Microarray analysis of a pyrethroid resistant African malaria vector, Anopheles funestus, from southern Africa
Ontology highlight
ABSTRACT:
ORGANISM(S): Anopheles funestus
SUBMITTER: Bob MacCallum
PROVIDER: E-MTAB-677 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Anopheles gambiae S form adults were drawn from the GAH laboratory colony that originated from the Ahafo region in Ghana. The GAH colony exhibits extensive insecticide resistance (bendiocarb, DDT, dieldrin, permethrin, deltamethrin). Gene expression was compared between blood-fed and sugar-fed females (3 hours after feeding) using a custom array focussing on around 300 detoxification-related genes.
2013-08-30 | E-MTAB-1621 | biostudies-arrayexpress
Project description:Aluminum (Al) toxicity is a major factor limiting crop yields on acid soils. In maize, Al tolerance is a complex phenomenon involving multiple genes and physiological mechanisms yet uncharacterized. To begin elucidating the molecular basis of maize Al toxicity and tolerance, we performed a detailed temporal analysis of root gene expression under Al stress using microarrays with an Al-tolerant and an Al-sensitive maize genotype. Seedlings of both genotypes were grown in hydroponics in a full nutrient solution containing 39uM of free Al3+ activity. Root samples were collected at 'time zero', and after 2, 6 and 24 hours of treatment. Time course experiment with 0h, 2h, 6h and 24 hours of Al treatment in two maize genotypes contrasting for Al tolerance. The experimental design used for the microarray study was of two interconnected loops, and utilized a total of 16 slide sets. Samples collected from each genotype at one time point were contrasted with the previous and subsequent time points in a loop (4 time points x 2 genotypes = 8 slide sets). Additionally, the loops were interconnected (with dye swap) so that the two genotypes were contrasted directly at each time point (4 time points x 2 replicates = 8 slide sets). The design was balanced for dye distribution throughout samples and biological replicates. Each sample was labeled twice with Cy3 and twice with Cy5; each biological replicate had four samples labeled with Cy3 and four samples labeled with Cy5. The Sample signal intensity values were log2 transformed and analyzed by two interconnected ANOVA mixed models using PROC MIXED in SAS (Jin et al., 2001; Wolfinger et al., 2001). The normalization ANOVA model yij = µ + Ai + Dj + (A x D)ij + eij was applied to account for experiment-wide sources of variation associated with array (Ai, degrees of freedom (df) = 15, random effect), dye (Dj, df = 1, fixed effect), and their interactions. The residuals (eij) were treated as normalized values and analyzed in the following ANOVA model (gene model), where effects were evaluated for each gene individually: rikl = µ + Ai + Gk + Tl + (G x T)kl + ekl. Gk is the kth genotype (i.e. C100-6 or L53; df = 1) and represents the effect of each genotype on the expression of every gene, Tl represents the lth treatment (i.e. 0, 2, 6 or 24 hours of Al treatment; df = 3), and (G x T)kl the interaction between genotype and treatment (df = 3). Array (Ai) was included as a random effect to control for spot effects (Jin et al., 2001). Least square means were calculated, and estimates of differential expression were calculated as the difference between least-square means for each of the terms in the model. ANOVA results linked below as Supplementary files.
2010-05-26 | E-GEOD-10308 | biostudies-arrayexpress
Project description:Genomic analysis of detoxification genes in the mosquito Aedes aegypti.
2008-02-09 | E-TABM-413 | biostudies-arrayexpress
Project description:Genomic analysis of detoxification genes in the mosquito Aedes aegypti
2008-02-09 | E-TABM-414 | biostudies-arrayexpress
Project description:Temporal gene expression changes in head tissues from mated females was determined at four time points post-mating, from 0-2 hours out to 72 hours. Each time point assayed post-mating showed a unique post-mating gene expression response, with 48 hours post-mating having the largest number of genes with expression changes. At most time points, a marked change in expression of genes expressed in the head fat body and encode products that function in metabolism was observed. Additionally, gene expression was analyzed at 24 hours post-mating in brain tissues, identifying the repressed expression of several genes encoding ion channels. All microarrays were dual channel with direct comparisons of mated females versus virgin females. For each experiment, four independent biological samples were analyzed using a dye-swap design. Samples consisted of adult heads or dissected CNS collected either at 0-2, 24, 48, or 72 hours post-mating.
