Hu et al. 2021 (PRJNA646476)
General Details
| Title | Identification of translated small open reading frames in lymphocytes |
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| Organism | |
| Number of Samples | 10 |
| Release Date | 2020/07/15 00:00 |
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| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
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Repository Details
| SRA | SRP272078 |
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| ENA | SRP272078 |
| GEO | |
| BioProject | PRJNA646476 |
Publication
| Title | |
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| Authors | Hu F,Lu J,Matheson LS,Díaz-Muñoz MD,Saveliev A,Xu J,Turner M |
| Journal | Bioinformatics (Oxford, England) |
| Publication Date | 2021 Oct 11 |
| Abstract | The annotation of small open reading frames (smORFs) of <100 codons (<300 nucleotides) is challenging due to the large number of such sequences in the genome. In this study, we developed a computational pipeline, which we have named ORFLine, that stringently identifies smORFs and classifies them according to their position within transcripts. We identified a total of 5744 unique smORFs in datasets from mouse B and T lymphocytes and systematically characterized them using ORFLine. We further searched smORFs for the presence of a signal peptide, which predicted known secreted chemokines as well as novel micropeptides. Four novel micropeptides show evidence of secretion and are therefore candidate mediators of immunoregulatory functions. Freely available on the web at https://github.com/boboppie/ORFLine. Supplementary data are available at Bioinformatics online. © The Author(s) 2021. Published by Oxford University Press. |
| PMC | PMC8504629 |
| PMID | 33970232 |
| 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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| SRR12228554 | PRJNA646476 | Mus musculus | LN CD19+ B cells | Ribo-Seq |  |
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| SRR12228555 | PRJNA646476 | Mus musculus | LN CD19+ B cells | Ribo-Seq | |
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| SRR12228556 | PRJNA646476 | Mus musculus | LN CD19+ B cells | Ribo-Seq | |
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| SRR12228557 | PRJNA646476 | Mus musculus | LN CD19+ B cells | Ribo-Seq | |
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| SRR12228558 | PRJNA646476 | Mus musculus | LN CD19+ B cells | Ribo-Seq | |
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| SRR12228559 | PRJNA646476 | Mus musculus | LN CD19+ B cells | Ribo-Seq | |
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| SRR12228560 | PRJNA646476 | Mus musculus | LN CD19+ B cells | Ribo-Seq | |
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| SRR12228561 | PRJNA646476 | Mus musculus | LN CD19+ B cells | Ribo-Seq | |
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| SRR12228562 | PRJNA646476 | Mus musculus | LN CD19+ B cells | Ribo-Seq | |
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| SRR12228563 | PRJNA646476 | Mus musculus | LN CD19+ B cells | Ribo-Seq | |
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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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