biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsNuno MIraTwo-color microarrayCandida albicansCandida albicanshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-8672In this work the effect of the hormone progesterone in the ability of C. albicans SC5314 to form biofilms was investigated as well as the transcriptomic response of the yeast to this compound. The analysis was performed always comparing the genomic expression of the biofilm cells cultivated in the presence and absence of progesterone with the transcriptome of planktonic cells (in mid-exponential phase) which was used to reference the analysis.biostudies-arrayexpressSample Collection - Cells were cultivated (in RPMI, at pH 4) after 24h of formation of a biofilm on the surface of a polystyrene plate, either or not in the presence of progesteroneHybridization - Samples were prepared for hybridization using Agilent’s Two-Color Microarray-Based Gene expression (Quick Amp labelling protocol) and the Gene Expression Hybridization Kit. 10 μL each Cy3-labeled and Cy5-labeled cDNA were used per array (8 X 15 k, design ID 065138), in a total volume of 50 μL.Scaning - Hybridized microarrays were scanned with an Axon 4000B scanner (Axon Instruments, Union City, CA, USA) and data were acquired with GenePix Pro 5.1 software (Axon Instruments, Union City, CA, USA). Data was analyzed using the LIMMA package in Bioconductor (www.bioconductor.org). Three biological replicates and three technical replicates were performed. Lowess normalization and background correction were applied to each array separately, and quantile normalization was used to allow log ratios to be compared across arrays. Only genes exhibiting log2FC >1.0 and having an associated p-value below 0.01 were selected for further analysisNucleic Acid Extraction - Nucleic acids were extracted with the RiboPure extraction kit from Ambion, following the instructions of the manufacturerLabeling - , 6 µg of total RNA was incubated with 1.4 µg of anchored Oligo(dT)20 primer (Invitrogen, Carlsbad, CA, USA) in a total volume of 18.5 µl for 10 min at 70°C. First-strand buffer (Invitrogen, Carlsbad, CA, USA), 0.5 mMdATP, dTTP, and dGTP; 50 µM dCTP; 10 mM dithiothreitol; 2 µl Superscript III reverse transcriptase (Invitrogen, Carlsbad, CA, USA); and 2 µl Cy3-dCTP or Cy5-dCTP (Amersham, PA53021 and A55021) were added to a total volume of 40 µl, incubated at 42°C for 2 h followed by 1 h at 42°C with an additional 1 µl of Superscript III. RNA was degraded by addition of 1 µl of RNase A at 50 µg/mL and 1 µl of RNase H at 1 unit/µl and incubated at 37°C for 30 min. The labelled cDNAs were purified using a QIAquick PCR purification kit (Qiagen, Hilden, Germany), using a modified protocol.MIAME ScoreRaw DataOrganizationAssays and DataProcessed DataMAGE-TAB FilesArray DesignsNuno MIraData Transformation - Lowess normalization and background correction were applied to each array separately, and quantile normalization was used to allow log ratios to be compared across arrays. Only genes exhibiting log2FC >1.0 and having an associated p-value below 0.01 were selected for further analysisfalseEffect of progesterone in biofilm formation by Candida albicansIn this work the effect of the hormone progesterone in the ability of C. albicans SC5314 to form biofilms was investigated as well as the transcriptomic response of the yeast to this compound. The analysis was performed always comparing the genomic expression of the biofilm cells cultivated in the presence and absence of progesterone with the transcriptome of planktonic cells (in mid-exponential phase) which was used to reference the analysis.2020-01-31T00:00:00Z2022-02-03T13:25:01.248Z2022-02-03T13:25:01.248ZE-MTAB-8672EFO_0002944EFO_0003814EFO_0003813EFO_0005518EFO_0003816EFO_0003815