RMacScw
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB84147 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| ERR14183553_1.fastq.gz | Fastqsanger.gz | |||
| ERR14183553_2.fastq.gz | Fastqsanger.gz | |||
| ERR14161570_1.fastq.gz | Fastqsanger.gz | |||
| ERR14161570_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 6 |
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Project description:Macrovipera schweizeri (Milos viper), genomic and transcriptomic data
| PRJEB84146 | ENA
Project description:Snakebite is a neglected tropical disease and a globally important driver of death and morbidity. Vipers of the genus Macrovipera (Viperidae: Viperinae) are among the snakes of higher medical importance in the Old World. Despite the medical relevance of Macrovipera venoms, the knowledge regarding them is heterogeneously distributed with virtually all works conducted so far focusing on subspecies of Macrovipera lebetinus, while other species within the genus are largely overlooked. Here we present the first proteomic evaluation of the venom from the Greek endemic Milos viper (Macrovipera schweizeri). In line with clinical symptoms typically elicited by Macrovipera envenomations, Milos viper venom primarily comprises coagulotoxic and cytotoxic protein families, such as metalloproteinases (svMP) and serine proteases (svSP). We conducted comparative bioactivity assays on venoms from M. schweizeri and the M. lebetinus subspecies M. lebetinus cernovi, M. lebetinus obtusa, and M. lebetinus turanica, and showed that they all exhibit similarities in levels of cytotoxicity proteolytic activity, and inhibition of prokaryotic growth. Lastly, we compared 1D-SDS-PAGE and RP-HPLC Macrovipera spp. venom profiles, as well as our proteomic data with previously published Macrovipera venom proteomes. The analyses performed reveal that a general venom profile seems to be conserved across blunt-nosed vipers, and that, similarly to M. lebetinus venom, M. schweizeri venom is able to cause significant tissue damage. The present work represents an important starting point to the development of comparative studies across the full taxonomic range of Macrovipera spp., and can potentially help optimize the treatment of envenomations caused by M. schweizeri.
2023-10-24 | PXD043615 | Pride
Project description:This dataset was used to benchmark the Virtual Inference of Protein-activity by Regulon Readout algorithm (VIPER). Despite recent advances in molecular profiling, proteome-wide assessment of protein activity in individual samples remains a highly elusive target. In stark contrast, protein activity quantitation is increasingly critical to the dissection of key regulatory processes and to the elucidation of biologically relevant mechanisms. Importantly, its value extends to the study of drug activity, as most small molecules inhibit activity of their cognate protein substrates without affecting the protein’s or associated mRNA’s abundance. VIPER leverages the increasingly accurate and context specific knowledge of regulatory networks. Specifically, it uses the expression of the transcriptional targets most directly regulated by a given protein in an individual sample as a reporter for the computational inference of its activity.
2013-09-01 | GSE45838 | GEO
Project description:Milos Island hydrothermal vent metagenome
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Project description:This dataset was used to benchmark the Virtual Inference of Protein-activity by Regulon Readout algorithm (VIPER). Despite recent advances in molecular profiling, proteome-wide assessment of protein activity in individual samples remains a highly elusive target. In stark contrast, protein activity quantitation is increasingly critical to the dissection of key regulatory processes and to the elucidation of biologically relevant mechanisms. Importantly, its value extends to the study of drug activity, as most small molecules inhibit activity of their cognate protein substrates without affecting the protein’s or associated mRNA’s abundance. VIPER leverages the increasingly accurate and context specific knowledge of regulatory networks. Specifically, it uses the expression of the transcriptional targets most directly regulated by a given protein in an individual sample as a reporter for the computational inference of its activity. BCL6 knock down experiments were performed in OCI-Ly7 and Pfeiffer GCB-DLBCL cell lines. Both cell lines were maintained in 10% FBS supplemented IMDM medium and transiently transfected with either a BCL6-specific or a non-target control siRNA oligo in triplicate. Total RNA was isolated 48h after transfection and gene expression was profiled on H-GU133plus2 Affymetrix gene chips.
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Project description:Vipera berus berus (European viper)
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Project description:In a post-hoc exploratory analysis of the KING trial to seek molecular markers of outcome, RNAseq was performed on resected tumor specimens at the time of diagnostic surgery before the recurrence from 57 study patients from all arms with adequate selinexor exposure and evidence of either clinical benefit or resistance defined above. RNAseq data were used to infer the activity for 6,203 master regulator proteins using the VIPER algorithm.
2021-12-01 | GSE186332 | GEO