Investigation Title	Transcription profiling of non-obese diabetic (NOD) mice with or without the scid mutation and BDC2.5 TCR gene knock-in to study T-cell mediated B-cell damage and repair	
Comment[Submitted Name]	RAD.Study[study_id=2440]: T Cell Mediated B-cell Damage and Repair in NOD Mice.	
Experimental Design	genetic_modification_design	strain_or_line_design	transcription profiling by array	
Experimental Design Term Source REF	The MGED Ontology	mo	EFO	
Comment[ArrayExpressReleaseDate]	2006-10-03	
Comment[AEMIAMESCORE]	4	
Comment[ArrayExpressAccession]	E-CBIL-18	
Comment[MAGETAB TimeStamp_Version]	2010-07-29 15:26:40 Last Changed Rev: 13058	
Experimental Factor Name	Genetic Background (NOD vs. NOD.scid)	Genetic Modification (BDC2.5 TCR Transgenic)	
Experimental Factor Type	strain_or_line	genetic_modification	
Experimental Factor Term Source REF	
Person Last Name	Katz	Rankin	Liu	
Person First Name	Jonathan	Sara	Junmin	
Person Mid Initials	
Person Email	jonathan.katz@cchmc.org		junmin@pcbi.upenn.edu	
Person Phone	
Person Fax	
Person Address	Cincinnati Children's Hospital Research Foundation and College of Medicine; 3333 Burnet Ave.; Cincinnati; Ohio; 45229-3039; USA.	Affymetrix/Genomics Core; Cincinnati Childrens Hospital Research Foundation; Cincinnati; OH; 45229; USA.	
Person Affiliation	University of Cincinnati	University of Cincinnati	
Person Roles	submitter	investigator	data_coder	
Person Roles Term Source REF	The MGED Ontology	The MGED Ontology		
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	2006-10-03	
PubMed ID	15671250	
Publication DOI	15671250	
Publication Author List	Vukkadapu Sankaranand S, Belli Jenine M, Ishii Koji, Jegga Anil G, Hutton John J, Aronow Bruce J, Katz Jonathan D	
Publication Title	Dynamic interaction between T cell-mediated beta-cell damage and beta-cell repair in the run up to autoimmune diabetes of the NOD mouse.	
Publication Status	journal_article	
Publication Status Term Source REF	
Experiment Description	Dynamic interaction between T-cell mediated beta-cell damage and beta-cell repair in the run up  to autoimmune diabetes of the NOD mice.	
Protocol Name	cbil.upenn.edu:RAD.Protocol:4546:Protocol	cbil.upenn.edu:RAD.Protocol:925:Protocol	cbil.upenn.edu:RAD.Protocol:263:Protocol	cbil.upenn.edu:RAD.Protocol:904:Protocol	
Protocol Type	nucleic_acid_extraction	labeling	hybridization	feature_extraction	
Protocol Description	Tissue is dissected and total RNA is extracted using a standard guanidinium isothiocyanate method.	See pages 2.1.10-2.1.17 of the GeneChip Expression Analysis Technical Manual for all details. First-strand cDNA is synthesized from (5.0 to 20.0 ug) high-quality total RNA, using the GeneChip T7-Oligo(dT) Promoter Primer Kit or random primers provided with the SuperScript Choice Kit. Second-strand synthesis is carried out in: 1X second-strand reaction buffer, 200 uM each dNTP mix, 10 U E. coli DNA ligase, 40 U E. coli DNA polymerase I, 2 U E. coli RNase H in a final volume of 150 uL. The double-stranded cDNA is cleaned-up using the components supplied with the GeneChip Sample Cleanup Module. Enzo BioArray HighYield RNA Transcript Labeling Kit (Affymetrix, P/N 900182) is used to synthesize biotin-labeled cRNA target. The latter is cleaned up using the components supplied with the GeneChip Sample Cleanup Module.	The fragmented cRNA is mixed with the hybridization cocktail, and heat shocked at 99C for 5 minutes.  In the meanwhile, the probe array is filled with hybridization buffer and incubated at 45C for 10 minutes with rotation.  The heated hybridization cocktail is then transferred to a 45C heat block for 5 minutes, and spun at maximum speed in a microcentrifuge for 5 minutes.  Fill the probe array cartridge with the clarified hybridization cocktail and place probe array in rotisserie box in 45C oven. Hybridize for 16 hours.	RMA is the Robust Multichip Average. It consists of three steps: a background adjustment (optional), quantile normalization (optional), and finally summarization.	
Protocol Parameters	
Protocol Hardware			Affymetrix Fluidics Station 400	
Protocol Software				RMAExpress quantification	
Protocol Contact	
Protocol Term Source REF	The MGED Ontology	The MGED Ontology	The MGED Ontology	The MGED Ontology	
SDRF File	E-CBIL-18.sdrf.txt	
Term Source Name		mgd	ncbitax	mo	cbil_cv	The MGED Ontology	ArrayExpress	The MGED Ontology	mo	EFO	
Term Source File		http://www.informatics.jax.org/	http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.cbil.upenn.edu/anatomy.php3	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