2010-09-23 | E-GEOD-22390 | biostudies-arrayexpress
Project description:This microarray experiment aimed at studying the response of Aedes aegypti 4th stage-larvae to various xenobiotics, including insecticides, polycyclic aromatic hydrocarbons, herbicides and heavy metals.
2008-12-31 | E-TABM-353 | biostudies-arrayexpress
Project description:Emerging evidence implicates transcriptional dyseregulation within skeletal muscle in the pathogenesis of Kennedy disease/spinal bulbar muscular atrophy (KD/SBMA). We therefore broadly characterized gene expression in skeletal muscle of three independently generated mouse models of this disorder. The mouse models included a polyglutamine expanded (polyQ) AR knock-in model (AR113Q KI), a polyQ AR transgenic model (AR97Q Tg), and a transgenic mouse which overexpresses wild type AR solely in muscle (HSA-AR Tg). We performed microarray analysis of lower hindlimb muscles taken from these three models using high density oligonucleotide arrays. Changes in gene expression relative to wild type controls were evaluated separately in each strain. We validated our results using quantitative RT-PCR. Patterns of gene expression that are common to all lines and unique to each are described. When considered globally, the degree of overlap between the three models is approximately equivalent, and several patterns of gene expression relevant to the disease process were observed. Notably, patterns of gene expression typical of loss of AR function were observed in all three models, as were alterations in genes involved in cell adhesion, energy balance, Huntingtonâ??s disease, muscle atrophy and myogenesis. By comparing patterns of gene expression in three independent models of KD/SBMA, we have been able to identify candidate genes that might mediate the core myogenic features of KD/SBMA. Keywords: Gene expression in transgenic mice and disease state analysis We used microarray (38.5K oligo mouse array, which contain 35,302 of 70mer oligonucleotide probes largely derived from constitutively expressed exons and 3,482 of controls) to analyze gene expression in limb muscles of transgenic mice. Three mouse models of KD/SBMA were used: HSA-AR, AR113Q knock-in and AR97Q. HSA-AR transgenic male mice (n=5) and their WT brothers (n=8, all mice were 110-130 days of age) were used in this experiment. ARQ113-Knock In males (n=3, 3-4 months of age), and transgenic AR97Q males and WT brothers (n= 6 of each) were used in this study. For both HSA-AR and AR113Q samples, the log2 ratio of experimental samples (Cy5) and reference RNA(Cy3) was obtained, and log2 ratios from mutant samples were then subtracted from log2 ratios from WT controls. AR97Q males (Cy5) were simply compared with their WT brothers (Cy3) using a log2 ratio, rather than being first compared with reference RNA.
2010-10-12 | E-GEOD-10190 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE16720: Comparison of precocious and non-precocious salmon brain GSE16721: Comparison of gene expression in the salmon parr precocious and non-precocious testis Refer to individual Series
2010-05-16 | E-GEOD-16860 | biostudies-arrayexpress
Project description:The objective was to compare gene expression in salmon precocious and non-precocious parr testis tissue. Nine microarray hybridisations were carried out in total as part of this loop design. Total RNA from 3 pools(PG1-PG3) each of 4 precocious fish testes were compared with 3 pools (NP1-NP3) each of 10 non-precocious fish testes. There were no direct dye swaps but there was overall dye balance in the loop
2010-05-16 | E-GEOD-16721 | biostudies-arrayexpress
Project description:The use of whole genome microarrays for monitoring mutagenised or otherwise engineered genetic derivatives is a potentially powerful tool for checking genomic integrity. Using comparative genomic hybridization of a number of unrelated, directed deletion mutants in Escherichia coli K-12 MG1655 we identified unintended secondary genomic deletions in the flhDC region in fnr, crp, and creB mutants. These deletions were confirmed by PCR and phenotypic tests. Our findings show that non-motile progeny are found in some populations of MG1655 directed deletion mutants, and studies on the effects of gene knock-outs should be viewed with caution when the mutants have not been screened for the presence of secondary deletions, or confirmed by other methods. We used the CGH method to genetically characterize a series of regulatory gene deletion mutants we had made in MG1655 using the lamda-Red method of Datsenko and Wanner. A number of strains were tested using CGH, and each strain was tested only once. Genomic DNA isolated from wt MG1655 was used as a reference in all hybridisations.
2007-09-30 | E-GEOD-7695 | biostudies-arrayexpress