{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Laura Carreto"],"organism":["Candida albicans"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MEXP-3247"],"description":["Candida albicans strain with RLM1 deletion was compared to wild type strain. Growth in YPD medium. Two comparisons were performed on microarray in dye-swap hybridizations."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Hybridization - Note: Agilent gasket slides (G2534-60012) and Agilent SureHyb hybridization chambers (G2534A) were used for the hybridization. Hybridization and microarray washes were performed as described in the Agilent two-color gene expression microarray protocol v5.7, using Agilent Gene Expression Hybridization Kit (5188-5242) and Agilent Gene Expression Wash Buffer kit (5188-5327), following the manufacturer's instructions.      For a dual chanel hybridization, 200 ng of Cy5 labeled cDNA were combined with 200 ng of Cy3 labeled cDNA and 11 ul of 10X Blocking Agent were added. Nuclease-free water was used to bring the volume to 55 ?l. The volume of 110 ul was completed by adding 55 ul  of Agilent GE Hybridization Buffer HI-RPM (2x concentrated). The reagents were mixed by careful pipe","Growth Protocol - Inoculate 10 ml of YPD (2% glucose, 1% yeast extract, 2% Bacto peptone) with single colonies and grown overnight at 30C and 150rpm. Use each overnight culture to inoculate 20 ml of YPD to an initial OD640 of 0.4. Then, incubate the cultures in the same conditions, at 30C and 150rpm. After 4h of growth, corresponding to at least two cell population duplications, harvest cells and follow the RNA extraction protocol. (Parameters: time unit = hours, temperature unit = C, media = YPD)","Nucleic Acid Extraction - RNA extraction was performed by using the hot acidic phenol method.    1. During harvest centrifugation, accurately determine OD600. For the normalization it is important that all steps are as quantitative as possible (i.e. always yielding identical amounts of total RNA per OD600 of a particular strain under a particular condition). [NOTE: actual numbers may vary from the yields listed here.]   2. Harvest cells by brief (3 min) centrifugation step at 14000rpm at 4C. Pour off and then aspirate remaining supernatant quickly. Briefly wash cells with cold water, centrifuge for 1 min, discard the supernatant quickly and immerse the tube in liquid nitrogen immediately.   3. Take frozen cells (-80 C) and ressuspend in Acid Phenol (from Sigma, 5:1, pH 4.7 put at 65 C befo","Labeling - RT REACTION (ratio 7 aa-dUTP : 3 dTTP):  1. Prepare the following RNA/primer mix on ice: 40 ug of  total RNA, 6 ul of oligo dT12-18 primer (0.25 ug/ul, Invitrogen Cat. No. 18418-012) and H2O up to 13 ul reaction volume.   2. Incubate at 70 C for 10 minutes.   3. After a short spindown chill on ice for 5 minutes.   4. During the 70 C incubation of the RNA/primer mix prepare the following labeling mix. (If multiple cDNA synthesis reactions are going to be performed a single labeling mix can be prepared by scaling up the volumes proportionally). On ice add, in the following order: 3 ul of dGAC-mix (1 mM each), 0.9 ul of 1 mM dTTP, 2.1 ul of 1 mM aa-dUTP (Sigma, A-0410), 6 ul of 5X first strand buffer and 3 ul of 0.1 M DTT (total volume = 15 ul).  5. Add the labeling mix to the RNA/"],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","Additional Files","MAGE-TAB Files","Array Designs"],"data_protocol":["Assay Data Transformation - The processed signal from Agilent Feature Extraction protocol GE2_105_Dec08 was obtained. Replicated features on the array were averaged prior to normalization of the Log2 intensity ratios (M values) using Lowess smother."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"pubmed_abstract":["Candida albicans cell wall is important for growth and interaction with the environment. RLM1 is one of the putative transcription factors involved in the cell wall integrity pathway, which plays an important role in the maintenance of the cell wall integrity. In this work we investigated the involvement of RLM1 in the cell wall biogenesis and in virulence. Newly constructed C. albicans Δ/Δrlm1 mutants showed typical cell wall weakening phenotypes, such as hypersensitivity to Congo Red, Calcofluor White, and caspofungin (phenotype reverted in the presence of sorbitol), confirming the involvement of RLM1 in the cell wall integrity. Additionally, the cell wall of C. albicans Δ/Δrlm1 showed a significant increase in chitin (213%) and reduction in mannans (60%), in comparison with the wild-typ"],"study_type":["transcription profiling by array"],"species":["Candida albicans"],"pubmed_title":["Participation of Candida albicans Transcription Factor RLM1 in Cell Wall Biogenesis and Virulence."],"pubmed_authors":["Laura Carreto","Delgado-Silva Y, Vaz C, Carvalho-Pereira J, Carneiro C, Nogueira E, Correia A, Carreto L, Silva S, Faustino A, Pais C, Oliveira R, Sampaio P."],"additional_accession":[]},"is_claimable":false,"name":"Sampaio_UMinho_Candida albicans Mutant vs Wt_YPD","description":"Candida albicans strain with RLM1 deletion was compared to wild type strain. Growth in YPD medium. Two comparisons were performed on microarray in dye-swap hybridizations.","dates":{"release":"2012-01-01T00:00:00Z","modification":"2022-11-21T08:46:39.364Z","creation":"2022-03-14T19:18:45.215Z"},"accession":"E-MEXP-3247","cross_references":{"pubmed":["24466000"],"EFO":["EFO_0002768"],"doi":["10.1371/journal.pone.0086270"]}}