Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Adenovirus transcriptome

ABSTRACT: direct RNA seq of adenovirus mRNA using nanopore

PROVIDER: PRJEB34619 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR3562100_1.fastq.gz	Fastqsanger.gz
	ERR3562101_1.fastq.gz	Fastqsanger.gz
	ERR3562102_1.fastq.gz	Fastqsanger.gz
	ERR3596019_1.fastq.gz	Fastqsanger.gz
	ERR3596019_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 5

Similar Datasets

Novel splicing and open reading frames revealed by long-read direct RNA sequencing of adenovirus transcripts

Project description:Adenovirus is a common human pathogen that relies on host cell processes for transcription and processing of viral RNA and protein production. Although adenoviral promoters, splice junctions, and cleavage and polyadenylation sites have been characterized using low-throughput biochemical techniques or short read cDNA-based sequencing, these technologies do not fully capture the complexity of the adenoviral transcriptome. By combining Illumina short-read and nanopore long-read direct RNA sequencing approaches, we mapped transcription start sites and cleavage and polyadenylation sites across the adenovirus genome. In addition to confirming the known canonical viral early and late RNA cassettes, our analysis of splice junctions within long RNA reads revealed an additional 35 novel viral transcripts. These RNAs include fourteen new splice junctions which lead to expression of canonical open reading frames (ORF), six novel ORF-containing transcripts, and fifteen transcripts encoding for messages that potentially alter protein functions through truncations or fusion of canonical ORFs. In addition, we also detect RNAs that bypass canonical cleavage sites and generate potential chimeric proteins by linking separate gene transcription units. Of these, an evolutionary conserved protein was detected containing the N-terminus of E4orf6 fused to the downstream DBP/E2A ORF. Loss of this novel protein, E4orf6/DBP, was associated with aberrant viral replication center morphology and poor viral spread. Our work highlights how long-read sequencing technologies can reveal further complexity within viral transcriptomes.

2022-08-30 | PXD034464 | Pride

HeLa Adenovirus timecourse

Project description:A timecourse of adenovirus infection of human HeLa cells, using RNA-seq

2012-10-27 | E-MTAB-1277 | biostudies-arrayexpress

Direct RNA sequencing of adenovirus

Project description:Direct RNA sequencing reveals m6A modifications on adenovirus RNA are necessary for efficient splicing

| PRJEB35652 | ENA

The reannotation of adenovirus Ad5

Project description:Non-canonical splicing and novel gene products revealed by direct RNA sequencing of adenovirus transcripts

| PRJEB35667 | ENA

Trial Investigating an Immunostimulatory Oncolytic Adenovirus for Cancer

Project description:This Phase I/II trial evaluates LOAd703 in patients with cancer (pancreatic, biliary, colorectal or ovarian) together with their standard of care chemotherapy or using gemcitabine immune-conditioning. LOAd703 is administered by intratumoral image-guided injections. Maximum 50 patients can be enrolled. LOAd703 is an immunostimulatory gene therapy using an selection replication competent adenovirus as a gene vehicle. The virus is derived from serotype 5 adenovirus with the fiber from serotype 35. It expresses the transgenes trimerized membrane-bound isoleucine zipper (TMZ) TMZ-CD40L and 41BBL under control of a cytomegalovirus (CMV) promoter.

| 2249969 | ecrin-mdr-crc

A new look at adenovirus splicing

2014-03-25 | GSE54583 | GEO

Project description:Direct RNA-seq using Nanopore Sequencing on Embryonic Stem Cells

| PRJNA830448 | ENA

Primary neonatal mouse cardiomyocytes: empty adenovirus infection vs. Mettl14-overexpression adenovirus infection

Project description:The adenovirus carrying Mettl14 gene infects primary neonatal mouse cardiomyocytes, which is in contrast with the primary neonatal mouse cardiomyocytes infected with empty virus. The purpose is to explore the effect of Mettl14 on the global mRNA m6A modification level in primary neonatal rat cardiomyocytes.

2021-12-05 | GSE186358 | GEO

N6-methyladenosine modification is not a general trait of positive-sense RNA viral genomes

Project description:<p>Despite the nuclear localization of the m6A machinery, the genomes of multiple exclusively-cytoplasmic RNA viruses, such as chikungunya (CHIKV) and dengue (DENV), are reported to be extensively m6A-modified. However, these findings are mostly based on m6A-seq, an antibody-dependent technique with a high rate of false positives. Here, we addressed the presence of m6A in CHIKV and DENV RNAs. For this, we combined m6A-seq and the antibody-independent SELECT and nanopore direct RNA sequencing techniques with functional, molecular, and mutagenesis studies. Following this comprehensive analysis, we found no evidence of m6A modification in CHIKV or DENV transcripts. Furthermore, depletion of key components of the host m6A machinery did not affect CHIKV or DENV infection. Moreover, CHIKV or DENV infection had no effect on the m6A machinery’s localization. Our results challenge the prevailing notion that m6A modification is a general feature of cytoplasmic RNA viruses and underscore the importance of validating RNA modifications with orthogonal approaches.</p>

2024-01-25 | MTBLS6978 | MetaboLights

A new look at adenovirus splicing

Project description:Adenovirus type 2 RNA splicing sites were mapped by using deep cDNA sequencing. The majority of the previously identified splice sites were detected. In addition, novel splicing sites were identified Total RNA obtained from four time stages of human primary lung fibroblast cells IMR-90 infected by adenovirus type 2 compared to the control mock-infected by adenovirus type 2.

2014-03-25 | E-GEOD-54583 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data