Investigation Title	Comparative genomic hybridization of Candida albicans and Candida dublinienis	
Comment[Submitted Name]	Candida dubliniensis genomic hybrdisation	
Experimental Design	comparative_genome_hybridization_design	comparative genomic hybridization by array	
Experimental Design Term Source REF	mo	EFO	
Comment[ArrayExpressReleaseDate]	2004-04-30	
Comment[AEMIAMESCORE]	3	
Comment[ArrayExpressAccession]	E-MEXP-99	
Comment[MAGETAB TimeStamp_Version]	2010-08-11 16:53:46 Last Changed Rev: 13058	
Experimental Factor Name	organism	
Experimental Factor Type	organism	
Experimental Factor Term Source REF	
Person Last Name	Coleman	Moran	Thewes	Hube	Stokes	Sullivan	
Person First Name	David	Gary	Sascha	Bernhard	Cheryl	Derek	
Person Mid Initials	C	P	
Person Email		gpmoran@dental.tcd.ie	
Person Phone		+353 1 612 7245	
Person Fax		+353 1 612 7295	
Person Address		Lincoln Place, Dublin, Ireland, na, Ireland	
Person Affiliation	Microbiology Laboratory	Microbiology Laboratory	Microbiology Laboratory	Microbiology Laboratory	Microbiology Laboratory	Microbiology Laboratory	
Person Roles		submitter	
Person Roles Term Source REF		mo	
Quality Control Type	technical_replicate	
Quality Control Term Source REF	mo	
Replicate Type	
Replicate Term Source REF	
Normalization Type	
Normalization Term Source REF	
Date of Experiment	
Public Release Date	2004-04-30	
PubMed ID	15470115	
Publication DOI	15470115	
Publication Author List	 Gary Moran; Cheryl Stokes; Sascha Thewes; Bernhard Hube; David Coleman; Derek Sullivan	
Publication Title	Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence associated genes in Candida dubliniensis	
Publication Status	journal_article	
Publication Status Term Source REF	mo	
Experiment Description	Comparative genomic hybridisation between Candida albicans and Candida dublinienis using Eurogentec Candida albicans whole genome microarrays	
Protocol Name	P-MEXP-3298	P-MEXP-3299	P-MEXP-3504	P-MEXP-3502	P-MEXP-4591	P-MEXP-4590	P-MEXP-3503	P-MEXP-3505	P-MEXP-3301	
Protocol Type	grow	nucleic_acid_extraction	labeling	labeling	labeling	labeling	labeling	labeling	hybridization	
Protocol Description	Candida strains were grown at 37?C in Yeast extract Peptone Dextrose  (YEPD) broth	Candida total genomic DNA was prepared by organic extraction with phenol/chloroform following Zymolysae 20T (Seikagu Corp., Japan) digestion of cell walls and proteinase K treatment, as described by Gallagher et al., 1992. J Gen Microbiol. Vol 138: 1901-1911.	Candida dubliniensis genomic DNA was labelled with Cy3 (Amersham biosciences) following reduction of the chromosome fragment size by sonication to produce fragments 500 - 5,000 bp in size. Labeling was carried out with the RadPrime random priming labeling kit (Invitrogen). After labeling, reaction products were purified with Nucleospin PCR clean up columns (Macherey-Nagel) and concentrated to a final volume < 5 microliters with a Microcon YM-30 column (Millipore). 	Candida albicans  genomic DNA was labelled with Cy5 dUTP (Amersham Biosciences) following sonication of chromosomal fragments to produce fragments of 500 - 5,000 bp in size. Genomic DNA was labelled by random priming with the RadPrime kit (Invitrogen). After labeling, reaction products were purified with Nucleospin PCR clean up columns (Macherey-Nagel) and concentrated to a final volume < 5 microliters with a Microcon YM-30 column (Millipore).	Candida dubliniensis genomic DNA was labelled with Cy5 (Amersham biosciences) following reduction of the chromosome fragment size by sonication to produce fragments 500 - 5,000 bp in size. Labeling was carried out with the RadPrime random priming labeling kit (Invitrogen). After labeling, reaction products were purified with Nucleospin PCR clean up columns (Macherey-Nagel) and concentrated to a final volume < 5 microliters with a Microcon YM-30 column (Millipore). 	 