E-GEOD-45123 - Single Feature Polymorphism (SFP) Data from Drosophila Genomic DNA

Status
Released on 15 March 2013, last updated on 2 June 2014
Organism
Drosophila melanogaster
Samples (12)
Array (1)
Protocols (7)
Description
Natural populations of the fruit fly, Drosophila melanogaster, segregate genetic variation that leads to cardiac disease phenotypes. Drosophila is well-known as a model for studying the mechanisms by which human disease genes cause pathology, including heart disease, but it is less well appreciated that they may also model the genetic architecture of disease, since flies presumably also have diseases that have a genetic basis. It is reasoned that most of these aberrant inbred line effects would be due to capture of rare variants of large effect as homozygotes, allowing the variants to be mapped rapidly using contemporary genomic approaches. In order to map the genetic variants in flies, we used single feature polymorphism (SFP) analysis to contrast the genome-wide genotype frequencies between pools of flies with aberrant and normal heart phenotype. SFP analysis is an indirect method for genome-wide genotyping that utilizes differential hybridization of genomic DNA to probes on a DNA chip that was initially designed for gene expression profiling, but can be used for species where genotyping chips are not available. DNA was prepared from three independent pools of 15 flies for each of the two types, as well as from the two parental lines. The samples were sheared and labeled with biotin, then hybridized to Affymetrix Drosophila expression microarray chips. Mismatch hybridization, namely a significant difference in the hybridization intensity between the parental lines, was detected from all perfect match (PM) probes, located in over 9,000 probes with an estimated False Discovery Rate of 11%.
Experiment type
comparative genomic hybridization by array 
Contacts
zhi zhang <zhizhang@sanfordburnham.org>, Greg Gibson, Rolf Bodmer, Zhi Zhang
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-45123.idf.txt
Sample and data relationshipE-GEOD-45123.sdrf.txt
Raw data (1)E-GEOD-45123.raw.1.zip
Array designA-AFFY-35.adf.txt
Links