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Sample GSM435274 Query DataSets for GSM435274
Status Public on Aug 05, 2009
Title dsim_w501_female_heads_RNA_rep2
Sample type RNA
 
Source name adult female heads
Organism Drosophila simulans
Characteristics sex: female
age: adult, 5-7 days post-eclosion
tissue: adult heads
genotype: w501
sample size: 100 flies
Biomaterial provider Rita M. Graze
Treatment protocol Flies were collected between 3:30-5:30 pm on consecutive days, lightly anesthetized (under CO2) and snap frozen in liquid nitrogen. The heads were separated and collected in a cold room using a sieve chilled on dry ice (Telonis-Scott et al. 2008). Each independent sample was stored at -80°C prior to RNA extractions.
Growth protocol Flies were propagated in bottles at 25°C on dextrose medium.
Extracted molecule total RNA
Extraction protocol Samples were homogenized using a motorized pestle in 1ml of TRIzol® in pre-chilled microcentrifuge tubes. Total RNA was then isolated according to the DGRC© RNA extraction protocol (Bogart and Andrews, 2006).
Label biotin
Label protocol For each of the RNA samples the starting material for sample processing was 5 ul of total RNA in DEPC H2O (7 ug total RNA). cDNA was synthesized using the GeneChip© WT Double-Stranded cDNA Synthesis Kit (Affymetrix, PN 900813) according to GeneChip© WT Double-Stranded target assay procedure A: First strand cDNA synthesis protocol. The resulting samples were then cleaned, fragmented and labeled using the Sample Cleanup Module (Affymetrix, PN 900371) and WT Double stranded DNA Terminal Labeling Kit (Affymetrix, PN 900812) following procedures B through D of the WT target assay protocol.
 
Hybridization protocol cDNA samples were hybridized to GeneChip© Drosophila Tiling 1.0R Arrays according to standard manufacturer protocols.
Scan protocol GeneChips were scanned at the University of Pennsylvania School of Medicine Microarray Facility according to standard manufacturer protocols.
Description total RNA from adult female heads
Data processing The Tiling Analysis Software from Affymetrix was used to produce .bar files containing raw intensities, then the bar2txt program from the affy file manipulation tools (http://www.affymetrix.com/Auth/support/developer/downloads/Tools/tiling_util.tgz) was used to convert the .bar files to plain txt.
 
Submission date Jul 31, 2009
Last update date Aug 04, 2009
Contact name Rob J Kulathinal
Organization name University of Florida
Department Department of Biology
Lab McIntyre Lab
Street address 1376 Mowry Road
City Gainesville
State/province FL
ZIP/Postal code 32610
Country USA
 
Platform ID GPL5919
Series (1)
GSE17453 Regulatory divergence in Drosophila melanogaster and D. simulans: a genome-wide analysis of allele-specific expression

Supplementary file Size Download File type/resource
GSM435274.CEL.gz 22.4 Mb (ftp)(http) CEL
GSM435274.bar.gz 18.2 Mb (ftp)(http) BAR
Processed data provided as supplementary file

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