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SRX22920576: GSM7979050: 24h Induced BCBL-1; Homo sapiens; OTHER
1 OXFORD_NANOPORE (PromethION) run: 1.7M spots, 2.4G bases, 2.1Gb downloads

External Id: GSM7979050_r1
Submitted by: University of Florida
Study: High-density resolution of the Kaposi's Sarcoma associated Herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing [BCBL-1-direct-cDNA-Seq]
show Abstracthide Abstract
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. 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.
Sample: 24h Induced BCBL-1
SAMN38882161 • SRS19888536 • All experiments • All runs
Organism: Homo sapiens
Library:
Name: GSM7979050
Instrument: PromethION
Strategy: OTHER
Source: TRANSCRIPTOMIC
Selection: other
Layout: SINGLE
Construction protocol: Total RNA was isolated from cultured cells using the TRIzol reagent (Ambion) as per manufacturer's protocol. Poly(A)-tailed RNA was selected from 75 μg of each RNA sample using Dyna Beads mRNA purification kit (Invitrogen, Catalog No. 61006). Direct-cDNA sequencing libraries were prepared by using SQK-DCS109 (ONT) library preparation kit with 100 ng of each polyA-selected RNA sample.
Runs: 1 run, 1.7M spots, 2.4G bases, 2.1Gb
Run# of Spots# of BasesSizePublished
SRR272423251,674,1292.4G2.1Gb2024-05-20

ID:
30985463

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