Comment[ArrayExpressAccession]	E-MTAB-1811
MAGE-TAB Version	1.1
Investigation Title	Transcription profiling of the radicle and micropylar endosperm cap of Lepidium seeds during germination in response to temperature
Comment[Submitted Name]	Transcription profiling of the radicle and micropylar endosperm cap of Lepidium seeds during germination in response to temperature
Experiment Description	An experiment was performed to compare global transcription patterns in two tissues of Lepidium sativum seeds at different temperatures during imbibition for 10h. RNA extractions from the two tissues were hybridized to Affymetrix ATH1 Arabidopsis microarrays. The two tissues were the radicle and the micropylar endosperm cap that covers it. The interaction of these two tissues is thought to control the timing of germination though alterations in the extensibility of the radicle and the physical resistance of the micropylar endosperm cap to radicle penetration. Only seeds without endosperm rupture were sampled.
Experimental Design	stimulus_or_stress_design	in_vivo_design	co-expression_design
Comment[AEExperimentType]	transcription profiling by array
Comment[AEExperimentDisplayName]	Transcription profiling by array of radicle and micropylar endosperm cap from Lepidium seeds during germination in response to temperature
Experimental Factor Name	temperature	organism part
Experimental Factor Type	temperature	organism part
Quality Control Type	biological replicate
Quality Control Term Source REF	EFO
Public Release Date	2013-10-06
Person Last Name	Leubner
Person First Name	Gerhard
Person Mid Initials
Person Email	gerhard.leubner@rhul.ac.uk
Person Phone
Person Address	Egham Hill TW20 0EX Egham, Surrey
Person Affiliation	Royal Holloway University of London, School of Biological Sciences
Person Roles	submitter
PubMed ID
Publication Author List	Antje Voegele, Tina Steinbrecher, Anita Kleiber, DanuM-BM-^Ze TarkowskM-CM-!, Terezie UrbanovM-CM-!, Veronika Ture?kovM-CM-!, Karin Weitbrecht, Kai Graeber, Miroslav Strnad and Gerhard Leubner-Metzger
Publication Title	The Molecular Biomechanics of the Micropylar Endosperm as a Major Mediator of the Germination Responses of Lepidium sativum Seeds to Sub- and Supra-Optimal Temperatures
Publication Status	completed manuscript
Protocol Name	P-MTAB-34006	P-MTAB-34007	P-MTAB-34008	P-MTAB-34009
Protocol Type	growth protocol	treatment protocol	nucleic acid extraction protocol	nucleic acid labeling protocol
Protocol Description	After-ripened Lepidium sativum L. FR1 ('Gartenkresse, einfache') seeds (Juliwa, Heidelberg, Germany) were incubated in petri dishes on two layers of filter paper with 6 ml 1/10 Murashige-Skoog salts in continuous white light (ca. 100 M-5molM-^Us-1M-^Um-2) at the temperature indicated. 	Four biological replicates of seeds were sampled after 10h of imbibition at 11 degrees C, 18 degrees C, 27 degrees C and 32 degrees C.  Two tissues (micropylar endosperm cap and radicle) were dissected from individual seeds. The dissected tissues (ca. 200 endosperm caps (Cap), and ca. 50 radicles (Rad)) were pooled for each sample, frozen in liquid nitrogen and stored at -80 M-:C.	CTAB/Chloroform extraction followed by RNA clean-up with the Qiagen Rneasy kit, followed by quantity and quality controls	The Affymetrix 3' IVT-Express Labeling Kit (#901229) was used to synthesize Biotin-labeled cRNA. From each RNA sample 100 ng was used as input for the labeling reactions.
Protocol Term Source REF	EFO	EFO	EFO	EFO
Term Source Name	EFO	ArrayExpress
Term Source File	http://www.ebi.ac.uk/efo	http://www.ebi.ac.uk/arrayexpress
SDRF File	E-MTAB-1811.sdrf.txt