Comment[ArrayExpressAccession] E-MEXP-3675
Investigation Title Transcriptional landscape modeling in Candida albicans defines a core filamentation response
Comment[Submitted Name] Transcriptional landscape modeling in Candida albicans defines a core filamentation response
Comment[AEExperimentDisplayName] Transcription profiling by array of Candida albicans grown in different pH and media over time
Comment[MIAMExpressLogin] elaalb
Comment[MIAMExpressSubmissionID] 8261
Experiment Description comparison of. C.albicans grown on different pH and media over time
Experimental Design reference_design co-expression_design time_series_design growth_condition_design
Comment[AEExperimentType] transcription profiling by array
Experimental Factor Name TIME GROWTH_CONDITION
Experimental Factor Type time growth_condition
Person Last Name Albrecht-Eckardt
Person First Name Daniela
Person Email daniela.albrecht@hki-jena.de
Person Phone 03641527831
Person Affiliation BioControl Jena GmbH
Person Address Research and Development, Wildenbruchstr. 15, Jena, Thüringen, 07745, Germany
Person Roles submitter
Person Roles Term Source REF MGED Ontology
Quality Control Type biological_replicate
Public Release Date 2012-12-29
Comment[ArrayExpressSubmissionDate] 2012-07-10 15:27:40
Publication Status not yet submitted
Protocol Name P-MTAB-27439 P-MTAB-27440 P-MTAB-27441 P-MTAB-27442 P-MTAB-27443
Protocol Description 1. Mix 5 l of each Cy 3 and Cy5 labelled cDNA probe
2. Add 5 ?l of calf thymus DNA
3. Add 35 ?l of EGT hybridization buffer
4. Incubate at 65°C for 2 min
5. Add a clean Lifterslips coverslide onto the printed area and inject the probe under the cover slide
6. Incubate overnight at 42°C in a humid chamber (Corning hybridization chamber)
(Parameters: Chamber type = Corning Microarray Technology- CMT-Hyb chamber, Quantity of label target used = 60, Mass unit = Micro gram, Tiny time unit = seconds, Volume unit = Nano litre, temperature = 42) For pH shift, samples were grown at 37°C in M199 medium (9.8 g/l M199 powder, PAA; 35.7 g/l HEPES, 2.2 g/l sodium carbonate; adjusted to different pH values with either sodium hydroxide or hydrochloride acid) with pH4 and transferred to M199 pH8 for hyphae- inducing conditions.
For the other shifts, cells were transferred from a preculture in SDG medium into either SDG with 10% human serum (serum shift, green) or into SDN medium with 20g/l N- acetylglucosamine as exclusive carbon source.
Time values in the experiment are hours after transfer into new pH or medium. "PixelSize=10"
"Wavelengths=635 532"
"NormalizationMethod=None"
"NormalizationFactors=1 1"
"StdDev=Type 1"
"RatioFormulations=W1/W2 (635/532)"
"BackgroundSubtraction=LocalFeature"
"ImageOrigin=1880, 2880"
"FocusPosition=0"
"PMTGain=700 585"
"ScanPower=100 100"
"ScanRegion=188,288,2040,5708"
(Parameters: Scanning hardware = Axon- GenePix4000B, Scanning software = GenePix Pro [Axon Instruments]) no background correction
printtiploess + Gquantile normalization
For RNA isolation cells were harvested by centrifugation and resuspended in 400 µl AE buffer (50 mM sodium acetate, 10 mM EDTA). Next, 40 µl 10% SDS and an equal volume of phenol/chloroforme/isoamylalcohol was added. Mixtures were incubated at 65°C for 5 min, followed by an incubation at ?80°C until they were frozen. After a second incubation at 65°C (until samples were thawn) the mixtures were centrifugated for 2 min at 12000×g. The upper liquid phase was transferred into a new reaction tube. After addition of 10% volume sodium acetate pH 5.3 and 1 volume 2-propanol, RNA was precipated for 30 min at ?20°C. Samples were centrifugated for 10 min at 12000×g, supernantant were discarded and RNA pellets washed twice with 70% ethanol (prepared with RNAse free water). Finally, RNA was solved in RNAase free water.
(Parameters: Extracted product = total_RNA, Amplification = none)
Protocol Type hybridization specified_biomaterial_action image_acquisition bioassay_data_transformation nucleic_acid_extraction
Protocol Term Source REF MGED Ontology MGED Ontology MGED Ontology MGED Ontology MGED Ontology
Term Source Name MGED Ontology ArrayExpress
Term Source File http://mged.sourceforge.net/ontologies/MGEDontology.php http://www.ebi.ac.uk/arrayexpress
SDRF File E-MEXP-3675.sdrf.txt