Specification Sheet: Genefficiency Methylation

Tuesday 23 August 2011

Applications:: Genomic services

Specifications for Oxford Gene Technology (OGT) microarray service for methylation studies

Measurable	OGT arrays (Agilent)
360° QC	DNA QC upon sample arrival QC of labelling efficiency and incorporation LIMS sample tracking
Microarray platform	OGT design printed on Agilent SurePrint™ HD or G3 CGH microarrays Agilent: G4492A Human CpG Island Arrays and Mouse G4811A CpG Island Arrays
Species covered	Catalogue: Human, mouse Bespoke: Designed using eArray
Array density	1x244k, 2x105k, 4x44k (OGT design on any Agilent G3 array formats)
Experimental design consultancy	Available on request
Sample preparation consultancy	Available on request
Starting sample	Post-methylation immunoprecipitation DNA
Starting sample requirement	5 μg of purified genomic DNA prior to preparation (e.g. immunoprecipitation of methylated DNA). All processed DNA is used
Labelling method	Enzymatic labelling
Slide format	1x244k, 2x105k, 4x44k, 8x15k; G3: 1x1M, 2x400k, 4x180k, 8x60k. Printed using Agilent SurePrint™ technology inconsistent
No. of controls	Number depends on array density; minimum 1,600
Replicate no. of probes	Tiling array: Variable numbers of multiple single probes per CNV region
Tm equalised	Due to the high CG content in CpG islands, the standard Tm restriction was lifted to achieve appropriate spacing
Genome coverage	237,220 probes in/within 95 bp of CpG islands
Database version	Enriched content sourced from UCSC hg18 (NCBI Build 36.1, March 2006)
Custom sequences	Available on request
Custom design by OGT	Available on request
Single/dual colour	Dual
Dynamic range	5 logs
Data analysis	Tailored to customer requirements (includes feature extraction, QC report, CytoSure™ analysis software)
Data format	Tailored to customer requirements TIFF images, XML files, TXT files (raw data), customer report, relevant data analysis files (e.g. CytoSure), QC report