Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cloning and multi-omic analysis of chimpanzee cytomegalovirus: a resource for comparative functional genomics

ABSTRACT: Cloning and multi-omic analysis of chimpanzee cytomegalovirus: a resource for comparative functional genomics

PROVIDER: PRJNA718552 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR14108137.fastq.gz	Fastqsanger.gz
	SRR14108138.fastq.gz	Fastqsanger.gz
	SRR14108139.fastq.gz	Fastqsanger.gz
	SRR14108155.fastq.gz	Fastqsanger.gz
	SRR14108156.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 18

Similar Datasets

Cloning and Decoding of Chimpanzee Cytomegalovirus - A Resource for Comparative Functional Genomics

Project description:The chimpanzee cytomegalovirus (CCMV) is the closest relative of human CMV (HCMV). Because of the high conservation between these two species and the ability of human cells to fully support CCMV replication, CCMV holds great potential as a model system for HCMV. To make the CCMV genome available for precise and rapid gene manipulation techniques, we captured the genomic DNA of CCMV strain Heberling as a bacterial artificial chromosome(BAC). Selected BAC clones were reconstituted to infectious viruses, growing to similar high titers as parental CCMV. DNA sequencing confirmed the integrity of our clones and led to the identification of two polymorphic loci within the CCMV genome. To re-evaluate the CCMV coding potential, we analyzed the transcriptome and proteome of infected cells and identified several novel ORFs, splice variants, and regulatory RNAs. We further characterized the dynamics of viral gene expression and found that in strong parallel to HCMV, CCMV proteins cluster into five distinct temporal classes. In addition, our datasets revealed that the host response to CCMV infection and the de-regulation of cellular pathways are in line with known hallmarks of HCMV infection. In a first functional experiment, we investigated a proposed frameshift mutation in UL128 that was suspected to restrict CCMV’s cell tropism. In fact, repair of this frameshift re-established productive CCMV infection in endothelial and epithelial cells, expanding the options of CCMV as an infection model. Thus, BAC-cloned CCMV can serve as a powerful tool for systematic approaches in comparative functional genomics, exploiting the close phylogenetic relationship between CCMV and HCMV.

2021-12-20 | PXD027434 | Pride

Cloning and multi-omic analysis of chimpanzee cytomegalovirus: a resource for comparative functional genomics

Project description:We assess the viral and host transcriptome during CCMV BAC virus infection

2021-06-01 | GSE171149 | GEO

NextGen Consortium: The iPSCORE (iPSC Collection for Omic Research) Resource

Project description:NextGen Consortium: The iPSCORE (iPSC Collection for Omic Research) Resource

| PRJNA285374 | ENA

Massively parallel dissection of human accelerated regions in human and chimpanzee neural progenitors [chimpanzee]

Project description:Human accelerated regions (HARs) are evolutionarily conserved sequences that acquired human-specific nucleotide changes and reside in genomic regions associated with unique human traits and disease. The majority of HARs (96%) are noncoding, a few of which have been shown to be functional enhancers. Here, we comprehensively tested human and chimpanzee sequences of HARs (N=714) for enhancer activity using a lentivirus-based massively parallel reporter assay (lentiMPRA) in human and chimpanzee iPSC derived neural progenitors at two differentiation time points. We found that 43% (306/714) function as enhancers and over two-thirds (204/306) showed consistent differences in activity between human and chimpanzee sequences across conditions. We also tested all possible permutations of substitutions in seven HARs and found significant positive and negative interactions. Our study provides a comprehensive resource of functional neurodevelopmental HAR enhancers and shows that multiple interacting sites drive evolutionary activity differences.

2018-02-17 | GSE110759 | GEO

Longitudinal Multi-omic Immune Resource Reveals Dynamic Responses in Healthy Human Aging

Project description:Longitudinal Multi-omic Immune Resource Reveals Dynamic Responses in Healthy Human Aging

| PRJNA1185831 | ENA

Longitudinal Multi-omic Immune Resource Reveals Dynamic Responses in Healthy Human Aging

Project description:Longitudinal Multi-omic Immune Resource Reveals Dynamic Responses in Healthy Human Aging

| PRJNA1185830 | ENA

NextGen Consortium: The iPSCORE (iPSC Collection for Omic Research) Resource - Whole Genome Sequence

Project description:NextGen Consortium: The iPSCORE (iPSC Collection for Omic Research) Resource - Whole Genome Sequence

| PRJNA378453 | ENA

Massively parallel dissection of human accelerated regions in human and chimpanzee neural progenitors [human]

2018-02-17 | GSE110758 | GEO

ChIP-seq analysis of human and chimpanzee iPS cells

Project description:ChIP-seq for H3K4me3 and H3K27me3 were conducted for iPS cells of human-1 (409-B2/HPS0076), human-2 (Nips-B2/HPS0223), chimpanzee-1 (kiku/0138F-1), and chimpanzee-2 (mari/0274F-2). The reads were mapped to the respective genomes (hg38 for human and panTro5 for chimpanzee).

2022-10-26 | GSE201295 | GEO

Transcriptome analysis of human and chimpanzee iPS cells

Project description:mRNA-seq were conducted for iPS cells of human-1 (409-B2/HPS0076), human-2 (Nips-B2/HPS0223), chimpanzee-1 (kiku/0138F-1), and chimpanzee-2 (mari/0274F-2). To compare gene expression levels, the reads were first mapped to the chimpanzee genome (panTro5), and mapped reads were then mapped to the human genome (hg38). Gene expression was anlyzed based on the hg38 annotation.

2022-10-26 | GSE201296 | 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