Comment[ArrayExpressAccession]	E-GEOD-51729
MAGE-TAB Version	1.1						
Public Release Date	2014-05-20
Investigation Title	Apple pedicel vascular development array						
Comment[Submitted Name]	Apple pedicel vascular development array
Experiment Description	This SuperSeries is composed of the SubSeries listed below. Refer to individual Series						
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	Celton						
Person First Name	Jean-Marc						
Person Email	jean-marc.celton@angers.inra.fr						
Person Affiliation	INRA-IRHS						
Person Address	INRA-IRHS, 42 rue Georges Morel, Beaucouzé, France						
Person Roles	submitter						
Protocol Name	P-GSE51729-1	P-GSE51729-5	P-GSE51729-6	P-GSE51729-2	P-GSE51729-3	P-GSE51729-4	P-GSE51729-7
Protocol Description	All statistical analyses on the gene expression data were performed using the R language, version 2.5.1 (R Development Core Team, 2011) and the package LIMMA (Smyth G.K., 2005) from the Bioconductor project. For the processing step, data were normalized by the lowess method in LIMMA. ID_REF =  VALUE = Normalized log2 signal intensity	400ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse-transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1,5mmol of Cyanine-3 (Cy3) or Cyanine-5 (Cy5) (Interchim, France), then purified with NucleoSpin Gel and PCR Clean-up column kits (Macherey-Nagel, GmbH & Co. KG, Germany). Purified labeled cDNA were quantified using NanoDrop ND-1000 (Nanodrop Technologies, DE, USA). Labelled samples were combined as 30 pmol for each dye and co-hybridized to the Medtr_v1 12x135K arrays.	The hybridization performed on a NimbleGen Hybridization System 4 (mix mode B) at 42° overnigth. Afterwards, the slide were washed, dried, and scanned.	Trees were trained according to horticultural practices. No thinning reagent was applied	orchard conditions Trees were grown in orchard at the INRA experimental station ' la Rétuzière', Champigné, France	Macherey-Nagel NucleoSpin RNA Plant RNA was purified using NucleoSpin RNA Plant extraction kit (Macherey-Nagel) according to the manufacturer specifications	Slides were scanned at 532/635nm at 2 μm resolution and high sensitivity with a Roche-NimbleGen MS200. NimbleScan Software v2.4 was used to extract pair-data files from the scanned images.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	TISSUS	PHENOTYPE	AGE				
Experimental Factor Type	tissus	phenotype	age				
Publication Title	Additional amphivasal bundles in pedicel pith exacerbate central fruit dominance and induce self-thinning of lateral fruitlets in apple.						
Publication Author List	Celton JM, Dheilly E, Guillou MC, Simonneau F, Juchaux M, Costes E, Laurens F, Renou JP						
PubMed ID	24550240						
Publication DOI	10.1104/pp.114.236117						
Comment[SecondaryAccession]	GSE51729						
Comment[GEOReleaseDate]	2014-05-20						
Comment[ArrayExpressSubmissionDate]	2013-10-25						
Comment[GEOLastUpdateDate]	2014-05-21						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-51729.sdrf.txt