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Sample GSM1635276 Query DataSets for GSM1635276
Status Public on Oct 01, 2015
Title ZA-4_PA-3
Sample type RNA
 
Channel 1
Source name PA
Organism Rhagoletis pomonella
Characteristics individual: PA-3
dev_time_point: L3 feeding larva
fruit: apple
tissue: whole 3rd instar larvae
Growth protocol Infested apple and snowverry fruit were collected from field sitse near Bellingham, WA, USA, and staged in the lab at 21C, 14:10 LD.
Wandering larvae and pupae were collected daily, allowed to sit at 21C for 10 days, then transferred to 4C for 20 weeks of simulated winter
Following 20 weeks at 4C, diapausing pupae were moved to 21C. Pupae breaking diapause were reared to adulthood.
Adults were crossed in several cages to produce F1 offspring that were layed as eggs into agar domes.
Eggs were transplanted into snowberry and apple fruits, then reared to the third larval instar.
Feeding 3rd instar larvae were snap frozen and RNA-extracted.
Extracted molecule total RNA
Extraction protocol larvae were homogenized in tri-reagent and total RNA was extracted from each individual using the Ambion RiboPure® Kit
Label Cy3
Label protocol Labeled aRNA from four individuals from each time point was generated using Quick-Amp labeling Kit (Agilent Technologies, Inc.) following the manufacturer recommendations.
We used 250ng of total RNA for reverse transcription to synthesize 1st strand cDNA, then generated labeled aRNA according to the manufacturer’s protocol
 
Channel 2
Source name ZA
Organism Rhagoletis zephyria
Characteristics individual: ZA-4
dev_time_point: L3 feeding larva
fruit: apple
tissue: whole 3rd instar larvae
Growth protocol Infested apple and snowverry fruit were collected from field sitse near Bellingham, WA, USA, and staged in the lab at 21C, 14:10 LD.
Wandering larvae and pupae were collected daily, allowed to sit at 21C for 10 days, then transferred to 4C for 20 weeks of simulated winter
Following 20 weeks at 4C, diapausing pupae were moved to 21C. Pupae breaking diapause were reared to adulthood.
Adults were crossed in several cages to produce F1 offspring that were layed as eggs into agar domes.
Eggs were transplanted into snowberry and apple fruits, then reared to the third larval instar.
Feeding 3rd instar larvae were snap frozen and RNA-extracted.
Extracted molecule total RNA
Extraction protocol larvae were homogenized in tri-reagent and total RNA was extracted from each individual using the Ambion RiboPure® Kit
Label Cy5
Label protocol Labeled aRNA from four individuals from each time point was generated using Quick-Amp labeling Kit (Agilent Technologies, Inc.) following the manufacturer recommendations.
We used 250ng of total RNA for reverse transcription to synthesize 1st strand cDNA, then generated labeled aRNA according to the manufacturer’s protocol
 
 
Hybridization protocol A total of 825 ng of labeled aRNA per sample was used for the hybridization,
and hybridization and washing were performed according to the manufacturer's protocol using the Gene Expression Hybridization Kit and Gene Expression Wash Buffers (Agilent Technologies, Inc.).
We used a two-color hybridization design, with six biological (individual larva) replicates, and 2-3 technical replicates per biological replicate.
Scan protocol The arrays were washed according to the manufacturer's protocol and then scanned on an Agilent G2505C scanner
Images were quantified using Agilent Feature Extraction Software (version 10.1.1.1).
Description ZA-R_PA-G
Data processing Data were background corrected and loess normalized using LIMMA
Processed data file (linked as supplementary file on Series record) reports Limma-generated log2 fold change values, estimated after normalization and background correction
 
Submission date Mar 17, 2015
Last update date Oct 01, 2015
Contact name Gregory Ragland
E-mail(s) gragland@ksu.edu
Phone 7855326139
Organization name Kansas State University
Department Entomology
Street address 123 West Waters Hall
City Manhattan
State/province KS
ZIP/Postal code 66506
Country USA
 
Platform ID GPL19895
Series (1)
GSE66975 Gene expression in Rhagoletis pomonella and R. zephyria transplanted into snowberry and apple fruits

Supplementary file Size Download File type/resource
GSM1635276_US83800208_252850010007_S01_GE2-v5_10_Apr08_1_2.txt.gz 12.7 Mb (ftp)(http) TXT
Processed data are available on Series record

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