Investigation Title	Transcription profiling of Mus musculus wild type vs mutant with knocked out Lsh to investigate mouse embryonic fibroblasts (MEFs)	
Comment[Submitted Name]	Mouse Lsh KO - expression. Stancheva Lab	
Experimental Design	genetic_modification_design	in_vivo_design	co-expression_design	transcription profiling by array	transcription profiling by array	
Experimental Design Term Source REF	The MGED Ontology		The MGED Ontology	EFO	EFO	
Comment[SecondaryAccession]		
Comment[ArrayExpressReleaseDate]	2009-11-30	
Comment[AEMIAMESCORE]	4	
Comment[ArrayExpressAccession]	E-MEXP-2385	
Comment[MAGETAB TimeStamp_Version]	2010-10-14 06:06:08 Last Changed Rev: 14677	
Experimental Factor Name	GENOTYPE	
Experimental Factor Type	genotype	
Experimental Factor Term Source REF	
Person Last Name	de las Heras	
Person First Name	Jose	
Person Mid Initials	I	
Person Email	j.delasheras@ed.ac.uk	
Person Phone	441316513374	
Person Fax	
Person Address	Wellcome Trust Centre, Mayfield Rd., Edinburgh, Scotland, EH9 3JR, United Kingdom	
Person Affiliation	University of Edinburgh	
Person Roles	submitter	
Person Roles Term Source REF	The MGED Ontology	
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	2009-11-30	
PubMed ID	
Publication DOI	
Publication Author List	
Publication Title	
Publication Status	
Publication Status Term Source REF	
Experiment Description	Expression profiling of mouse embryonic fibroblasts (MEFs), "wild type" vs. Lsh knock-out.	
Protocol Name	P-MTAB-5492	P-NGEN-5	P-NGEN-9	P-NGEN-13	P-MTAB-5490	P-MTAB-5491	
Protocol Type	nucleic_acid_extraction	labeling	hybridization	feature_extraction	bioassay_data_transformation	bioassay_data_transformation	
Protocol Description	total RNA was extracted using Invitrogen's Trizol reagent. <br><br>Quality was assessed by gel electrophoresis and spectrophotometry (using a Nanodrop spectrophotometer).<br><br>cDNA was synthesised using an anchored poly(dT) primer (20mer) and INvitrogen's SuperscriptII reverse transcriptase. RNA was hydrolysed in basic conditions, and cDNA measured using a Nanodrop sprectrophotometer. About 2.5ug of cDNA were sent to Nimblegen for labelling (Cy3) and hybridisation using their own protocols. <br>(Parameters: Extracted product = total_RNA, Amplification = none)	Title: NimbleGen Sample Labeling (Expression) v1.0. Description: 	Title: NimbleGen Hybridization & Washing (Expression) v1.0. Description: 	Title: NimbleGen One-Color Array Scanning (Expression) v1.0. Description: 	Raw data (one colour) were quantile normalised, and probesets summarised using the median polish algorithm.	Normalised and summarised probeset data were processed with Limma (BioConductor) to fit a linear model, and obtain statistics for each probeset.	
Protocol Parameters	
Protocol Hardware	
Protocol Software	
Protocol Contact	
Protocol Term Source REF				The MGED Ontology	The MGED Ontology	The MGED Ontology	
SDRF File	E-MEXP-2385.sdrf.txt	
Term Source Name	EFO		The MGED Ontology	ArrayExpress	The MGED Ontology	EFO	
Term Source File	http://www.ebi.ac.uk/efo/		http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/arrayexpress	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/efo/	
Term Source Version