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| Status |
Public on May 20, 2024 |
| Title |
High-density resolution of the Kaposi’s Sarcoma associated Herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing [iSLK-WTBAC-PCR-cDNA-Seq] |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
Kaposi’s sarcoma-associated herpesvirus is etiologic agent of Kaposi’s Sarcoma and two B-cell malignancies. Recent advancements in sequencing technologies have led to high resolution transcriptomes for several human herpesviruses that densely encode genes on both strands. However, for KSHV progress remained limited due to overall low percentage of KSHV transcripts even during lytic replication. To address this challenge, we have developed a target enrichment method to increase the KSHV-specific reads for both short- and long-read sequencing platforms. Furthermore, we combined this approach with the Transcriptome Resolution through Integration of Multi-platform Data (TRIMD) pipeline developed previously to annotate transcript structures. TRIMD first builds a scaffold based on long-read sequencings and validates each transcript feature with supporting evidence from Illumina RNA-Seq and deepCAGE sequencing data. Our stringent innovative approach identified 994 unique KSHV transcripts, thus providing the first high-density KSHV lytic transcriptome. We describe a plethora of novel coding and non-coding KSHV transcript isoforms with alternative untranslated regions, splice junctions and open-reading frames, thus providing deeper insights on gene expression regulation of KSHV. Interestingly, as described for Epstein-Barr Virus, we identified transcription start sites that augment long-range transcription and may increase the number of latency-associated genes potentially expressed in KS tumors.
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| Overall design |
Multi-platform RNA sequencing of reactivated BCBL-1 cells to study the transcriptome of Kaposi's Sarcoma associated Herpesvirus on a high resolution.
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| Contributor(s) |
Shekhar R, O'Grady T, Keil N, Feswick A, Moraga D, Tibbets SA, Flemington EK, Renne R |
| Citation(s) |
38922687 |
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| Submission date |
Dec 18, 2023 |
| Last update date |
Aug 16, 2024 |
| Contact name |
Rolf Renne |
| E-mail(s) |
[email protected]
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| Organization name |
University of Florida
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| Street address |
1200 Newell Dr.
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| City |
Gainesville |
| State/province |
FL |
| ZIP/Postal code |
32610 |
| Country |
USA |
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| Platforms (1) |
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| Samples (3) |
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| This SubSeries is part of SuperSeries: |
| GSE250435 |
High-density resolution of the Kaposi’s Sarcoma associated Herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing |
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| Relations |
| BioProject |
PRJNA1054068 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE250434_RAW.tar |
410.4 Mb |
(http)(custom) |
TAR (of GTF) |
SRA Run Selector |
| Raw data are available in SRA |
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