Comment[ArrayExpressAccession]	E-MTAB-1523
Investigation Title	Response of grapevine shoot apex expression to grafting with rootstocks
Comment[Submitted Name]	Response of grapevine shoot apex expression to grafting with rootstocks
Comment[AEExperimentType]	transcription profiling by array
Comment[AEExperimentDisplayName]	Transcription profiling by array of grapevine scion shoot apex to investigate responses to different rootstock genotypes
Experimental Design	strain_or_line_design
Experiment Description	The transcriptional response in the shoot apex to hetero-grafting Cabernet Sauvignon (CS) with the rootstocks 1103 Paulsen (CS/1103P) and Riparia Gloire de Montpellier (CS/RG) compared to the auto-grafted control (CS/CS) four months after grafting. Gene expression profiling was done using the Nimblegen whole genome array with 4 biological replicates of 5 pooled shoot apices.
Experimental Factor Name	strain
Experimental Factor Type	strain
Person Last Name	Cookson
Person First Name	Sarah Jane
Person Email	sarah.cookson@bordeaux.inra.fr
Person Phone	33557575923
Person Address	BM-btiment ISVV, 210 chemin de Leysotte, CS 50008, 33882 Villenave d'Ornon cedex, France
Person Affiliation	UMR 1287 Ecophysiologie et GM-inomique fonctionelle de la Vigne, Institut des Sciences de la Vigne et du Vin
Person Roles	submitter
Quality Control Type	biological_replicate
Public Release Date	2014-01-11
PubMed ID	24083813
Publication Author List	Cookson SJ, Ollat N.
Publication Title	Grafting with rootstocks induces extensive transcriptional re-programming in the shoot apical meristem of grapevine.
Publication Status
Protocol Name	P-MTAB-31364	P-MTAB-31365	P-MTAB-31366	P-MTAB-31367	P-MTAB-31368	P-MTAB-31381	P-MTAB-31370	P-MTAB-31371
Protocol Type	grow	specified_biomaterial_action	specified_biomaterial_action	nucleic_acid_extraction	labeling	hybridization	image_acquisition	bioassay_data_transformation
Protocol Description	After the formation of a successful graft union, plants were transferred to a greenhouse for one month for rooting (the greenhouse is designed to preferentially heat the root system).After callusing and rooting, grafted plants were planted in 7 L pots filled with calcareous clay soil and cultivated in an experimental plot outside (at the end of May). The plants were trained to one stem, side branches and inflorescences were removed. The plants were supplied with a nutrient solution several times a day. The composition of the nutrient solution was: 2.5 mM KNO3, 0.25 mM MgSO4.7H2O, 0.62 mM NH4NO3, 1 mM (NH4)H2PO4, 9.1 mM MnCl2.4H2O, 46.3 mM H3BO3, 2.4 mM ZnSO4.H2O, 0.5 mM CuSO4 and 0.013 mM (NH4)6Mo7O24. Iron was supplied as 8.5 mg/L Sequestrene 138 (EDDHA 5.9% Fe). Tap water introduced 0.69 mM Mg2+, 0.22 mM K+ and 0.22 mM SO42-, and final pH was 6.0. The climatic conditions from 1st June until 30th September 2010 were: average air temperature 20.6 M-0C; the average daily mean global radiation was 1962 joules/cmM-2; the average relative humidity 68.1 %.	Vitis vinifera cv. M-^QCabernet-Sauvignon NM-^R (CS, clone 15), V. riparia cv. M-^QRiparia Gloire de MontpellierM-^R (RG, clone 1030) and the V. berlandieri x V. rupestris hybrid cv. M-^Q1103 PaulsenM-^R (1103P, clone 198) hardwood was collected from a vineyard in January and stored as one meter long stems in a cold chamber (4 M-0C) until grafting in March.The scion CS was grafted onto RG and 1103P as well as auto-grafted onto CS rootstocks. Stored stems were taken out of the cold chamber the day before grafting and soaked in water at room temperature in order to rehydrate. One bud cuttings were made for scions and two-node de-budded cuttings were made for rootstocks shortly before grafting. Mechanical omega grafting was performed on scion/rootstock pairs of approximately the same diameter. Grafts were briefly dipped into melted wax and settled for callusing for 21 days at 28M-0C, 100% humidity.	Four pools of 5 shoot apex zones (approximately 4 mm in length) were harvested at the end of the night for each scion/rootstock combination in July (4 months after grafting) and immediately snap frozen in liquid nitrogen. 	Total RNA was extracted using the Spectrum Plant Total RNA kit (Sigma-Aldrich) according to the manufacturerM-^Rs instructions. 	2 ug of RNA were used for cDNA synthesis according to the NimbleGen Gene Expression protocol. cDNA samples were labeled with Cy3 using a NimbleGen One-Color DNA labeling kit.	The microarrays used were the grape whole genome NimbleGen microarrays (Roche, probeset design 090918 Vitus exp HX12). The microarray hybridizations were done for the 12 samples (three scion/rootstock combinations with four biological replicates) by the Plateforme Biopuces, Institut National des Sciences AppliquM-ies, Toulouse, France according to the manufacturerM-^Rs instructions. 	The slide was scanned using an MS200 from Tecan, after which resulting images were imported into NimbleScan software for grid alignment and expression data analyses. Raw data are in .xys.	The microarray data were analyzed using the statistical package R, version 2.14.0 (R Development Core Team, 2005) with various Bioconductor packages (http://www.bioconductor.org, Gentleman et al., 2004). Microarray quality controls were performed using the arrayQualityMetrics package (Kauffmann et al., 2009). Expression intensities were background corrected, quantile-normalized and summarized using the RMA function of the oligo package (Carvalho & Irizarry, 2010). Value are expressed in log2.
SDRF File	E-MTAB-1523.sdrf.txt
Publication DOI	10.1186/1471-2229-13-147