Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptional analysis of Leishmania infantum antimony resistant strains using full-genome DNA microarrays

ABSTRACT: The aim of the experiment is to detect any gene expression modulation in an antimony resistant L.infantum Sb2000.1 strain compared to an antimony sensitive L.infantum WT strain. We want to identify the modulated genes associated with an antimony resistant phenotype. The Sb2000.1 resistant strain used is about 1000 times more resistant to SbIII than the WT sensitive strain. The full-genome DNA microarrays includes one 70-oligonucleotide probe for each gene of L. infantum. Keywords: drug resistance Two-condition experiment, resistant strain Sb2000.1 vs wild-type. Five biological replicates for each strain, independently grown and harvested. One replicate per array

ORGANISM(S): Leishmania infantum

SUBMITTER: Philippe Leprohon

PROVIDER: E-GEOD-16965 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Gene expression modulation is associated with gene amplification, supernumerary chromosomes and chromosome loss in antimony-resistant Leishmania infantum.

Leprohon Philippe P Légaré Danielle D Raymond Frédéric F Madore Eric E Hardiman Gary G Corbeil Jacques J Ouellette Marc M

Nucleic acids research 20090107 5

Antimonials remain the first line drug against the protozoan parasite Leishmania but their efficacy is threatened by resistance. We carried out a RNA expression profiling analysis comparing an antimony-sensitive and -resistant (Sb2000.1) strain of Leishmania infantum using whole-genome 70-mer oligonucleotide microarrays. Several genes were differentially expressed between the two strains, several of which were found to be physically linked in the genome. MRPA, an ATP-binding cassette (ABC) gene ...[more]

PMID: 19129236

Similar Datasets

Comparative Genomic Hybridization of Leishmania major methotrexate resistant strains vs wild-type LV39

Project description:CGH analysis of the drug resistant strain L. major MTX60.4 vs the wild-type strain LV39 The full-genome DNA microarrays includes one 70-oligonucleotides probe for each gene of L.major LV39 Keywords: drug resistance Two-condition experiment, resistant strain MTX60.4 vs wild-type LV39. Three biological replicates for each strain, independently grown and harvested. One replicate per array

2008-05-31 | E-GEOD-11623 | biostudies-arrayexpress

Transcriptional analysis of Leishmania major methotrexate resistant strains using full-genome DNA microarrays

Project description:Transcriptional analysis of the drug resistant strain L. major MTX60.4 compared to the wild-type strain LV39 The full-genome DNA microarrays includes one 70-oligonucleotides probe for each gene of L.major LV39 Keywords: drug resistance Two-condition experiment, resistant strain MTX60.4 vs wild-type LV39. Four biological replicates for each strain, independently grown and harvested. One replicate per array

2010-05-25 | E-GEOD-9948 | biostudies-arrayexpress

Transcriptional analysis of Leishmania infantum methotrexate resistant strains using full-genome DNA microarrays

Project description:Transcriptional analysis of the drug resistant strain L. infantum MTX20.5 compared to the wild-type strain The full-genome DNA microarrays includes one 70-oligonucleotides probe for each gene of L. infantum Keywords: drug resistance Two-condition experiment, resistant strain MTX20.5 vs wild-type. Four biological replicates for each strain, independently grown and harvested. One replicate per array

2010-05-25 | E-GEOD-9947 | biostudies-arrayexpress

Methotrexate resistant Leishmania strains

Project description:This SuperSeries is composed of the following subset Series: GSE9947: Transcriptional analysis of Leishmania infantum methotrexate resistant strains using full-genome DNA microarrays GSE9948: Transcriptional analysis of Leishmania major methotrexate resistant strains using full-genome DNA microarrays Keywords: SuperSeries Refer to individual Series

2010-05-25 | E-GEOD-9949 | biostudies-arrayexpress

Whole-genome comparative RNA expression profiling of axenic and intracellular amastigote forms of Leishmania infantum

Project description:Transcriptional analysis of L. infantum promastigote compared to L. infantum intracellular amastigote and transcriptional analysis of L. infantum promastigote compared to L. infantum axenic amastigote. The full-genome DNA microarrays includes one 70-oligonucleotides probe for each gene of L.infantum. Keywords: stage and culture condition Intracellular amastigote analysis: Two-condition experiment, promastigote stage vs intracellular amastigote stage. Six biological replicates for each stage, independently grown and harvested. One replicate per array Axenic amastigote analysis: Two-condition experiment, promastigote stage vs axenic amastigote stage. Four biological replicates for each stage, independently grown and harvested. One replicate per array.

