Investigation Title	Transcription profiling of Medicago truncatula wild type and symbiotic mutant material 	
Comment[Submitted Name]	Medicago truncatula nodulation-related transcriptome	
Experimental Design	time_series_design	development_or_differentiation_design	strain_or_line_design	transcription profiling by array	
Experimental Design Term Source REF	mo:1.1.3	mo:1.3.1.1	mo	EFO	
Comment[ArrayExpressReleaseDate]	2004-06-28	
Comment[AEMIAMESCORE]	2	
Comment[ArrayExpressAccession]	E-MEXP-129	
Comment[MAGETAB TimeStamp_Version]	2010-10-15 01:04:56 Last Changed Rev: 14677	
Experimental Factor Name	Strain	Time	Inoculation	
Experimental Factor Type	strain_or_line	time	infect	
Experimental Factor Term Source REF	
Person Last Name	Gough	Niebel	Gamas	El Yahyaoui	Ben Amor	Gouzy	Vernie	Kuester	Hohnjec	Puehler	Becker	
Person First Name	Clare	Andreas	Pascal	Fikri	Besma	Jerome	Tatiana	Helge	Natalija	Alfred	Anke	
Person Mid Initials	
Person Email								Helge.Kuester@Genetik.Uni-Bielefeld.DE	
Person Phone								+49 521 106 4819	
Person Fax	
Person Address								Universitaetsstrasse 25, Bielefeld, NRW, 33615, Germany	
Person Affiliation	Laboratoire des Interactions Plantes Micro-organismes	Laboratoire des Interactions Plantes Micro-organismes	Laboratoire des Interactions Plantes Micro-organismes	Laboratoire des Interactions Plantes Micro-organismes	Laboratoire des Interactions Plantes Micro-organismes	Laboratoire des Interactions Plantes Micro-organismes	Laboratoire des Interactions Plantes Micro-organismes	Lehrstuhl Genetik	Lehrstuhl Genetik	Lehrstuhl Genetik	Lehrstuhl Genetik	
Person Roles								submitter	
Person Roles Term Source REF								mo	
Quality Control Type	
Quality Control Term Source REF	
Replicate Type	
Replicate Term Source REF	
Normalization Type	
Normalization Term Source REF	
Date of Experiment	
Public Release Date	2004-06-28	
PubMed ID	15466239	
Publication DOI	15466239	
Publication Author List	El Yahyaoui F; Kuster H; Ben Amor B; Hohnjec N; Puhler A; Becker A; Gouzy J; Vernie T; Gough C; Niebel A; Godiard L; Gamas P	
Publication Title	Expression profiling in Medicago truncatula identifies more than 750 genes differentially expressed during nodulation, including many potential regulators of the symbiotic program	
Publication Status	journal_article	
Publication Status Term Source REF	mo	
Experiment Description	This experiment constitutes an expression profiling approach to identify genes differentially regulated during the symbiotic interaction between the model legume Medicago truncatula and the nitrogen-fixing bacterium Sinorhizobium meliloti. Macro- and microarrays containing 6144 probes were generated on the basis of three cDNA libraries dedicated to the study of root symbiotic interactions. The experiment performed on wild-type and symbiotic mutant material led to the identification of genes either up- or down-regulated at different stages of the nodulation process.	
Protocol Name	P-MEXP-4287	P-MEXP-4300	P-MEXP-4289	P-MEXP-4299	P-MEXP-4291	P-MEXP-4292	P-MEXP-4295	P-MEXP-4294	
Protocol Type	grow	specified_biomaterial_action	nucleic_acid_extraction	pool	labeling	labeling	hybridization	hybridization	
Protocol Description	Plant growth chamber conditions were the following: temperature: 22C; 75% hygrometry; light intensity: 200 uE.m-2.s-1; light-dark photoperiod: 16h-8h.	Medicago truncatula wild type A17 or mutant TR122 root nodules were inoculated with wild type Sinorhizobium meliloti PCR2011 pXLGD4 (GMI6526) or S. meliloti strain PCR2011 nodA::Tn5#2208.	Total RNA was then extracted with Trizol (Invitrogen, Cergy Pontoise Cedex, France).	No pooling applied	Twenty ug of total RNA were reverse transcribed in the presence of 50 uCi [alpha-33P]dCTP with SuperscriptII RTase (Invitrogen), using anchored oligodT17 primer and 0.5 mM d[A, G, T]TP. A cold chase (1 h with 2 mM dCTP) was carried out after 1 h incubation at 42C. Reaction was stopped and RNA degraded in 0.3 M NaOH (30 min at 68C). After neutralisation in 0.4 M Tris-HCl pH 7.5, cDNAs were purified on MicroSpin S-200 columns (Amersham Biosciences Europe GmbH, Orsay, France). The labelling efficiency was quantified by liquid scintillation counting. 	Twenty ug of total RNA was used to synthesize Cy5- or Cy3- labeled first strand cDNA targets as described in Kuester et al. (J Biotechnol 108: 95-113; 2004).	Membranes were prehybridized during 3-4 h at 65C in 15 mL of Church buffer. The hybridisation was performed at 65C for 16 h in 10 mL of fresh hybridization solution containing the denaturated labelled target (25 to 50 106 cpm). Membranes were rapidly rinsed with solution-A (2xSSC, 0.1%(w/v) SDS), washed at 65C for 15 min in 100 mL of solution-A then 100 mL of solution-B (0.2xSSC, 0.1%(w/v) SDS).	Hybridization and washing was carried out as described in Kuester et al. (J Biotechnol 108: 95-113 (2004).	
Protocol Parameters			Amplification;Extracted product;		Amount of nucleic acid labeled;Amplification;Label used;	Label used;Amplification;Amount of nucleic acid labeled;	Quantity of label target used;temperature;Chamber type;	temperature;Quantity of label target used;Chamber type;	
Protocol Hardware	
Protocol Software	
Protocol Contact	
Protocol Term Source REF				mo	
SDRF File	E-MEXP-129.sdrf.txt	
Term Source Name	mo		ArrayExpress	mo:1.1.3	mo:1.3.1.1	mo	EFO	
Term Source File	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://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/efo/	
Term Source Version				1.1.3	1.3.1.1