Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

HHV-5 (HCMV) genomes

ABSTRACT: Sequences of complete human cytomegalovirus genomes from infected cell cultures and clinical specimens

PROVIDER: PRJEB2153 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR011942.fastq.gz	Fastqsanger.gz
	ERR011943.fastq.gz	Fastqsanger.gz
	ERR011944.fastq.gz	Fastqsanger.gz

Items per page:

1 - 3 of 3

Similar Datasets

HHV-5 (HCMV) genomes

Project description:High-throughput sequence analysis of variants of human cytomegalovirus strains Towne and AD169

| PRJEB2152 | ENA

Clinical HCMV

Project description:Human cytomegalovirus sequences from clinical samples

| PRJEB22095 | ENA

ATRX reduces the accessibility of HCMV genomes during lytic infections

Project description:We investigated the role of the chromatin remodeling protein ATRX on chromatin accessibility of HCMV genomes during the IE phase of lytic infections

2024-08-28 | GSE262839 | GEO

miRNA array analysis in HCMV and HHV-6 infected human fibroblasts

Project description: Not available

| S-BSST598 | biostudies-other

From genomes to cultures: a parasitic Nanoarchaota system from a Yellowstone geothermal spring.

Project description:From genomes to cultures: a parasitic Nanoarchaota system from a Yellowstone geothermal spring.

2016-05-04 | MSV000079705 | MassIVE

Comprehensive Annotations of Human Herpesvirus 6A and 6B Genomes Reveals Novel and Conserved Genomic Features

Project description:Human herpesvirus 6 (HHV-6) A and B are highly ubiquitous betaherpesviruses, infecting the majority of the human population. Like other herpesviruses, our understanding of their protein coding potential is far from complete. Here we use ribosome profiling and RNA-seq to experimentally define the HHV-6 translation products and to follow their temporal expression. We identified hundreds of new open reading frames (ORF)s, including many upstream ORFs (uORF)s and internal ORFs (iORF)s, generating a complete atlas of HHV-6 translation products. Integrating data from human cytomegalovirus we uncover numerous uORFs and iORFs that are conserved between beta herpesviruses and we show uORFs are specifically enriched in late viral genes. We also identified three highly abundant viral long non coding RNAs (lncRNA)s and we show one of these lncRNAs generate a non-polyadenylated stable intron that is conserved between all sequenced beta herpesviruses. Overall, this work uncovers the full complexity of the HHV-6 family genomes and highlights novel features that are conserved between beta herpesviruses, providing a resource for future functional studies.

2019-08-13 | GSE135363 | GEO

Woolly mammoth genomes

Project description:Complete genome sequences for two woolly mammoths

| PRJEB7929 | ENA

HCMV paediatric cases

Project description:Longitudinal whole genome sequencing of cytomegalovirus from children

| PRJEB12814 | ENA

Next Generation Annotation of prokarotic genomes with EuGene-P: application to Sinorhizobium meliloti 2011

Project description:With a view to re-annotate the genome sequence of the nitrogen fixing bacterium Sinorhizobium meliloti, we generated oriented sequences of transcripts. To cover a large number of expressed genes we prepared RNA from bacteria grown in three very different physiological conditions including bacteria grown in liquid cultures (in both exponential and stationary growth phases) and from 10-day-old nodules in which bacteria were differentiated in nitrogen fixing bacteroids. The transcripts sequences were then integrated into EuGene-P, a new prokaryotic genome annotation tool able to integrate high throughput data including oriented RNA-Seq data directly into the prediction process, which led to the production of an accurate and complete annotation of the genome of S. meliloti strain 2011.

2013-04-01 | GSE44083 | GEO

A measles virus collective infectious unit that caused lethal human brain disease includes many locally restricted and few widespread copy-back defective genomes

Project description:During virus replication in cultured cells, copy-back defective viral genomes (cbDVG) can arise. CbDVG are powerful inducers of innate immune responses in vitro, but their occurrence and impact on natural infections of human hosts remain poorly defined. We asked whether cbDVG were generated in the brain of a patient who succumbed to subacute sclerosing panencephalitis (SSPE) about 20 years after acute measles virus (MeV) infection. Previous analyses of 13 brain specimens of this patient indicated that a collective infectious unit (CIU) drove lethal MeV spread. In this study, we identified 276 replication-competent cbDVG species, each present in over 100 copies in the brain. Six species were detected in multiple forebrain locations, implying that they travelled long-distance with the CIU. The cbDVG to full-length genomes ratio was often close to 1 (0.6-1.74). Most cbDVG were 324-2000 bases in length, corresponding to 2-12% of the full-length genome; all are predicted to have complementary terminal sequences. If improperly encapsidated, these sequences have the potential to form double-stranded structures that can induce innate immune responses. To assess this, we examined the transcriptome of all brain specimens. Several interferon- and inflammatory response genes were upregulated, but upregulation levels did not correlate with cbDVG levels in the specimens. Thus, the CIU that drove MeV pathogenesis in this brain includes, in addition to two complementary full-length genome populations, many locally restricted and few widespread cbDVG species. The widespread cbDVG species may have been positively selected but how they impacted pathogenesis remains to be determined.

2024-10-01 | GSE272560 | GEO

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