2010-05-14 | E-GEOD-13983 | biostudies-arrayexpress

Transcriptional analysis of wild-type Leishmania species between both stages using full-genome DNA microarrays

Project description:Transcriptional analyses of L. infantum promastigote compared to L. infantum intracellular amastigote, and L. major promastigote compared to L. major intracellular amastigote The full-genome DNA microarray includes one 70mer-oligonucleotide probe for each gene of L. infantum and for each gene of L.major LV39 Keywords: stage-specific comparison Leishmania infantum: Two-condition experiment, promastigote stage vs amastigote stage. Six biological replicates for each stage, independently grown and harvested. One replicate per array Leishmania major: Two-condition experiment, promastigote stage vs amastigote stage. Four biological replicates for each stage, independently grown and harvested. One replicate per array

2008-05-28 | E-GEOD-10407 | biostudies-arrayexpress

Genetic heterogeneity versus molecular analysis of prion susceptibility in neuroblasma N2a sublines

Project description:The neuroblastoma-derived cell line N2a is permissive to certain prion strains but resistant sublines unable to accumulate the pathological proteinase-K resistant form of the prion protein can be isolated. We compared for gene expression and phenotypes different N2a sublines that were susceptible or resistant to the 22L prion strain. Karyotypes and comparative genomic hybridization arrays revealed chromosomal imbalances but did not demonstrate a characteristic profile of genomic alterations linked to prion susceptibility. Likewise, we showed that this phenotype was not dependent on the binding of PrPres, the expression of the prion protein gene, or on its primary sequence. We completed this analysis by looking using real-time quantitative PCR at the expression of a set of genes encoding proteins linked to prion biology. None of the candidates could account by itself for the infection phenotype, nevertheless sublines had distinct transcriptional profiles. Taken together, our results do not support a role for specific genomic abnormalities and possible candidate proteins in N2a prion susceptibility. They also reveal genetic heterogeneity among the sublines and serve as a guidance for further investigation into the molecular mechanisms of prion infection. In a first approach, CGHa profiles were established for the parental cell line N2apcl, a sensitive (G9) and a resistant (F1) sublines, as compared to A/HeJ mouse strain normal DNA. To allow a more precise description of the differences between N2apcl and six of its derived sub-lines (58, D11, F1, G9, R4, R10), N2apcl DNA was used as reference DNA in a series of CGHa experiments, avoiding the potential copy number polymorphisms between the cell lines and A/HeJ murine DNAs.

2010-06-19 | E-GEOD-5374 | biostudies-arrayexpress

Shoot tip tissue: Tall Mokka vs Typica.

Project description:The closely related Coffea arabica cultivars ‘Tall Mokka’ and ‘Typica’, with excellent flavor, but differing distinctively in the size of aerial organs, branching pattern and branch numbers. Differential gene expression analysis of shoot tips of arabica coffee cultivars 'Tall Mokka' and 'Typica' were done using Potato cDNA microarray as cross-species platform. Using cross-species microarray hybridization, we identified a prolyl oligopeptidase (CaPOP) gene as differentially expressed between the shoot tips of ‘Tall Mokka’ and ‘Typica’. Isolation and sequencing of POP genes from coffee identified three paralogs, CaPOP1, CaPOP2 and CaPOP3. All three genes were present in both cultivars, which suggest that differences in the expression of CaPOP are caused by factor(s) regulating the transcription of CaPOPs. CaPOP1 differs in sequence from CaPOP2 primarily in having two large deletions in the promoter region. CaPOP genes are homologous to arabidopsis At1g20380, encoding a post-proline cleaving enzyme that acts on substrates shorter than 30 amino acids. Ectopic expression of CaPOP1 under its native promoter in transgenic arabidopsis resulted in more secondary branches than in the wild type. This is the first study to successfully isolate CaPOP genes and characterize their expression in the developing tissues of coffee. This study also identified a novel role for prolyl oligopeptidase in control of branching. Eight coffee trees of 'Typica' ('K') and six trees of 'Tall Mokka' ('M') cultivar were used in this study. The trees were equally divided into two groups 'A' and 'B' for each cultivar ('MA','MB', 'KA' and 'KB') and treated as biological replicates. Eight two channel microarray hybridizations were done in following pairs: MA x KA, MA x KB, MB x KA, MB x KB and dye swap replicate of each pair. Summary: Two-sample experiment: Tall Mokka vs. Typica . 8 Hybridizations. 2 Biological replicates per sample. 1 Dye swap per array.

2011-08-03 | E-GEOD-31179 | biostudies-arrayexpress

Effect of ovarian stimulation on oocyte gene expression in cow

Project description:The objective of the study was to analyze the impact of FSH on transcriptome changes of in vivo bovine oocytes. Oocytes were collected from naturally ovulated and superovulated animals at 2 hours pre-LH surge, 6 hours post-LH surge, and 22 hours post-LH surge. Six-condition experiment. Biological replicates: 1 . Technical replicate:2.

2011-07-31 | E-GEOD-27696 | biostudies-arrayexpress

Transcriptome changes in the cambial region of poplar (Populus alba L.) in response to water deficit

Project description:A transcriptome analysis of P. alba cambial zone was performed with the aim to unravel the gene network underlying the response to water deficit within the cambium and the differentiating derivatives cambial cells. Water stress was induced on one-year-old plant of Populus alba by withholding water for 9 days. At that time, leaf Î¨pd fell down to -0,8 MPa resulting in a significant reduction of the stomatal conductance, CO2 assimilation, consistent increment of stem shrinkage and cessation of the radial growth. These effects were almost fully reversed by re-hydration. The water deficit resulted in changes in gene expression that affected a few functional categories as protein metabolism, cell wall metabolism, stress response, transporters and transcriptional regulation. The function of up- and down-regulated genes is discussed considering the physiological response of the plants to water deficit. Three-condition experiment, Stress vs. Control, Re-hydrated vs. Stress and Re-hydrated vs Control. Each sample consists of a pool of two plants independently grown and harvested. Two technical replicates are performed for each of the three treatments. One swap replicate per array.

2010-05-16 | E-GEOD-18675 | 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