Investigation Title	Transcription profiling of 100 Arabidopsis Col/Ler recombinant inbred lines to generate a high-density genetic linkage map	
Comment[Submitted Name]	Arabidopsis Col/Ler RIL genotyping	
Experimental Design	genotyping_design	strain_or_line_design	transcription profiling by array	
Experimental Design Term Source REF		mo	EFO	
Comment[ArrayExpressReleaseDate]	2006-09-01	
Comment[AEMIAMESCORE]	4	
Comment[ArrayExpressAccession]	E-TABM-135	
Comment[MAGETAB TimeStamp_Version]	2010-09-07 05:11:26 Last Changed Rev: 13833	
Experimental Factor Name	Ecotype	StrainOrLine	
Experimental Factor Type	ecotype	strain_or_line	
Experimental Factor Term Source REF	
Person Last Name	Singer	
Person First Name	Tatjana	
Person Mid Initials	
Person Email	tsinger@salk.edu, tatjana_singer@hotmail.com	
Person Phone	
Person Fax	
Person Address	
Person Affiliation	Salk Institute for Biological Studies	
Person Roles	
Person Roles Term Source REF	
Quality Control Type	biological_replicate	
Quality Control Term Source REF	The MGED Ontology	
Replicate Type	
Replicate Term Source REF	
Normalization Type	
Normalization Term Source REF	
Date of Experiment	
Public Release Date	2006-09-01	
PubMed ID	
Publication DOI	
Publication Author List	Tatjana Singer, Yiping Fan, Hur-Song Chang, Tong Zhu, Samuel P. Hazen, Steven P. Briggs	
Publication Title	A High-Resolution Map of Arabidopsis Recombinant Inbred Lines by Whole-Genome Exon Array Hybridization	
Publication Status	
Publication Status Term Source REF	
Experiment Description	The aim of this study was to generate a high-density genetic linkage map of Arabidopsis. A custom-designed exon-specific whole-genome array was used to identify ~16,000 significant SFP markers between the parental accessions Col and Ler. Subsequently 100 Col/Ler recombinant inbred lines (RILs) were hybridized to the whole genome exon arrays and the SFP-markers genotyped in all lines.	
Protocol Name	P-TABM-612	P-TABM-614	P-TABM-615	Affymetrix:Protocol:Hybridization-DNA hybridization	P-AFFY-6	
Protocol Type	grow	nucleic_acid_extraction	labeling	hybridization	feature_extraction	
Protocol Description	Eight plants for WT or each RIL were grown for 30 days in one pot under long-day conditions. (16h light, 8h dark, 23 degree_C). 3-4 leaves per plant of all 8 plants in a pot were harvested and frozen in liquid nitrogen.	Total genomic DNA was isolated from leaf tissue with the DNeasy Plant Mini Kit (Qiagen, Valencia, California, United States) according to the manufacturer’s instructions.	1ug DNA was labeled by random priming with biotin14-dCTP (Bioprime DNA labeling system, Invitrogen, Carlsbad, California, United States). 2h, 37 degree_C		Title: Affymetrix CEL analysis. Description: 	
Protocol Parameters	
Protocol Hardware	
Protocol Software					MicroArraySuite 5.0	
Protocol Contact	
Protocol Term Source REF	
SDRF File	E-TABM-135.sdrf.txt	
Term Source Name		nasc	ncbitax	The MGED Ontology	ArrayExpress	The MGED Ontology	mo	EFO	
Term Source File		http://arabidopsis.info/catalogue.html	http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/arrayexpress	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/efo/	
Term Source Version