Whisnant et al. 2020 (PRJNA527127)
General Details
| Title | Ribosome profiling of HSV-1 infected cells |
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| Organism | |
| Number of Samples | 18 |
| Release Date | 2019/03/14 00:00 |
| Sequencing Types | |
| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
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Repository Details
| SRA | SRP188457 |
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| ENA | SRP188457 |
| GEO | |
| BioProject | PRJNA527127 |
Publication
| Title | |
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| Authors | Whisnant AW,Jürges CS,Hennig T,Wyler E,Prusty B,Rutkowski AJ,L'hernault A,Djakovic L,Göbel M,Döring K,Menegatti J,Antrobus R,Matheson NJ,Künzig FWH,Mastrobuoni G,Bielow C,Kempa S,Liang C,Dandekar T,Zimmer R,Landthaler M,Grässer F,Lehner PJ,Friedel CC,Erhard F,Dölken L |
| Journal | Nature communications |
| Publication Date | 2020 Apr 27 |
| Abstract | The predicted 80 open reading frames (ORFs) of herpes simplex virus 1 (HSV-1) have been intensively studied for decades. Here, we unravel the complete viral transcriptome and translatome during lytic infection with base-pair resolution by computational integration of multi-omics data. We identify a total of 201 transcripts and 284 ORFs including all known and 46 novel large ORFs. This includes a so far unknown ORF in the locus deleted in the FDA-approved oncolytic virus Imlygic. Multiple transcript isoforms expressed from individual gene loci explain translation of the vast majority of ORFs as well as N-terminal extensions (NTEs) and truncations. We show that NTEs with non-canonical start codons govern the subcellular protein localization and packaging of key viral regulators and structural proteins. We extend the current nomenclature to include all viral gene products and provide a genome browser that visualizes all the obtained data from whole genome to single-nucleotide resolution. |
| PMC | PMC7184758 |
| PMID | 32341360 |
| 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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| SRR8730340 | PRJNA527127 | Homo sapiens | human foreskin fibroblasts | Ribo-Seq | Harringtonine |  |
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| SRR8730341 | PRJNA527127 | Homo sapiens | human foreskin fibroblasts | Ribo-Seq | Harringtonine | |
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| SRR8730342 | PRJNA527127 | Homo sapiens | human foreskin fibroblasts | Ribo-Seq | Harringtonine | |
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| SRR8730343 | PRJNA527127 | Homo sapiens | human foreskin fibroblasts | Ribo-Seq | Harringtonine | |
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| SRR8730344 | PRJNA527127 | Homo sapiens | human foreskin fibroblasts | Ribo-Seq | Harringtonine | |
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| SRR8730345 | PRJNA527127 | Homo sapiens | human foreskin fibroblasts | Ribo-Seq | Harringtonine | |
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| SRR8730346 | PRJNA527127 | Homo sapiens | human foreskin fibroblasts | Ribo-Seq | Lactimidomycin | |
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| SRR8730347 | PRJNA527127 | Homo sapiens | human foreskin fibroblasts | Ribo-Seq | Lactimidomycin | |
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| SRR8730348 | PRJNA527127 | Homo sapiens | human foreskin fibroblasts | Ribo-Seq | Lactimidomycin | |
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| SRR8730349 | PRJNA527127 | Homo sapiens | human foreskin fibroblasts | Ribo-Seq | Harringtonine | |
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| SRR8730350 | PRJNA527127 | Homo sapiens | human foreskin fibroblasts | Ribo-Seq | Harringtonine | |
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| SRR8730351 | PRJNA527127 | Homo sapiens | human foreskin fibroblasts | Ribo-Seq | Harringtonine | |
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| SRR8730352 | PRJNA527127 | Homo sapiens | human foreskin fibroblasts | Ribo-Seq | Harringtonine | |
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| SRR8730353 | PRJNA527127 | Homo sapiens | human foreskin fibroblasts | Ribo-Seq | Harringtonine | |
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| SRR8730354 | PRJNA527127 | Homo sapiens | human foreskin fibroblasts | Ribo-Seq | Harringtonine | |
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| SRR8730355 | PRJNA527127 | Homo sapiens | human foreskin fibroblasts | Ribo-Seq | Lactimidomycin | |
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| SRR8730356 | PRJNA527127 | Homo sapiens | human foreskin fibroblasts | Ribo-Seq | Lactimidomycin | |
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| SRR8730357 | PRJNA527127 | Homo sapiens | human foreskin fibroblasts | Ribo-Seq | Lactimidomycin | |
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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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