Verification of a custom chip which measures abundance, isoforms and alleles in Drosophila
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila simulans
PROVIDER: GSE31750 | GEO | 2011/09/13
SECONDARY ACCESSION(S): PRJNA145327
REPOSITORIES: GEO
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Project description:Analysis of differential expression using the 3’ expression module revealed 34% probe sets showed evidence for a sex bias and alternative exon sex bias was identified for 164 genes. Intriguingly, allelic imbalance was detected for 37% of 6,579 probe sets examined which contained heterozygous SNP loci. Two different isogenic strains of D. simulans, st e and C167.4 and their male and female progeny were used as the basis for the verification study. Three replicates of RNA from female and male progeny of the cross st e x C167.4 made for a total of six RNA samples. In addition, DNA was used as a control for estimating allele imbalance. Three replicates of DNA target were prepared for female st e, femaleC167.4 and the female F1 progeny of the cross st e x C167.4, for a total of 9 gDNA samples.
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Project description:Microarrays have evolved from low-density cDNA or oligonucleotide arrays to high-density platforms, for several study species even covering the complete transcriptome. At the same time, transcriptomics experiments have become more complex and multifactorial in nature, requiring many microarrays to assess multiple biologically relevant hypotheses. Scientists using this technology are therefore painfully aware of the high financial cost of a typical microarray experiment. Unfortunately, this often leads to either a suboptimal experimental design in an effort to reduce the cost by using fewer microarrays, or to abandoning microarray technology altogether. In this study, we argue that for many studies high-density full genome microarrays are in fact technical overkill. By selectively reducing full genome probe sets to a lower number of probes, it is possible to significantly reduce the total cost of a microarray experiment. The study consists of four microarray analyses: a cadmium probe selection experiment, a temperature probe selection experiment, a cadmium validation experiment and a cadmium validation experiment.
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Project description:Microarrays have evolved from low-density cDNA or oligonucleotide arrays to high-density platforms, for several study species even covering the complete transcriptome. At the same time, transcriptomics experiments have become more complex and multifactorial in nature, requiring many microarrays to assess multiple biologically relevant hypotheses. Scientists using this technology are therefore painfully aware of the high financial cost of a typical microarray experiment. Unfortunately, this often leads to either a suboptimal experimental design in an effort to reduce the cost by using fewer microarrays, or to abandoning microarray technology altogether. In this study, we argue that for many studies high-density full genome microarrays are in fact technical overkill. By selectively reducing full genome probe sets to a lower number of probes, it is possible to significantly reduce the total cost of a microarray experiment. The study consists of four microarray analyses: a cadmium probe selection experiment, a temperature probe selection experiment, a cadmium validation experiment and a cadmium validation experiment.
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Project description:Microarrays have evolved from low-density cDNA or oligonucleotide arrays to high-density platforms, for several study species even covering the complete transcriptome. At the same time, transcriptomics experiments have become more complex and multifactorial in nature, requiring many microarrays to assess multiple biologically relevant hypotheses. Scientists using this technology are therefore painfully aware of the high financial cost of a typical microarray experiment. Unfortunately, this often leads to either a suboptimal experimental design in an effort to reduce the cost by using fewer microarrays, or to abandoning microarray technology altogether. In this study, we argue that for many studies high-density full genome microarrays are in fact technical overkill. By selectively reducing full genome probe sets to a lower number of probes, it is possible to significantly reduce the total cost of a microarray experiment. The study consists of four microarray analyses: a cadmium probe selection experiment, a temperature probe selection experiment, a cadmium validation experiment and a cadmium validation experiment.
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Project description:Stalk-eyed flies (family Diopsidae) are a model system for studying sexual selection due to the elongated and sexually dimorphic eye-stalks found in some species. These flies are of additional interest because their X chromosome is derived largely from an autosomal arm in other flies. To investigate how sex-biased expression arose on the novel X we compared gene expression between males and females using oligonucleotide microarrays and RNA from developing eyestalk tissue in the sexually monomorphic diopsid, Teleopsis quinqueguttata. We use probe sequence divergence to evaluate cross-species ascertainment bias and chromosome assignment to determine if sex linkage influence expression. Microarray analysis revealed sex-biased expression for only 1.9% of 3,748 genes expressed in eye-antennal imaginal discs. Analysis of probe sequences between species indicates that the lack of sex-biased expression is not due to ascertainment bias. These findings indicate that the the majority of sex-biased gene expression observed in developing heads of the dimorphic species, T. dalmanni, is causally related to development of dimorphic head shape. Two-condition experiment, female vs. male RNA using larval eye discs and adult heads for one species (Teleopsis quinqueguttata)
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