Comment[ArrayExpressAccession]	E-MTAB-840
Investigation Title	Genotyping by high throughput sequencing of four different cultivars of Lilium																															
Comment[Submitted Name]	Genotyping by high throughput sequencing of four different cultivars of Lilium
Experiment Description	The cDNA of 4 Lilium cultivars were sequenced in this study in order to develop SNP markers for mapping purpose. The four selected cultivars represent the four main hybrid groups in Lilium which are (Asiatic, Oriental, Longiflorum, and Trumpet). The SNP markers developed of this study will be implemented in mapping and association studies that aims to find SNP markers linked to virus resistance in Lilium. To achieve this target, SNP markers were generated from each cultivar separately, and of the four cultivars together trying to cover as much as variation in each cultivar and also to find SNP markers that can  distinguish the four cultivars. Doing so, we hope to identify different genes resistance to virus in the four hybrid groups of Lilium. 																															
Experimental Design	strain_or_line_design	genotyping_design																														
Comment[AEExperimentType]	genotyping by high throughput sequencing																															
Experimental Factor Name	STRAINORLINE																															
Experimental Factor Type	strain_or_line																															
Public Release Date	2013-01-17																															
Person Last Name	Borm																															
Person First Name	Theo																															
Person Email	theo_arrayexpress@borm.org																															
Person Roles	submitter																															
Person Affiliation	Wageningen University and Research Centre, Dept. of Plant Sciences, Laboratory of Plant Breeding																															
Person Address	Droevendaalsesteeg 1, 6708PB Wageningen, Netherlands.																															
Publication Author List	Arwa Shahin, Thomas van Gurp, Sander A. Peters, Richard G.F. Visser, Jaap M. van Tuyl, Paul Arens																															
Publication Title	SNP markers retrieval for a non-model species: a practical approach																															
Publication Status	under review																															
Protocol Name	P-MTAB-24564	P-MTAB-24565	P-MTAB-24566	P-MTAB-24567	P-MTAB-24568
Protocol Type	grow	specified_biomaterial_action	nucleic_acid_extraction	sequencing	scanning																											
Protocol Description	Plants were grown  in open field without any chemical treatment	Young leaves were picked and immediately frozen in liquid nitrogen and kept at -80 degree Celsius before RNA isolation	mRNA-extracted using Trizol protocol (Invitrogen. Carlsbad, CA, USA), and purified using the RNeasy MinElute kit (Qiagen, Hilden, Germany)	sequencing cDNA fragments using 454 GS FLX Titanium sequencing at Wageningen UR Greenomics (Wageningen, the Netherlands). The sequence data were coded as A, T, C, G.	SFF file was generated from 454 Roche machine																											
Protocol Hardware				454 GS FLX Titanium																												
Comment[SecondaryAccession]	ERP001106																															
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/ERR063465-ERR063468																															
SDRF File	E-MTAB-840.sdrf.txt