Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Parasite gene expression differences between RH-ERP, RH-JSR and GT1 of Toxoplasma gondii.

ABSTRACT: Parasite gene expression differences have been reported previously between RH-ERP, RH-JSR and GT1. To independently confirm these gene expression differences, we examined the parasite gene expression profiles of RH-ERP, RH-JSR and GT1 through microarray. Three type I strains of Toxoplasma gondii were compared with one array each, and these were used to verify data from previous studies.

ORGANISM(S): Toxoplasma gondii

SUBMITTER: Ninghan Yang

PROVIDER: E-GEOD-44191 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Genetic basis for phenotypic differences between different Toxoplasma gondii type I strains.

Yang Ninghan N Farrell Andrew A Niedelman Wendy W Melo Mariane M Lu Diana D Julien Lindsay L Marth Gabor T GT Gubbels Marc-Jan MJ Saeij Jeroen P J JP

BMC genomics 20130710

<h4>Background</h4>Toxoplasma gondii has a largely clonal population in North America and Europe, with types I, II and III clonal lineages accounting for the majority of strains isolated from patients. RH, a particular type I strain, is most frequently used to characterize Toxoplasma biology. However, compared to other type I strains, RH has unique characteristics such as faster growth, increased extracellular survival rate and inability to form orally infectious cysts. Thus, to identify candida ...[more]

PMID: 23837824

Similar Datasets

Parasite gene expression differences between RH-ERP, RH-JSR and GT1 of Toxoplasma gondii.

Project description:Parasite gene expression differences have been reported previously between RH-ERP, RH-JSR and GT1. To independently confirm these gene expression differences, we examined the parasite gene expression profiles of RH-ERP, RH-JSR and GT1 through microarray.

2013-08-20 | GSE44191 | GEO

Expression data from human foreskin fibroblasts (HFFs) infected with type I strains of Toxoplasma gondii.

Project description:Type I strains of Toxoplasma gondii exhibit phenotypic variation, but it is uncertain how differently type I strains modulate the host cell. We determined differential host modulation by type I strains through microarray. HFFs were infected with RH-ERP, RH-JSR and GT1 for 24 hours. Total RNA was isolated and hybridized to Affymetrix GeneChip Human Genome U133A 2.0 arrays.

2013-08-20 | E-GEOD-44189 | biostudies-arrayexpress

Global gene expression differences between GT1, RH-ERP2009 and RH-JSR

Project description:Previous studies have shown that continuous in vitro passage can result in changes to the global gene expression profiles in mammalian cells. To examine the extent of gene expression differences between highly homologous type I strains, we took advantage of the T. gondii Affymetrix microarray containing probes to more than 8,000 genes. We compared the RH-JSR and GT1 strains, two isolates that share the small plaque phenotype, to the large plaque isolate RH-ERP2009. Following hybridization and normalization of data, we used two independent methods to generate lists of genes with expression differences that were statistically significant and 2-fold or greater in at least one sample. The 1-way ANOVA (P ≤ 0.05) identified 520 genes that were significantly differentially expressed between GT1, RH-ERP2009 and RH-JSR. Statistical Analysis of Microarray (SAM) (FDR = .05%) analysis identified 475 transcripts that were differentially expressed. Both lists were combined (610 genes) and used to perform pairwise fold comparisons between the three samples. This process identified 113 genes that were similarly expressed in GT1 and RH-JSR and differentially expressed in RH-ERP2009. Differentially expressed genes were located across all chromosomes and showed no pattern of clustering to one particular region of the genome. Interestingly, three out of 34 ABC transporters (ToxoDB) were significantly upregulated in RH-ERP2009 (hypergeometric distribution, P = 0.01)

