Investigation Title	Transcription profiling of mouse lymphoma L5178Y and Human TK6 cells treated with Methylmethane Sulfonate ILSI-HESI Genotoxicity Study - MMS	
Comment[Submitted Name]	ILSI-HESI Genotoxicity Study - MMS	
Experimental Design	dose_response_design	compound_treatment_design	transcription profiling by array	
Experimental Design Term Source REF		mo	EFO	
Comment[ArrayExpressReleaseDate]	2005-02-13	
Comment[AEMIAMESCORE]	3	
Comment[ArrayExpressAccession]	E-TOXM-7	
Comment[MAGETAB TimeStamp_Version]	2010-10-14 03:23:15 Last Changed Rev: 14677	
Experimental Factor Name	compound	dose	compound	performer	time	
Experimental Factor Type	compound_treatment_design	dose	compound_treatment_design	performer	time	
Experimental Factor Term Source REF	
Person Last Name	Pettit	
Person First Name	Syril	
Person Mid Initials	D	
Person Email	spettit@ilsi.org 	
Person Phone	(202) 659-3306	
Person Fax	(202)659-3617	
Person Address	
Person Affiliation	ILSI Health and Environmental Sciences Institute	
Person Roles	submitter	
Person Roles Term Source REF		
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	2005-02-13	
PubMed ID	
Publication DOI	
Publication Author List	Newton RK, Aardema M, Aubrecht J	
Publication Title	The Utility of DNA Microarrays for Characterizing Genotoxicity	
Publication Status	
Publication Status Term Source REF	
Experiment Description	Mouse lymphoma L5178Y and Human TK6 cells are treated with Methylmethane Sulfonate [CAS:66-27-3;CHEBI:25255] and harvested a 4 and 24 hours for analysis.	
Protocol Name	P-TOXM-193	P-TOXM-190	P-TOXM-191	P-TOXM-194	P-TOXM-195	P-TOXM-199	
Protocol Type	compound	grow	grow	nucleic_acid_extraction	labeling	hybridization	
Protocol Description	100mL of a 5 x 10^5 cells/mL culture is exposed to a defined concentration of each test chemical (dissolved in DMSO for final concentration of <= 1%) and incubated for 4 hours at 37 degrees C.	Mouse lymphoma L5178Y TK+/- cells were maintained in RPMI 1640 media supplemented with 2 mg/mL sodium bicarbonate, 10ug/mL folic acid, 1.5 mg/mL L-glutamine, 0.11 mg/mL sodium pyruvate, 0.5 mg/mL Pluronit F68 and 100 U/mL final concentration each of a pen/strep mixture all adjusted to a pH of 7.2.  Media was supplemented with 10% heat-inactivated horse serum for cell growth.	Mouse TK6 cells were maintained in RPMI 1640 media supplemented with 2 mg/mL sodium bicarbonate, 10ug/mL folic acid and 100 U/mL final concentration each of a pen/strep mixture all adjusted to a pH of 7.2.  	Cells are washed twice with growth media through centrifugation for 5 min at 1200xg and resuspension.  Pellets are rinsed twice in ice-cold Dulbecco's PBS and finally subjected to TRIzol extraction protocol.  Samples are stored in DEPC treated water.	As recommonded by Affymetrix	As per manufacturers protocols.	
Protocol Parameters		Temperature max;	Temperature max;	Extracted product;Amplification;	Amplification;Amount of nucleic acid labeled;Amount of nucleic acid labeled;	Quantity of label target used;Temperature;Chamber type;	
Protocol Hardware	
Protocol Software	
Protocol Contact	
Protocol Term Source REF	The MGED Ontology			mo		mo	
SDRF File	E-TOXM-7.sdrf.txt	
Term Source Name	mo		The MGED Ontology	ArrayExpress	mo	EFO	The MGED Ontology	
Term Source File	http://mged.sourceforge.net/ontologies/MGEDontology.php		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/	http://mged.sourceforge.net/ontologies/MGEDontology.php	
Term Source Version