Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic analysis unveils bona fide molecular signatures of microglia under conditions of homeostasis and viral encephalitis

ABSTRACT: Transcriptomic analysis unveils bona fide molecular signatures of microglia under conditions of homeostasis and viral encephalitis

PROVIDER: PRJNA1130877 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR29680082_1.fastq.gz	Fastqsanger.gz
	SRR29680082_2.fastq.gz	Fastqsanger.gz
	SRR29680083_1.fastq.gz	Fastqsanger.gz
	SRR29680083_2.fastq.gz	Fastqsanger.gz
	SRR29680084_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 36

Similar Datasets

Transcriptomic analysis unveils bona fide molecular signatures of microglia under conditions of homeostasis and viral encephalitis

Project description:Microglia provide a front-line defense against neuroinvasive viral infection, however, determination of their bona fide transcriptional profiles under conditions of health and disease is challenging. Here, we used a combination of experimental tools to delineate the overall transcriptional landscape of microglia during viral infection. By exploiting the ribosomal tagging approach, we developed the concept of enrichment of relevant marker genes by comparing immunoprecipitated RNA with total RNA. Enriched transcripts corresponding to genes expressed in target cells were instrumental in defining bona fide signatures of microglia. With this approach, we generated a comprehensive and accurate transcriptome of microglia at the in situ environment under conditions of health and virus infection. These unified microglial signatures may serve as a benchmark to retrospectively assess ex vivo artefacts from available atlases. Leveraging the microglial translatome, we found enrichment of genes implicated in T-cell activation and cytokine production during the course of VSV infection. These data linked microglia with T-cell re-stimulation and further underscored that microglia shape anti-viral T-cell responses in the brain. Collectively, this study faithfully defines the transcriptional landscape of microglia in steady state and during viral encephalitis and highlights cellular interactions between microglia and T cells that contribute to the control of virus dissemination.

2024-08-09 | GSE271293 | GEO

CD74-NRG1 fusion as an bona fide oncogene

Project description:CD74-NRG1 fusion as an bona fide oncogene

| PRJNA762691 | ENA

Staphylococcus aureus bona fide sRNAs in the model strain HG003

Project description:Staphylococcus aureus bona fide sRNAs in the model strain HG003

| PRJNA414251 | ENA

Staphylococcus aureus bona fide sRNAs in the model strain HG003

Project description:Accurate annotation of regulatory RNAs is a complex task but nevertheless essential as sRNA molecular and functional studies ensue from it. Several formerly considered small RNAs (sRNA) are now known to be parts of UTR transcripts. In light of experimental data, we review hundreds of Staphylococcus aureus putative regulatory RNAs. We pinpoint those that are likely acting in trans and are not expressed from the opposite strand of a coding gene. We conclude that HG003, a NCTC8325 derivative strain, has about 50 bona fide sRNAs, indicating that these RNAs are less numerous than commonly stated.

2018-03-07 | GSE104971 | GEO

An unbiased approach to defining bona fide tumor neoepitopes that mediate cancer immunity

Project description:An unbiased approach to defining bona fide tumor neoepitopes that mediate cancer immunity

| PRJNA681865 | ENA

Generation of Bona Fide Human Induced Trophoblast Stem Cells from Term Umbilical Cord

Project description:Generation of Bona Fide Human Induced Trophoblast Stem Cells from Term Umbilical Cord

| PRJNA1188182 | ENA

Multi-omics unveils host perturbations by tick-borne encephalitis virus for therapeutic targets

Project description:Multi-omics unveils host perturbations by tick-borne encephalitis virus for therapeutic targets

2024-01-09 | PXD048439 |

BioE3 enables the identification of bona fide targets of E3 ligases

Project description:The post-translational modification of proteins by ubiquitination is a highly regulated process that involves a dynamic, three-step enzymatic cascade, where more than 600 E3 ligases play a critical role in recognizing specific substrates for modification. Separating bona fide targets of E3s from E3-interacting proteins remains a major challenge in the field. In this study, we present BioE3, a novel approach for identifying substrates of ubiquitin-like (UbL) E3 ligases of interest. Using BirA-E3 ligase fusion proteins and bioUbLs, the method facilitates site-specific biotinylation of UbL-modified substrates for proteomic identification. We demonstrate that the BioE3 system can identify both known and novel targets of two RING-type ubiquitin E3 ligases: RNF4, known to be involved in DNA damage response and the regulation of PML nuclear bodies, and MIB1, implicated in endocytosis, autophagy, and centrosomal protein homeostasis. We further show the versatility of BioE3 by identifying targets of an organelle-specific E3 (MARCH5) and a relatively uncharacterized E3 (RNF214). Furthermore, we show that BioE3 works with HECT-type E3 ligases and identify novel targets of NEDD4 involved in vesicular trafficking. BioE3 is a powerful tool that enables identification of bona fide substrates of UbL E3 ligases and how they change with chemical perturbations, which may be useful for the emerging applications in targeted protein degradation (TPD). BioE3 may also be applicable for UbLs beyond Ub and SUMO, as well as other E3 ligase classes. The resulting knowledge can shed light on the regulation of cellular processes by the complex UbL network, advancing our understanding of fundamental biological mechanisms.

2024-01-26 | PXD041685 | Pride

Generation of Bona Fide Human Induced Trophoblast Stem Cells from Term Umbilical Cord

Project description:Placentation disorders such as severe fetal growth restriction and preeclampsia have their origin in the first trimester of pregnancy, whereas symptoms typically present later on. To be able to study the pathogenesis of these diseases, there is a need for a reliable model system of early placenta development with known pregnancy outcomes. Therefore, we aimed to optimize the generation of human induced trophoblast stem cells (iTSCs) from term umbilical cord using a direct reprogramming approach. In this, we added three supplements—A-485 (CREBBP/EP300 inhibitor), BMP4 or EPZ-6438 (PRC2 inhibitor)—that could potentially boost iTSC induction. The generated iTSCs fulfilled the criteria for bona fide first-trimester trophoblasts and exhibited transcriptional similarity to TSCs derived from first-trimester placental tissue, while the supplements tested did not substantially enhance iTSC induction.

2025-01-15 | GSE282356 | GEO

Proteomic profiles of bona fide RNA-binding proteins across E. coli growth curve in M9LB media.

Project description:Dynamic interactions between RNA and RNA-binding proteins (RBPs) regulate a broad spectrum of bacterial functions. Here, we have characterised how the RBPome is dynamically rewired during the E. coli life cycle. We applied Orthogonal Organic Phase Separation (OOPS) coupled with an RNase digestion step to shortlist bona fide bacterial RBPs and assessed whether proteins bound RNA differentially express at different cell proliferation stages.

2024-03-20 | PXD043373 | Pride

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