Nicotiana glauca isolate:RH
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA335307 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Nicotiana glauca Genome sequencing and assembly
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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
Project description:Picea glauca isolate:SMarTFor_1 Genome sequencing
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Project description:Toxoplasma gondii RH strain:RH Genome sequencing
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Project description:Quercus glauca isolate:JXL012 Genome sequencing and assembly
| PRJNA833751 | ENA
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) 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
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
Project description:Toxoplasma gondii RH Genome sequencing project
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Project description:Nicotiana tabacum isolate:nk326_chen Genome sequencing and assembly
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