GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE45123 Query DataSets for GSE45123
Status Public on Mar 15, 2013
Title Single Feature Polymorphism (SFP) Data from Drosophila Genomic DNA
Organism Drosophila melanogaster
Experiment type Genome variation profiling by array
Summary 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.
Overall design 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%.
Contributor(s) Zhang Z, Bodmer R, Gibson G
Citation(s) 23638165
Submission date Mar 13, 2013
Last update date May 04, 2018
Contact name zhi zhang
Phone 858-646-3100-3801
Fax 858-795-5298
Organization name Sanford-Burnham Medical Research Institute
Department Development and Ageing
Lab Bodmer
Street address 10901 North Torrey Pines Rd.
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
Platforms (1)
GPL1322 [Drosophila_2] Affymetrix Drosophila Genome 2.0 Array
Samples (12)
GSM1097484 genomic DNA of yw, biological rep1
GSM1097485 genomic DNA of yw, biological rep2
GSM1097486 genomic DNA of yw, biological rep3
BioProject PRJNA193149

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE45123.xlsx.gz 51.5 Mb (ftp)(http) XLSX
GSE45123_RAW.tar 27.9 Mb (http)(custom) TAR (of CEL)
GSE45123_readme.txt.gz 202 b (ftp)(http) TXT
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap