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Sample GSM226641 Query DataSets for GSM226641
Status Public on Sep 11, 2007
Title TS-102
Sample type RNA
 
Source name Drosophila melanogaster larvae infected by Leptopilina boulardi, 9 to 12 hours post-infection, replicate 2.
Organism Drosophila melanogaster
Characteristics 40 second-instar (72 hours old at 22 degrees C) Drosophila melanogaster larvae (strain Oregon R) were attacked by females of the parasitic wasp, Leptopilina boulardi (strain Lb17). Fly larvae were collected 9 to 12 hours post-infection for tissue homogenization and RNA extraction.
Extracted molecule total RNA
Extraction protocol RNA was extracted using the standard Trizol method (Gibco), and was purified using RNeasy spin columns (Qiagen).
Label biotin
Label protocol RNA processing and hybridization protocols are available at www.affymetrix.com (Santa Clara, CA) and in the Genechip Expression Analysis Technical Manual. Two micrograms of total RNA were converted into double-stranded cDNA by using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit with the T7-(dT)24-primer [sequence 5’-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-(dT)24-3’]. The cDNA was purified as per protocol by using the GeneChip Sample Cleanup Modules. Purified cDNA was then used for in vitro transcription using the GeneChip Expression 3’-Amplification Reagents for IVT Labeling. Biotin-labeled cRNA was purified by GeneChip Sample Cleanup Modules and then randomly chemically fragmented to approximately 35 - 200 bp pieces.
 
Hybridization protocol Each fragmented cRNA sample was hybridized to the Affymetrix Drosophila Genome microarray for 16 hours at 60 rpm at 45°C. The microarray was washed and stained on the Affymetrix Fluidics Station 450 according to manufacture’s protocol. After washing out the nonhybridized material the array was incubated with phycoerythrin-streptavidin (SAPE, Molecular Probes, Eugene, OR). The signal intensity was amplified by second staining with biotin-labeled antistreptavidin antibody followed by SAPE staining.
Scan protocol Fluorescent images were read using Affymetrix GeneChip Scanner 3000. The microarrays were processed on the fluidics station under the control of the GeneChip Operating software (GCOS) and read according to the standard Affymetrix protocol. The signal, which represents the intensity of each gene, was extracted from the image. The target intensity value from each chip was scaled to 500. All RNA samples passed the quality control and ratio of 3’ to 5’ less than three.
Description Labeling, hybridization, and scanning protcols were carried out at the Weill Medical College Microarray Core Facility of Cornell University.
Data processing The GeneTraffic (Stratagene) software package was used for microarray data processing. Probe intensities were normalized using Robust Multi-Chip Analysis, using the three control replicates from each time point as the designated baseline.
 
Submission date Sep 02, 2007
Last update date Aug 28, 2018
Contact name Todd A Schlenke
E-mail(s) tschlen@emory.edu
Phone 404-727-0817
Fax 404-727-2880
Organization name Emory University
Department Department of Biology
Lab RRC room 1081
Street address 1510 Clifton Road NE
City Atlanta
State/province GA
ZIP/Postal code 30322
Country USA
 
Platform ID GPL1322
Series (1)
GSE8938 Contrasting infection strategies in generalist and specialist wasp parasitoids of Drosophila melanogaster.
Relations
Reanalyzed by GSE119084

Data table header descriptions
ID_REF
VALUE RMA signal

Data table
ID_REF VALUE
AFFX-BioB-5_at -0.459185308
AFFX-BioB-M_at -0.164790047
AFFX-BioB-3_at -0.41379754
AFFX-BioC-5_at 0.048294672
AFFX-BioC-3_at 0.291038845
AFFX-BioDn-5_at -0.145428027
AFFX-BioDn-3_at -0.394528916
AFFX-CreX-5_at 0.13715833
AFFX-CreX-3_at 0.009969217
AFFX-DapX-5_at 1.172646181
AFFX-DapX-M_at 0.865093447
AFFX-DapX-3_at 0.757792518
AFFX-LysX-5_at 1.240639012
AFFX-LysX-M_at 0.7396267
AFFX-LysX-3_at 1.053018592
AFFX-PheX-5_at 1.195477498
AFFX-PheX-M_at 0.822951624
AFFX-PheX-3_at 0.572225132
AFFX-ThrX-5_at 0.791471953
AFFX-ThrX-M_at 1.052781525

Total number of rows: 18952

Table truncated, full table size 444 Kbytes.




Supplementary file Size Download File type/resource
GSM226641.CEL.gz 3.5 Mb (ftp)(http) CEL
GSM226641.CHP.gz 6.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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