Thomaidou et al. 2021 (PRJNA703954)
General Details
| Title | Long-RNA sequencing and ribosome profiling of inflamed beta-cells reveal an extensive translatome landscape |
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| Organism | |
| Number of Samples | 30 |
| Release Date | 2021/02/22 00:00 |
| Sequencing Types | |
| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
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Repository Details
| SRA | SRP307513 |
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| ENA | SRP307513 |
| GEO | GSE167223 |
| BioProject | PRJNA703954 |
Publication
| Title | |
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| Authors | Thomaidou S,Slieker RC,van der Slik AR,Boom J,Mulder F,Munoz-Garcia A,'t Hart LM,Koeleman B,Carlotti F,Hoeben RC,Roep BO,Mei H,Zaldumbide A |
| Journal | Diabetes |
| Publication Date | 2021 Oct |
| Abstract | Type 1 diabetes (T1D) is an autoimmune disease characterized by autoreactive T cell-mediated destruction of the insulin-producing pancreatic β-cells. Increasing evidence suggest that the β-cells themselves contribute to their own destruction by generating neoantigens through the production of aberrant or modified proteins that escape central tolerance. We recently demonstrated that ribosomal infidelity amplified by stress could lead to the generation of neoantigens in human β-cells, emphasizing the participation of nonconventional translation events in autoimmunity, as occurring in cancer or virus-infected tissues. Using a transcriptome-wide profiling approach to map translation initiation start sites in human β-cells under standard and inflammatory conditions, we identify a completely new set of polypeptides derived from noncanonical start sites and translation initiation within long noncoding RNA. Our data underline the extreme diversity of the β-cell translatome and may reveal new functional biomarkers for β-cell distress, disease prediction and progression, and therapeutic intervention in T1D. © 2021 by the American Diabetes Association. |
| PMC | |
| PMID | 34554924 |
| 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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| SRR13762817 | PRJNA703954 | Homo sapiens | H1 | Ribo-Seq | Harringtonine |  |
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| SRR13762818 | PRJNA703954 | Homo sapiens | H1 | Ribo-Seq | Harringtonine | |
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| SRR13762819 | PRJNA703954 | Homo sapiens | H1 | Ribo-Seq | Harringtonine | |
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| SRR13762820 | PRJNA703954 | Homo sapiens | H1 | Ribo-Seq | Harringtonine | |
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| SRR13762821 | PRJNA703954 | Homo sapiens | H1 | Ribo-Seq | Harringtonine | |
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| SRR13762822 | PRJNA703954 | Homo sapiens | H1 | Ribo-Seq | Harringtonine | |
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| SRR13762823 | PRJNA703954 | Homo sapiens | H1 | RNA-Seq | |
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| SRR13762824 | PRJNA703954 | Homo sapiens | H1 | RNA-Seq | |
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| SRR13762825 | PRJNA703954 | Homo sapiens | H1 | RNA-Seq | untreated | |
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| SRR13762826 | PRJNA703954 | Homo sapiens | H1 | RNA-Seq | untreated | |
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| SRR13762827 | PRJNA703954 | Homo sapiens | H1 | RNA-Seq | |
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| SRR13762828 | PRJNA703954 | Homo sapiens | H1 | RNA-Seq | untreated | |
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| SRR13762829 | PRJNA703954 | Homo sapiens | H1 | Ribo-Seq | Harringtonine | |
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| SRR13762830 | PRJNA703954 | Homo sapiens | H1 | Ribo-Seq | Harringtonine | |
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| SRR13762831 | PRJNA703954 | Homo sapiens | H1 | Ribo-Seq | Harringtonine | |
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| SRR13762832 | PRJNA703954 | Homo sapiens | H1 | Ribo-Seq | Harringtonine | |
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| SRR13762833 | PRJNA703954 | Homo sapiens | H1 | Ribo-Seq | Harringtonine | |
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| SRR13762834 | PRJNA703954 | Homo sapiens | H1 | Ribo-Seq | Harringtonine | |
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| SRR13762835 | PRJNA703954 | Homo sapiens | H1 | RNA-Seq | |
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| SRR13762836 | PRJNA703954 | Homo sapiens | H1 | RNA-Seq | |
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| SRR13762837 | PRJNA703954 | Homo sapiens | H1 | RNA-Seq | untreated | |
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| SRR13762838 | PRJNA703954 | Homo sapiens | H1 | RNA-Seq | untreated | |
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| SRR13762839 | PRJNA703954 | Homo sapiens | H1 | RNA-Seq | |
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| SRR13762840 | PRJNA703954 | Homo sapiens | H1 | RNA-Seq | untreated | |
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| SRR13762841 | PRJNA703954 | Homo sapiens | H1 | RNA-Seq | Harringtonine | |
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| SRR13762842 | PRJNA703954 | Homo sapiens | H1 | RNA-Seq | Harringtonine | |
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| SRR13762843 | PRJNA703954 | Homo sapiens | H1 | RNA-Seq | Harringtonine | |
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| SRR13762844 | PRJNA703954 | Homo sapiens | H1 | RNA-Seq | Harringtonine | |
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| SRR13762845 | PRJNA703954 | Homo sapiens | H1 | RNA-Seq | Harringtonine | |
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| SRR13762846 | PRJNA703954 | Homo sapiens | H1 | RNA-Seq | Harringtonine | |
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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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