Investigation Title	Genotyping of human lymphoblastoid cell lines from pairs of HapMap indiviudals pooled in varying proportions using Illumina GoldenGate SNP arrays	
Comment[Submitted Name]	Control experiment for Illumina GoldenGate SNP arrays	
Experimental Design	genotyping_design	replicate_design	genotyping by array	
Experimental Design Term Source REF		The MGED Ontology	EFO	
Comment[ArrayExpressReleaseDate]	2010-03-30	
Comment[SecondaryAccession]		
Comment[AEMIAMESCORE]	4	
Comment[ArrayExpressAccession]	E-TABM-855	
Comment[MAGETAB TimeStamp_Version]	2010-08-13 13:28:43 Last Changed Rev: 13058	
Experimental Factor Name	Protocol	Individual	
Experimental Factor Type	protocol	individual	
Experimental Factor Term Source REF	
Person Last Name	Ritchie	
Person First Name	Matthew	
Person Mid Initials	
Person Email	mritchie@wehi.edu.au	
Person Phone	
Person Fax	
Person Address	
Person Affiliation	The Walter and Eliza Hall Institute of Medical Research	
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	2010-03-30	
PubMed ID	
Publication DOI	
Publication Author List	Matthew E Ritchie, Matthew S Forrest, Antigone S Dimas, Caroline Daelemans, Emmanouil T Dermitzakis, Panagiotis Deloukas, Simon Tavare	
Publication Title	Data analysis issues for allele-specific expression using Illumina	
Publication Status	
Publication Status Term Source REF	
Experiment Description	In this experiment genomic DNA samples from lymphoblastoid cell lines from pairs of HapMap indiviudals were pooled in varying proportions.  This design produces predictable changes in allelic imbalance for all SNPs which differ between individuals.  The mixtures were hybridized to Illumina GoldenGate SNP arrays.	
Protocol Name	P-TABM-4470	P-TABM-4467	P-TABM-4466	P-TABM-4468	P-TABM-4469	
Protocol Type	specified_biomaterial_action	nucleic_acid_extraction	labeling	hybridization	feature_extraction	
Protocol Description	gDNA samples from pairs of HapMap individuals (NA12892 and NA19092 in series A and NA07022 and NA19143 in series B) were mixed in different proportions (series A mixing proportions of NA12892:NA19092: 0%:100%, 5%:95%, 91%:9%, 83%:17%, 67%:33%, 64%:36%, 60%:40%, 56%:44%, 50%:50%, 44%:56%, 40%:60%, 36%:64%, 33%:67%, 17%:83%, 9%:91%, 5%:95% and 100%:0%.  Series B mixing proportions of NA07022:NA19143: 0%:100%, 91%:9%, 83%:17%, 67%:33%, 64%:36%, 60%:40%, 56%:44%, 50%:50%, 44%:56%, 40%:60%, 36%:64%, 33%:67%, 17%:83%, 9%:91% and 100%:0%).	Genomic DNA (gDNA) was extracted using standard phenol-chloroform separation. Genomic DNA was quantified using a spectrophotometer and Quant-it DNA Assay (Invitrogen).	Samples were processed according to the manufacturer's instructions for GoldenGate genotyping assays.	Samples were hybridized for 16 hours to a 96-sample Sentrix Array Matrix according to the manufacturer's instructions for GoldenGate genotyping assays.	The arrays were scanned on the Illumina BeadArray Reader and image analysis was perfomed using Illumina's default image analysis algorithm.	
Protocol Parameters	
Protocol Hardware	
Protocol Software	
Protocol Contact	
Protocol Term Source REF					The MGED Ontology	
SDRF File	E-TABM-855.sdrf.txt	
Term Source Name	EFO	ArrayExpress	The MGED Ontology	EFO	
Term Source File	http://www.ebi.ac.uk/efo/	http://www.ebi.ac.uk/arrayexpress	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/efo/	
Term Source Version