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: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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Project description:Multilevel analysis of transcription is facilitated by a new array design that includes modules for assessment of differential expression, isoform usage, and allelic imbalance in Drosophila. The ?2.5 million feature chip incorporates a large number of controls, and it contains 18,769 3' expression probe sets and 61,919 exon probe sets with probe sequences from Drosophila melanogaster and 60,118 SNP probe sets focused on Drosophila simulans. An experiment in D. simulans identified genes differentially expressed between males and females (34% in the 3' expression module; 32% in the exon module). These proportions are consistent with previous reports, and there was good agreement (? = 0.63) between the modules. Alternative isoform usage between the sexes was identified for 164 genes. The SNP module was verified with resequencing data. Concordance between resequencing and the chip design was greater than 99%. The design also proved apt in separating alleles based upon hybridization intensity. Concordance between the highest hybridization signals and the expected alleles in the genotype was greater than 96%. Intriguingly, allelic imbalance was detected for 37% of 6579 probe sets examined that contained heterozygous SNP loci. The large number of probes and multiple probe sets per gene in the 3' expression and exon modules allows the array to be used in D. melanogaster and in closely related species. The SNP module can be used for allele specific expression and genotyping of D. simulans.
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