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Sample GSM1097484 Query DataSets for GSM1097484
Status Public on Mar 15, 2013
Title genomic DNA of yw, biological rep1
Sample type genomic
 
Source name Drosophila genomic DNA of yw (wild type).
Organism Drosophila melanogaster
Characteristics genotype: yellow white
age: 1 week old female
Treatment protocol 1-week old female flies were anaesthetized with five minutes of FlyNap before semi-dissection. Whole body tissue are stored at -80c after semi-dissection.
Growth protocol ~15 female flies at 1 week old age are collected at room temperature (RT) on normal food source according to the different genotype.
Extracted molecule genomic DNA
Extraction protocol For each biological replicate genomic DNA was generated from 15 parental or selected F2 flies using DNA Easy prep kit (Qiagen). To avoid RNA contamination, genomic DNA was treated with 1.5μl RNAse at 37°C for 30 min. Linear amplification of genomic DNA was performed using the REPLI-g midi kit to a concentration of ~ 1μg/μl. Five μg of amplified genomic DNA was fragmented with 1 U RQ1 DNase (Promega) for 2 min at room temperature (18–22°C) in standard buffer followed by incubation with 2ul EDTA at 65°C for 10 min, and digestion was confirmed on 3% agarose gels by the existence of sheared products with ~50–100 bp length.
Label biotin
Label protocol 50 μl fragmented genomic DNA was used in the labeling reaction with 22.5 U terminal deoxynucleotidyl transferase (rTDT) (Promega) and 1 μL (1 mM) Biotin N6-ddATP (Enzo) under the following temperature cycle: 37°C for 90 min, 99°C for 15 min and 12°C for 5 min. Gel-shift assays were performed to confirm labeling efficiency. Subsequently, the labeled products were hybridized to Affymetrix Chips (Drosophila Genome 2.0) using standard Affymetrix protocols at the Salk Institute’s Genomic Facility Center.
 
Hybridization protocol Following fragmentation, 10 ug of labeled genomic DNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using Affymetrix GeneChip scanner 3000 7G.
Description Single Feature Polymorphism (SFP) data from genomic DNA pool of 15 yw flies
Drosophila_YW_1
Data processing All statistical analysis code was written in R language. The required coordinate file for SFP analysis of Drosophila Genome 2.0 was obtained from Bioconductor. Briefly, the raw .CEL files from scanned arrays were read into R as the log-transferred intensity of 25mer perfect match (PM) probes after background correction and quantile normalization to ensure that all arrays have the same overall distribution. All 12 arrays were evaluated with >99% present call using MAS5 algorithm assuming high quality of hybridization.
Matrices contain log-transformed intensity of perfect match (PM) probes
 
Submission date Mar 13, 2013
Last update date Mar 15, 2013
Contact name zhi zhang
E-mail(s) zhizhang@sanfordburnham.org
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
 
Platform ID GPL1322
Series (1)
GSE45123 Single Feature Polymorphism (SFP) Data from Drosophila Genomic DNA

Supplementary file Size Download File type/resource
GSM1097484_Drosophila_YW_1.CEL.gz 2.4 Mb (ftp)(http) CEL
Processed data are available on Series record

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