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Status |
Public on Aug 05, 2009 |
Title |
dsim_w501_female_heads_RNA_rep2 |
Sample type |
RNA |
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Source name |
adult female heads
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Organism |
Drosophila simulans |
Characteristics |
sex: female age: adult, 5-7 days post-eclosion tissue: adult heads genotype: w501 sample size: 100 flies
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Biomaterial provider |
Rita M. Graze
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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.
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Growth protocol |
Flies were propagated in bottles at 25°C on dextrose medium.
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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).
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Label |
biotin
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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.
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Hybridization protocol |
cDNA samples were hybridized to GeneChip© Drosophila Tiling 1.0R Arrays according to standard manufacturer protocols.
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Scan protocol |
GeneChips were scanned at the University of Pennsylvania School of Medicine Microarray Facility according to standard manufacturer protocols.
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Description |
total RNA from adult female heads
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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.
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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 |
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Platform ID |
GPL5919 |
Series (1) |
GSE17453 |
Regulatory divergence in Drosophila melanogaster and D. simulans: a genome-wide analysis of allele-specific expression |
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