Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Thiouracil Pulse-chase, Tachyzoites and Bradyzoites mRNA stability data

ABSTRACT: Pulse chase measurements using thiouracil (DTU) labeling via UPRT and chasing with uracil Data from tachyzoites is labeled "DTU Pulse Chase". Two independent pulse chase experiments were performed in tachyzoites, pulse chase 1 and 2. Duplicate arrays at each timepoint were performed for pulse chase 2 (2 a and b). Data from bradyzoites are labeled "DTU Bradyzoite Pulse Chase". Two independent pulse chase experiments were performed in bradyzoites and a single set of arrays were performed for each experiment. Just one chase timepoint was used in the bradyzoite experiments, the 2 hour chase. An RNA stablity experiment design type examines stability and/or decay of RNA transcripts. Keywords: RNA_stability_design

ORGANISM(S): Toxoplasma gondii

PROVIDER: GSE2947 | GEO | 2005/07/16

SECONDARY ACCESSION(S): PRJNA104765

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcription profiling of Toxoplasma gondii thiouracil pulse-chase, tachyzoites and bradyzoites mRNA stability data

Project description:Pulse chase measurements using thiouracil (DTU) labeling via UPRT and chasing with uracil Data from tachyzoites is labeled "DTU Pulse Chase". Two independent pulse chase experiments were performed in tachyzoites, pulse chase 1 and 2. Duplicate arrays at each timepoint were performed for pulse chase 2 (2 a and b). Data from bradyzoites are labeled "DTU Bradyzoite Pulse Chase". Two independent pulse chase experiments were performed in bradyzoites and a single set of arrays were performed for each experiment. Just one chase timepoint was used in the bradyzoite experiments, the 2 hour chase.

2005-07-07 | E-SMDB-2949 | biostudies-arrayexpress

Thiouracil Pulse-chase, Tachyzoites and Bradyzoites mRNA stability data

2005-07-16 | E-GEOD-2947 | biostudies-arrayexpress

Transcription profiling of parasites grown as either tachyzoites or bradyzoites for 40 hours pulsed with 2,4-dithiouracil (DTU) for 1 hour

2005-07-07 | E-SMDB-2373 | biostudies-arrayexpress

Synthesis vs. Abundance, Bradyzoite Development

Project description:Parasites grown as either tachyzoites or bradyzoites for 40 hours were pulsed with 2,4-dithiouracil (DTU) for 1 hour. Following the pulse, mRNA was extracted and either used directly in microarray experiments (Abundance Arrays) or biotinylated and purified to select DTU labeled RNAs that were then used in microarray experiments (Synthesis Arrays). Two independent tachyzoite and bradyzoite preparations were made and duplicate microarrays were performed for each sample. A development or differentiation experiment design type assays events associated with development or differentiation or moving through a life cycle. Development applies to organism(s) acquiring a mature state, and differentiation applies to cells acquiring specialized functions. Keywords: development_or_differentiation_design

2005-07-16 | GSE2946 | GEO

Synthesis vs. Abundance, Bradyzoite Development

2005-07-16 | E-GEOD-2946 | biostudies-arrayexpress

Toxoplasma gondii

Project description:Thiouracil Pulse-chase, Tachyzoites and Bradyzoites mRNA stability data

| PRJNA104765 | ENA

RNA sequencing of host transcriptome of human foreskin fibroblast cells infected with either bradyzoites and tachyzoite of Toxoplasma gondii

Project description:The purpose of this data set is to determine if bradyzoites impact the host transcripton in a similar manner as tachyzoites. We found that 3853 differentially expressed genes (DEGs) are shared between tachyzoite infected cells and bradyzoite infected cells (41%; 2161 up-reg., 1692 down-reg.) when compared to uninfected host samples, leaving 3356 tachyzoite specific DEGs (1488 up-reg., 1868 down-reg.), and 1951 DEGs specific to bradyzoite infection (1075 up-reg., 876 down-reg). We conclude therefore that bradyzoites manipulate the host cell and that this is unique when compared to tachyzoites.

2020-01-15 | GSE125121 | GEO

Temporal analysis of in vivo Toxoplasma gondii cysts shows novel and late stage specific transcripts.

Project description:The protozoan pathogen Toxoplasma gondii has the unique ability to develop a chronic infection in the brain of its host. The T. gondii develops cysts within the neurons that are resilient against the host immune response and current therapeutics. The bradyzoite parasites within the cyst have a sugar-protein-rich wall and a slow-replication cycle, allowing them to remain hidden from the host. This intracellular encysted lifestyle of T. gondii has made them recalcitrant to molecular analysis in vivo. Here, we have enriched for T. gondii brain cysts 21 to 150 days post-infection (DPI). RNA and protein from bradyzoites was isolated from each timepoint. Deep sequencing of transcripts expressed during these three timepoints showed many of the identified proteins are transcriptionally expressed at a high level. Approximately one-third are more enriched during bradyzoite conditions compared to tachyzoites, and approximately half are expressed at similar levels during each phase. We have expanded the transcriptional profile of in vivo bradyzoites to 120 DPI. The RNA sequencing depth of in vivo bradyzoite T. gondii was over 250-fold greater than was have been previously, which allowed us to identify low level transcripts and novel bradyzoite-specific isoforms.

2019-07-11 | GSE134099 | GEO

Cell-specific analysis of mRNA synthesis and decay

Project description:This SuperSeries is composed of the following subset Series: GSE2946: Synthesis vs. Abundance, Bradyzoite Development GSE2947: Thiouracil Pulse-chase, Tachyzoites and Bradyzoites mRNA stability data GSE2948: UPRT Transgenic cells, Human Arrays Abstract: Standard microarrays measure mRNA abundance, not mRNA synthesis, and therefore cannot identify the mechanisms that regulate gene expression. We have developed a method to overcome this limitation by using the salvage enzyme uracil phosphoribosyltransferase (UPRT) from the protozoan Toxoplasma gondii. T. gondii UPRT has been well characterized because of its application in monitoring parasite growth: mammals lack this enzyme activity and thus only the parasite incorporates (3)H-uracil into its nucleic acids. In this study we used RNA labeling by UPRT to determine the roles of mRNA synthesis and decay in the control of gene expression during T. gondii asexual development. We also used this approach to specifically label parasite RNA during a mouse infection and to incorporate thio-substituted uridines into the RNA of human cells engineered to express T. gondii UPRT, indicating that engineered UPRT expression will allow cell-specific analysis of gene expression in organisms other than T. gondii. Refer to individual Series

2006-03-07 | E-GEOD-4401 | biostudies-arrayexpress

RESTRICTION checkpoint controls bradyzoite development in Toxoplasma gondii

Project description:The Toxoplasma gondii G1 RESTRICTION checkpoint operates the switch between parasite growth and differentiation. The Cdk-related G1 kinase TgCrk2 forms alternative complexes with atypical cyclins (TgCycP1, TgCycP2 and TgCyc5) in the rapidly dividing developmentally incompetent RH and slower dividing developmentally competent ME49 tachyzoites and bradyzoites. The TgCycP1 expression interferes with bradyzoite differentiation. The TgCycP2 regulates G1 in the developmentally competent ME49 but not in the developmentally incompetent RH tachyzoites. Examination of TgCycP2 and TgCyc5 in alkaline induced and spontaneous bradyzoite differentiation (rat embryonic brain cells) models confirmed TgCycP2 role in bradyzoite replication and revealed that stress induced TgCyc5 is critical for efficient tissue cyst maturation.

2022-04-23 | GSE200962 | 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