2009-10-26 | GSE16115 | GEO

Global gene expression differences between GT1, RH-ERP2009 and RH-JSR

Project description:Previous studies have shown that continuous in vitro passage can result in changes to the global gene expression profiles in mammalian cells. To examine the extent of gene expression differences between highly homologous type I strains, we took advantage of the T. gondii Affymetrix microarray containing probes to more than 8,000 genes. We compared the RH-JSR and GT1 strains, two isolates that share the small plaque phenotype, to the large plaque isolate RH-ERP2009. Following hybridization and normalization of data, we used two independent methods to generate lists of genes with expression differences that were statistically significant and 2-fold or greater in at least one sample. The 1-way ANOVA (P â¤ 0.05) identified 520 genes that were significantly differentially expressed between GT1, RH-ERP2009 and RH-JSR. Statistical Analysis of Microarray (SAM) (FDR = .05%) analysis identified 475 transcripts that were differentially expressed. Both lists were combined (610 genes) and used to perform pairwise fold comparisons between the three samples. This process identified 113 genes that were similarly expressed in GT1 and RH-JSR and differentially expressed in RH-ERP2009. Differentially expressed genes were located across all chromosomes and showed no pattern of clustering to one particular region of the genome. Interestingly, three out of 34 ABC transporters (ToxoDB) were significantly upregulated in RH-ERP2009 (hypergeometric distribution, P = 0.01) Three type I strains of Toxoplasma gondii, GT1, RH-ERP2009 and RH-JSR, were compared for global gene expression differences. Three biological replicates were obtained for each strain.

2010-06-20 | E-GEOD-16115 | biostudies-arrayexpress

Expression data from Human foreskin fibroblasts (HFFs) infected with Toxoplasma gondii.

Project description:Toxoplasma strains have been shown to modulate host cell transcription. We have found a type II Toxoplasma gene, GRA15, which activates the nuclear translocation of the NF-kappaB p65 transcription factor. We used microarrays to determine how GRA15II modulates host cell transcription. HFFs were infected with type I (RH), type I GRA15II (RH GRA15II), type II (Pru), type II GRA15KO (Pru GRA15KO), type III (cep), or type III GRA15II (cep GRA15II) parasites for 18-24 hours. Some samples were also stimulated with TNF-alpha. Total RNA was isolated and hybridized to Affymetrix GeneChip Human Genome U133A 2.0 arrays.

2011-01-10 | E-GEOD-25468 | biostudies-arrayexpress

Expression data from RAW264.7 murine macrophages infected with Toxoplasma gondii and subsequently stimulated with interferon-gamma

Project description:Toxoplasma strains are known to inhibit the expression of several interferon-gamma induced genes, and a type II strain was shown to dysregulate genome-wide responses to interferon-gamma in human fibroblasts (Kim et al., 2007, J Immunol.). In this study we aimed to determine the effect of infection with three clonal lineages of Toxoplasma, type I, II, and III strains on genome-wide interferon-gamma induced transcription in murine macrophages. We also assessed the effect of the two main Toxoplasma modulators of mouse macrophage transcription, ROP16 and GRA15 (Jensen et al., 2011, Cell Host Microbe). We used Affymetrix microarrays to analyze host cell transcription after Toxoplasma infection and interferon-gamma stimulation. RAW264.7 murine macrophages were left uninfected or infected with type I (RH), type I ?rop16 (RH ?rop16), type II (Pru), type II ?gra15 (Pru ?gra15), or type II (CEP) parasites at an MOI ~5 for 18 hours and subsequently stimulated with murine IFN-? for six hours. Plaque assays were done to assess parasite viability. Total RNA was isolated and hybridized to Affymetrix Mouse 430A 2.0 gene chips.

2013-02-19 | E-GEOD-34913 | biostudies-arrayexpress

Human foreskin fibroblasts (HFFs) infected with type I strains of Toxoplasma gondii

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-08-20 | E-GEOD-44246 | biostudies-arrayexpress

Expression data from WT or p65-/- mouse embryonic fibroblasts (MEFs) infected with Toxoplasma gondii.

Project description:Toxoplasma strains have been shown to modulate host cell transcription. We have found a type II Toxoplasma gene, GRA15, which activates the nuclear translocation of the NF-kappaB p65 transcription factor. We used microarrays to determine how GRA15II modulates host cell transcription, and whether this transcription is dependent on the p65 transcription factor. WT or p65-/- MEFs were infected with type I (RH), type I GRA15II (RH GRA15II), type II (Pru), or type II GRA15KO (Pru GRA15KO) parasites for 18-24 hours. Total RNA was isolated and hybridized to Affymetrix GeneChip Human Genome U133A 2.0 arrays.

2011-01-10 | E-GEOD-25469 | biostudies-arrayexpress

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

Expression data from host cells infected with different strains of Toxoplasma gondii

Project description:This SuperSeries is composed of the following subset Series: GSE25468: Expression data from Human foreskin fibroblasts (HFFs) infected with Toxoplasma gondii. GSE25469: Expression data from WT or p65-/- mouse embryonic fibroblasts (MEFs) infected with Toxoplasma gondii. Refer to individual Series

2011-01-10 | E-GEOD-25476 | 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