Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell RNA-sequencing of wildtype (ME49∆KU80) or mutant (ME49∆KU80∆BFD1) parasites under unstressed or stressed conditions

ABSTRACT: Single-cell RNA-sequencing of wildtype (ME49∆KU80) or mutant (ME49∆KU80∆BFD1) parasites under unstressed or stressed conditions

PROVIDER: PRJNA546578 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Single-cell RNA-sequencing of wildtype (ME49∆KU80) or mutant (ME49∆KU80∆BFD1) parasites under unstressed or stressed conditions

Project description:To profile cell-cycle progression and the asynchronous process of differentiation, we performed single-cell RNA-sequencing (scRNA-Seq) of T. gondii using Seq-Well (Gierahn et al., 2017). Wild-type or ∆BFD1 parasites were grown under unstressed or stressed conditions (24, 48 or 72 h), mechanically released from host cells, and analyzed.

2020-01-16 | GSE132238 | GEO

Host gene expression response to Toxoplasma gondii infection is not different between RH?ku80 and RH?ku80?rop5 parasites.

Project description:The normally virulent type-I RH parasite is rendered avirulent when lacking ROP5. The avirulent phenotype is a consequence of interaction with the host innate immune system. We sought to understand if ROP5 alters host gene expression in order to escape host defenses. We saw no gene expression differences between host cells infected with wt (RH?ku80) or RH?ku80?rop5 parasites. We have included uninfected HFF samples that were harvested in parallel with the infected samples. Host gene expression in response to infection with Toxoplasma gondii. Two independent samples per sample type. Three sample types: HFF infected with RH?ku80, HFF infected with RH?ku80?rop5, and uninfected HFF.

2012-09-13 | E-GEOD-32104 | biostudies-arrayexpress

RNA-sequencing of parasites overexpressing conditionally stabilized BFD1 to identify genes regulated by BFD1

Project description:WT (ME49∆KU80), ∆BFD1, or ∆BFD1/DD-BFD1-Ty parasites were treated with the stabilizing ligand Shield-1 (all three) or vehicle alone (WT and ∆BFD1/DD-BFD1-Ty) to identify genes differentially regulated by overexpression of BFD1.

2020-01-16 | GSE139537 | GEO

Host gene expression response to Toxoplasma gondii infection is not different between RH∆ku80 and RH∆ku80∆rop5 parasites

Project description:The normally virulent type-I RH parasite is rendered avirulent when lacking ROP5. The avirulent phenotype is a consequence of interaction with the host innate immune system. We sought to understand if ROP5 alters host gene expression in order to escape host defenses. We saw no gene expression differences between host cells infected with wt (RH∆ku80) or RH∆ku80∆rop5 parasites. We have included uninfected HFF samples that were harvested in parallel with the infected samples.

2012-09-13 | GSE32104 | GEO

Stage-specific RNA-sequencing to identify genes differentially expressed between Toxoplasma gondii tachyzoites and bradyzoites

Project description:Using a differentiation reporter strain, unstressed parasites (tachyzoites) or stressed, reporter positive parasites (bradyzoites) were isolated by flow cytometry and analyzed for differential gene expression.

2020-01-16 | GSE132248 | GEO

Ku80/Ku70 complex associated RNA in HEK293T cells

Project description:We report the Ku80/Ku70 complex associated RNA in HEK293T cells using RNA-seq following PAR-Clip.

2024-04-09 | GSE219220 | GEO

TgCrk2 interactome in Toxoplasma gondii RH and ME49 parasites

Project description:Although apicomplexans lack conventional R-point regulators, presence of the quiescent G1 forms of 43 parasites, including mature T. gondii bradyzoites suggests that a functional RESTRICTION checkpoint 44 exists in apicomplexan parasites. We showed that Cdk-related G1 kinase TgCrk2 forms alternative 45 complexes with atypical cyclins (TgCycP1, TgCycP2 and TgCyc5) in the rapidly dividing developmentally 46 incompetent RH and slower dividing developmentally competent ME49 tachyzoites and bradyzoites. 47 Examination of individual cyclins verified the correlation of cyclin expression with growth dependence and 48 development capacity of type I RH and type II ME49 strains. We demonstrated that rapidly dividing RH 49 tachyzoites are dependent on TgCycP1 and expression of TgCycP1 interferes with bradyzoite 50 differentiation. By using an auxin-induced degradation (AID) model, we established that TgCycP2 51 regulates G1 duration in the developmentally competent ME49 tachyzoites but not in the developmentally 52 incompetent RH tachyzoites. We also tested the functions of TgCycP2 and TgCyc5 in alkaline induced in 53 vitro model and in ex vivo model of spontaneous bradyzoite differentiation (rat embryonic brain cells). 54 Based on functional and global gene expression analyses, we determined that TgCycP2 also regulates 55 bradyzoite replication, while stress- or host-induced TgCyc5 was critical for efficient bradyzoite conversion 56 and tissue cyst maturation.

2022-08-12 | PXD033109 | Pride

Transcriptome of Plasmodium berghei wildtype parasites and KIN knockout parasites [RNA-seq]

Project description:The ability to sense, respond and adapt to changes in nutrient availability is a survival requisite. This might be particularly important for malaria parasites, which encounter major alterations in nutrients levels throughout infection. How these parasites deal with nutrient fluctuations and maintain infection without killing their hosts before transmission remains unknown. Here, we show that blood-stage malaria parasites respond to dietary-restriction through a rearrangement of their transcriptome accompanied by a significant reduction in their multiplication rate. A kinome analysis combined with chemical and genetic approaches identified KIN, a putative AMP-activated kinase homologue, as a master regulator that senses host nutrients both in vitro and in vivo, and mediates the transcriptional response to the host nutritional status. Diet-responsive genes include the plant-like ApiAP2 transcription regulators, which appear to act as downstream effectors of KIN. Overall, these findings reveal key components of a parasite nutrient-sensing mechanism that is critical to modulate replication and virulence in malaria parasites.

2017-07-14 | GSE69627 | GEO

A sexually dimorphic "pre-stressed" translational signature in CA3 pyramidal neurons of BDNF Val66Met mice

Project description:BDNF Val66Met mice, a model that is genetically susceptible to stress, recapitulated the translational effects of acute stress in the absence of applied stressors. However, unstressed heterozygous BDNF Val66Met mice did not display activation of immediate early genes, indicating a “pre-stressed” translational phenotype.

2017-06-28 | GSE100579 | GEO

A. borkumensis cells: control vs. 1-octanol-stressed cells

Project description:Transcriptional profiling of Alcanivorax borkumensis cells, grown on either pyruvate or hexadecane as carbon source, that were stressed with 1- octanol. The gene expression was measured 15 min, 30 min, 60 min and 90 min after 1-octanol addition. Two-condition experiment, 1-octanol-stressed vs. unstressed cells; different time points were investigated after 1-octanol was spiked in (15 min, 30 min, 60 min, 90 min); for each condition 3 replicates were used, for the control condition 4 replicates (pyruvate cultures) and 3 replicates (hexadecane cultures) were used for analysis

2013-02-27 | E-GEOD-44687 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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