Comment[ArrayExpressAccession]	E-GEOD-48529
MAGE-TAB Version	1.1						
Public Release Date	2014-06-24
Investigation Title	Comparative genomics of a fluconazole-resistant variant Candida albicans strain CaLY188.						
Comment[Submitted Name]	Comparative genomics of a fluconazole-resistant variant Candida albicans strain CaLY188.
Experiment Description	To investigate the diversity of gene contents of Candida albicans strain by array-based comparative genomic hybridization (array CGH; aCGH). A fluconazole-resistant variant Candida albicans strain CaLY188 was selected to carry out the comparative genomics microarray. Two-condition experiment, CaLY188 vs.SN152. Biological replicates: 2 control, 2 transfected, independently grown and harvested. One replicate per array.						
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl					
Person Last Name	li	Li	Li				
Person First Name	xingxing	Xingxing	Dedong				
Person Email	xingxingsf@163.com						
Person Affiliation	Second Military Medical University						
Person Address	Second Military Medical University, Guohe Road, Shanghai, China						
Person Roles	submitter						
Protocol Name	P-GSE48529-1	P-GSE48529-5	P-GSE48529-6	P-GSE48529-2	P-GSE48529-3	P-GSE48529-4	P-GSE48529-7
Protocol Description	After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed. Two hybridizations were performed by using a reversal fluorescent strategy in one test and control and the other hybridization without performing reversal fluorescent. ID_REF =  VALUE = The geometric mean of lowess normalized log2 ratio (test/control) for the two independent experiments was calculated.	The genomic DNA was sonicated to generate fragments 50M-bM-^@M-^S2000 bp in size,then the DNA fragment was labeled by fluorescent dye (Cy5 and Cy3-dCTP) with random primer and Klenow enzyme.	standard CapitalBio Methods	strains were grown routinely in YPD medium at 30M-0C with shaking overnight, diluted to an OD600 of 0.1 in fresh YPD and were allowed to grow to an OD600 of 0.8. Cells were then harvested, flash-frozen and stored at -80M-0C.	Candida albicans cells were propagated in YPD medium.	For DNA extraction, 200M-NM-<l of 25:24:1 phenol/chloroform/isoamyl alcohol were added to the cells resuspended in lysis buffer, together with 300 mg of acid-washed glass beads. The mixture was vortexed for 3 minutes before the addition of 200M-NM-<l of TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH8.0). Following a 5 minutes centrifugation at 9300 g and 4M-bM-^DM-^C for phase separation (Eppendorf centrifuge 5415D), the DNA in the aqueous phase was precipitated with 1 ml ethanol (96%, v/v) at room temperature, resuspended in 400M-NM-<l of TE containing 60 mg RNaseA (GE healthcare), and incubated at 37M-bM-^DM-^C for 6 hours, the DNA was precipitated with 40M-NM-<l of 3 M ammonium acetate and 1 ml of cold absolute ethanol at -20M-bM-^DM-^C for 15 minutes, followed by a 5 minutes centrifugation at 9300 g at 4M-bM-^DM-^C. The DNA pellet was carefully washed with 1 ml ethanol (70%, v/v), left to dry at room temperature, and resuspended in 50M-NM-<l of TE buffer. DNA was purified using the PCR Clean-up NucleoSpin Extract M-bM-^EM-! Kit (Macherey-Nagel, Germany) according to manufacturerM-bM-^@M-^Ys directions.	Luxscan 10K (CapitalBio)
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	STRAIN						
Experimental Factor Type	strain						
Comment[SecondaryAccession]	GSE48529						
Comment[GEOReleaseDate]	2014-06-24						
Comment[ArrayExpressSubmissionDate]	2013-07-03						
Comment[GEOLastUpdateDate]	2014-06-24						
Comment[AEExperimentType]	comparative genomic hybridization by array						
SDRF File	E-GEOD-48529.sdrf.txt