Candida albicans genomic DNA was labelled with Cy3 dUTP (Amersham Biosciences) following sonication of chromosomal fragments to produce fragments of 500 - 5,000 bp in size. Genomic DNA was labelled by random priming with the RadPrime kit (Invitrogen). After labeling, reaction products were purified with Nucleospin PCR clean up columns (Macherey-Nagel) and concentrated to a final volume < 5 microliters with a Microcon YM-30 column (Millipore).	In this labeling protocol, Candida albicans genomic DNA was labelled with Cy5 dUTP (Amersham biosciences) folowing fragmentation of chromosomes by restriction endonuclease digestion with Tru1I and RsaI (Fermentas). These digests were then heat inactivated, extracted once with a mixture phenol:chloroform:isoamyl alcohol (25:24:1) and ethanol precipitated. The two separate aliquots of digested DNA were combined to give a mixture of Tru1I and RsaI fragments (50 to 4,000 bp) for labeling.  Labeling was carried out with the RadPrime random priming labeling kit (Invitrogen). After labeling, reaction products were purified with Nucleospin PCR clean up columns (Macherey-Nagel) and concentrated to a final volume < 5 ml with a Microcon YM-30 column (Millipore). 	Candida dubliniensis genomic DNA was labelled with Cy3 dUYP (Amersham biosciences) following  restriction endonuclease digestion with Tru1I and RsaI (Fermentas).  For restriction endonuclease digests, two 1 mg aliquots of DNA were separately digested with Tru1I or RsaI (Fermentas). These digests were then heat inactivated, extracted once with a mixture of phenol:chloroform:isoamyl alcohol (25:24:1) and ethanol precipitated. The two separate aliquots of digested DNA were combined to give a mixture of Tru1I and RsaI fragments (50 to 4,000 bp) for labeling. Labeling was carried out with the RadPrime random priming labeling kit (invitrogen). After labeling, reaction products were purified with Nucleospin PCR clean up columns (Macherey-Nagel) and concentrated to a final volume < 5 microliters with a Microcon YM-30 column (Millipore). 	Cy5 and Cy3 labeling reactions were mixed together in 60 µl of DIG EasyHyb buffer (Roche Diagnostics GmbH, Mannheim, Germany) for hybridisation. The mixture was denatured at 98?C for 5 min and chilled on ice. Microarray slides (Eurogentec, Seraing, Belgium) were placed in a hybridisation chamber (Corning GmbH, Berlin, Germany), covered with a plastic coverslip and the labeling reaction was carefully applied at the edges of the slide. The chamber was sealed and incubated in the dark at 42?C for 16-18h. Slides were washed at high stringency at room temperature as follows: (i) 5 min in 1x SSC, 0.03% SDS,  (ii) 5 min in 0.2x SSC and (iii) 5 min in 0.05x SSC. Following washing, the slide was dried thoroughly by centrifugation at low speed for 5 min in a 50 ml disposable plastic tube (Greiner Bio-One GmbH, Germany) and scanned immediately.	
Protocol Parameters	min temperature;media;	Extracted product;Amplification;	Amount of nucleic acid labeled;Amplification;Label used;	Amplification;Amount of nucleic acid labeled;Label used;	Amplification;Label used;Amount of nucleic acid labeled;	Label used;Amount of nucleic acid labeled;Amplification;	Amplification;Label used;Amount of nucleic acid labeled;	Amount of nucleic acid labeled;Label used;Amplification;	Quantity of label target used;Chamber type;time;Volume;temperature;	
Protocol Hardware	
Protocol Software	
Protocol Contact	
Protocol Term Source REF	
SDRF File	E-MEXP-99.sdrf.txt	
Term Source Name	The MGED Ontology		ArrayExpress	mo	EFO	
Term Source File	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