7 protocols
AccessionNameType
P-MTAB-31594
normalization data transformation protocol
Basic data preprocessing was done in Partek Genomics Suite 6.6 (6.12.0712) with these options: Background correction - GCRMA algorithm, Normalization - Quantile normalization, Log Probes using Base - 2, Probeset summarization - Median polish.
P-MTAB-31593
hybridization
Fragmented cRNA (10 ug) was hybridized in GeneChip 640 Hybridization Oven (Affymetrix) to a GeneChip?? Drosophila Genome 2.0 Array (Affymetrix) according to standard protocol. The washing and staining of the arrays with phycoerythrin-conjugated streptavidin (Molecular Probes, Eugene, OR) was completed in Fluidics Station 450 (Affymetrix). Arrays were scanned using GeneChip 3000 7G Scanner (Affymetrix).
P-MTAB-31592
nucleic acid labeling protocol
Total RNA (100 ng) was amplified and labelled using standard protocols for GeneChip 3??? IVT Express Kit (Affymetrix).
P-MTAB-31590
treatment protocol
Third instar larvae (approx. 88 hrs after egg-laying) were rinsed briefly in water and placed in wells of a microtiter plate (96-well, flat bottom) containing approx. one cm2 of wet tissue paper. The control assay plate was covered with Parafilm and kept in dark at 25 degrees Celsius for 2 hours. Then Drosophila larvae were rinsed briefly in water again and transfered back to vials with instant fly food and RU486 (3.5 ug/ml). After 6 hours they were harvested and kept frozen until RNA extraction.
P-MTAB-31588
growth protocol
24 hrs after egg-laying, 30 first instar larvae were transfered to food vials (standard corn-meal diet).The animals were allowed to feed and develop at 25 degrees Celsius into third instar larvae. 84 hrs after egg-laying larvae were transfered to instant fly food (1 g mixed with 3.5 ml water solution of RU486, final concentration of RU486 3.5 ug/ml).
P-MTAB-31591
nucleic acid extraction protocol
Total RNA from 15 larvae/sample was extracted using RiboZol RNA extraction reagent according to the manufacturer?s instructions (Amresco) and subsequently cleaned with NucleoSpin RNA II kit (Macherey-Nagel).
P-MTAB-31589
treatment protocol
Third instar larvae (approx. 88 hrs after egg-laying) were rinsed briefly in water and placed in wells of a microtiter plate (96-well, flat bottom) containing approx. one cm2 of tissue paper. IJs (of H. bacteriophora harbouring GFP-labelled P. luminescens) were washed with tap water, diluted to the final density 10 IJs/?l and 10 ?l of required nematode suspension was added to each well containing one Drosophila larva. The assay plate was covered with Parafilm and kept in dark at 25 degrees Celsius for 2 hours. Then Drosophila larvae were rinsed briefly in water again and transfered back to vials with instant fly food and RU486 (3.5 ug/ml). After 6 hours they were checked for GFP signal (due to Photorhabdus septicaemia) and kept frozen until RNA extraction.