | Mus musculus | mESC | Ribo-Seq | untreated | |
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| Run Accession | Study Accession | Scientific Name | Cell Line | Library Type | Treatment | GWIPS-viz | Trips-Viz | Reads | BAM | BigWig (F) | BigWig (R) |
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