Browse
Submit Data
Databases
API
Help

Dataset Information

25 Views

3 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 1008

Pandoraviruses: Amoeba Viruses with Genomes Up to 2.5 Mb Reaching That of Parasitic Eukaryotes

ABSTRACT: Data from ProteomeXchange, PXD ID: PXD000213. Published as part of Science 2013, 341(6143): 281-286 . From the Abstract: {{i}} ... We report the isolation of two giant viruses, one off the coast of central Chile, the other from a freshwater pond near Melbourne (Australia), without morphological or genomic resemblance to any previously defined virus families. Their micrometer-sized ovoid particles contain DNA genomes of at least 2.5 and 1.9 megabases, respectively. ... {{/i}}

INSTRUMENT(S): Instrument

ORGANISM(S): Pandoravirus, Acanthamoeba_castellanii

DISEASE(S): Not Available

SUBMITTER: Philippe N, et al.

PROVIDER: GPM11210019586 | GPMDB |

REPOSITORIES: GPMDB

ACCESS DATA

Json Xml

Similar Datasets

Proteomic analyses of Pandoravirions

Project description:With its 2.5 Mb DNA genome packed in amphora-shaped particles of bacterium-like dimension (1.2 µm in length, 0.5 µm in diameter), the Acanthamoeba-infecting Pandoravirus salinus remained the most spectacular and intriguing virus since its description in 2013. Following its isolation from shallow marine sediment off the coast of central Chile, that of its relative Pandoravirus dulcis from a fresh water pond near Melbourne, Australia, suggested that they were the first representatives of an emerging worldwide-distributed family of giant viruses. This was further suggested when P. inopinatum discovered in Germany, was sequenced in 2015. We now report the isolation and genome sequencing of three new strains (P. quercus, P.neocaledonia, P. macleodensis) from France, New Caledonia, and Australia. Using a combination of transcriptomic, proteomic, and bioinformatic analyses, we found that these six viruses share enough distinctive features to justify their classification in a new family, the Pandoraviridae, distinct from that of other large DNA viruses.

2018-06-15 | PXD008167 | Pride

Characterisation of a FAK-proximal nuclear interactome

2022-06-01 | PXD025861 | Pride

Characterisation of a Hic-5-proximal nuclear interactome

2022-06-01 | PXD025868 | Pride

Characterisation of a nucleo-adhesome

Project description:In addition to central functions in cell adhesion signalling, integrin-associated proteins have wider roles at sites distal to adhesion receptors. In experimentally defined adhesomes, we noticed that there is clear enrichment of proteins that localise to the nucleus, and conversely, we now report that nuclear proteomes contain a class of adhesome components that localise to the nucleus. We here defined a nucleo-adhesome, providing experimental evidence for a remarkable scale of nuclear localisation of adhesion proteins, establishing a framework for interrogating nuclear adhesion protein functions.

2022-06-01 | PXD025870 | Pride

Quantitative mass spectrometry analysis of 70S ribosomes from iSAT

Project description:The ribosome is one of the largest and the most complicated enzymes in cells, making up 25% of the bacterial cell’s dry mass, and is responsible for protein synthesis in all organisms on earth. In 2013, Jewett et al. reported an in vitro system named integrated rRNA synthesis, ribosome assembly, and translation (iSAT) reaction, which provided a defined system for ribosome biogenesis in a near-physiological environment.In this project, the r-protein composition in 30S and 50S ribosomeal subunits assembled in the iSAT reaction was quantified by mass spectrometry compared to 15N labeled 70S ribosomes.

