Comment[ArrayExpressAccession]	E-GEOD-47008
MAGE-TAB Version	1.1					
Public Release Date	2013-11-01
Investigation Title	Solanum torvum transcriptional responses to nematodes					
Comment[Submitted Name]	Solanum torvum transcriptional responses to nematodes
Experiment Description	Solanum torvum Sw is worldwide employed as rootstock for eggplant cultivation because of its vigour and resistance/tolerance to the most serious soil-borne diseasesas bacterial, fungal wilts and root-knot nematodes.  A 30,0000 features custom combimatrix chip was designed and microarray hybridizations were conducted for both control and 14 dpi (day post inoculation) with Meloidogyne incognita-infected roots samples. We also tested the chip with samples from the phylogenetically-related nematode-susceptible eggplant species Solanum melongena.The genes identified from S. torvum catalogue, bearing high homology to knownnematode resistance genes, were further investigated in view of their potential role in the nematode resistance mechanism. total RNA was extracted from control and 14 days post-infection (infection with root-knot nematode Meloidogyne  incognita)  from roots of Solanum torvum and Solanum melongena. Three biological replicates were used for each condition and genotype for a total of 12 samples.					
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl				
Person Last Name	Bagnaresi	Bagnaresi				
Person First Name	Paolo	Paolo				
Person Email	paolo.bagnaresi@entecra.it					
Person Affiliation	CRA-GPG					
Person Address	Genomics, CRA-GPG, Via S. Protaso 302, Fiorenzuola D'Arda, Italy					
Person Roles	submitter					
Protocol Name	P-GSE47008-1	P-GSE47008-4	P-GSE47008-5	P-GSE47008-2	P-GSE47008-3	P-GSE47008-6
Protocol Description	Data extraction was carried out using CombiMatrix Microarray Imager software, and a quantile normalization of raw medians and log2 transformation were performed using SPSS v.15.0 software. Further statistical processing was performed using the SAM analysis (T-MEV 4.3) ID_REF =  VALUE = quantile-normalized value	Total RNA (1M-NM-<g) was used as a template to synthesize antisense RNA (aRNA) with the SuperScriptM-bM-^DM-" Indirect RNA Amplification System Kit (Invitrogen) incorporating Alexa Fluor 647 Reactive Dye according to manufacturer's instructions	Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt's solution, 100 ng/ul Salmon Sperm DNA, 0.05% SDS) for 60 minutes at 45 M-0C. 5 ug of labeled aRNA were fragmented by incubation with Fragmentation Solution (40mM Tris Acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc) for 20 min at 95 M-0C. Hybridization was performed at 45M-0C for 16 hours in hybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 25% DiFormamide, 100 ng/ul Salmon Sperm DNA, 0.04% SDS). Hybridization washings were performed as the following: - wash with 6X SSPET wash solution (6X SSPE, 0.05% Tween-20). - wash with 3X SSPET wash solution (3X SSPE, 0.05% Tween-20). - wash with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20). - wash with PBST wash solution (2X PBS, 0.1% Tween-20). - 2 washes with 2X PBS	Seeds of Solanum torvum Sw accession TG1 [1] and eggplant (Solanum melongena L.) breeding line 1F5(9) were sown in a seed-plot for germination. Seedlings about 10 cm tall at the second-leaf stage were singly transplanted into 10 cm diameter plastic pots, each containing 500 cc of mixture sterilized sandy soil: 70% sand+ 15% leca + 10% clay (sterilized at 70M-oM-=M-0C for 24 hours) + 5% organic matter. The pots were maintained in controlled chambers at 24M-oM-=M-12M-oM-=M-0C, 60% relative humidity, with a 16-h light/8-h dark regimen. Plants were watered with tap water at necessity and fertilized every two weeks with a 20-20-20 NPK fertilizer.	total RNA samples were extracted by means of the Nucleospin RNA plant Kit (MACHEREY-NAGEL GmbH & Co., DM-CM-<ren, Germany) at 0 and 14 dpi.	After hybridization and washing, the microarray was dipped in imaging solution, covered with LifterSlipM-bM-^DM-", and then scanned using a Perkin Elmer ScanArray 4000XL and the accompanying acquisition software (ScanArray Express Microarray Analysis System v4.0). Multiple scanning at different PMT was provided for each hybridization.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	INFECTION BY NEMATODE	ORGANISM				
Experimental Factor Type	infection by nematode	organism				
Comment[SecondaryAccession]	GSE47008					
Comment[GEOReleaseDate]	2013-11-01					
Comment[ArrayExpressSubmissionDate]	2013-05-16					
Comment[GEOLastUpdateDate]	2013-11-03					
Comment[AEExperimentType]	transcription profiling by array					
SDRF File	E-GEOD-47008.sdrf.txt