2023-05-10 | PXD038716 | Pride

Chromatin immunoprecipitation of Oct4 and nanog in mouse embryonic stem cells to enable comparison of regulatory networks obtained by ChIP-Chip and ChIP-PET

Project description:Genome-wide approaches have begun to elucidate the transcriptional and epigenetic regulatory networks responsible for pluripotency in embryonic stem (ES) cells. Chromatin Immunoprecipitation (ChIP) followed either by hybridization to a microarray platform (ChIP-chip), or by DNA sequencing (ChIP-PET), has identified the genomic-binding targets of the ES cell transcription factors Oct4 and Nanog in humans and mice, respectively. A central issue that remains to be resolved is the concordance of the data obtained by these methods, given the differences between the two techniques. Here, we report the identification of the Oct4 and Nanog genomic targets in mouse ES cells by ChIP-Chip and have compared the data with binding data identified previously by ChIP-PET. Binding data have also been combined with Oct4 and Nanog RNAi knockdown expression profiling data in ES cells. Surprisingly, we find a substantial difference between the regions that identified exclusively by one of the two techniques. In both studies, however, targets identified by either technique contain a number of genes that are differentially expressed on Oct4 or Nanog knockdown, and have been implicated in cell-fate determination events. This study provides a comparison between the data obtained by different genomic platform, and offers a more comprehensive picture of the stem cell transcriptional network.

2008-11-04 | E-TABM-410 | biostudies-arrayexpress

DNA methylation profiles of human bone samples

Project description:The main goal of the study was to measure the epigenetic age (also known as DNA methylation age) of human bone tissue and to relate it to chronological age. Toward this end, we used the epigenetic clock software described in Horvath S (2013) DNA methylation age of human tissues and cell types. Genome Biology.2013, 14:R115. DOI: 10.1186/10.1186/gb-2013-14-10-r115 PMID: 24138928 Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 486,000 CpGs. The trabecular bone pieces were obtained from the central part of the femoral head of Spanish (Caucasian) patients with hip fractures (due to osteoporosis) or subjects with osteoarthritis. About 85% of the cell population in this bone tissue are osteocytes and the remainder are osteoblasts, bone marrow, etc.

2015-06-03 | E-GEOD-64490 | biostudies-arrayexpress

Characterisation of FAK- and ILK-dependent nuclear subproteomes

Project description:In addition to central functions in cell adhesion signalling, integrin-associated proteins have wider roles at sites distal to adhesion receptors. In experimentally defined adhesomes, there is clear enrichment of proteins that localise to the nucleus, and conversely, we now report that nuclear proteomes contain a subset of adhesome components that localise to the nucleus of cancer cells. We have defined a nucleo-adhesome, providing evidence for the remarkable scale of nuclear localisation of adhesion proteins, establishing a framework for interrogating nuclear adhesion protein functions. Here, we examined whether there was a role for focal adhesion kinase (FAK) and integrin-linked kinase (ILK) in specifying the nucleo-adhesome and, more broadly, the nuclear proteome in squamous cell carcinoma (SCC) cancer cells.

2022-06-09 | PXD020179 | Pride

Genome-wide map of cohesin positions in RT112 bladder cancer cells

Project description:Bladder cancer is one of the most common genitourinary malignancies worldwide. It is a heterogeneous disease at the clinical, pathological, and genetic levels. In an exome-sequencing study of bladder cancer, we identified genes mutated in bladder cancer coding for proteins involved in chromatin modification, cell division, and DNA repair. STAG2, a constituent of the cohesin complex, was commonly mutated or lost, mainly in tumors of low stage or grade. Loss of STAG2 expression was often observed in genomically stable tumors, suggesting that STAG2 may act as a tumor suppressor through mechanisms other than chromosome segregation (Balbás-Martínez et al. 2013). In addition to mediating sister chromatid cohesion, cohesin plays a central role in DNA looping and organization of the genome into Topologically Associating Domains (TADs). Two variant cohesin complexes that contain either STAG1 or STAG2 are present in all cell type. Here we addressed their genome wide binding in bladder cancer cells.

2021-03-15 | GSE111913 | GEO

Transcriptional profiling of ovarian cancer samples with different grades

Project description:We have previously demonstrated (Calura E et al., 2013) that different epithelial ovarian cancer (EOC) histotypes have different, defined characteristics at the microRNA level, which might highlight a different originating tissue for the disease. From these results we have invesigated whole-genome gene expression on a cohort of samples with different FIGO grades, in order to investigate the link between the tumor grade and gene expression.

2014-12-12 | E-MTAB-1814 | 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