biostudies-arrayexpressEmer HickeyCandida albicanshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15594Changes in carbon source influence genome-wide gene expression in Candida albicans, thereby modulating key virulence traits such as adhesion, morphogenesis, and stress resistance. To investigate the biological consequences of alternative nutrient utilisation, this experiment examined how growth on inulin, a complex polysaccharide commonly encountered in host and dietary environments, alters the C. albicans transcriptome compared to growth on glucose, a readily metabolisable sugar.biostudies-arrayexpressLibrary Construction - The library preparation was performed using the NEBNext Ultra II Directional RNA Library Prep Kit with poly(A) enrichment, following the manufacturer’s standard protocol. Libraries were quantified and quality-checked prior to sequencing.Sequencing - Prepared libraries were sequenced on an Illumina NovaSeq 6000 platform following the manufacturer’s instructions. Paired-end sequencing was performed with a read length of 150 bp (PE150), generating high-throughput data suitable for transcriptome profiling. Cluster generation and sequencing chemistry were carried out using standard Illumina reagents. Base calling and quality scoring were performed automatically using Illumina’s real-time analysis software. The sequencing was done on a Novaseq 6000 - SP flowcell 150bp paired end - yielding 400m read pairsSample Collection - SC5314 C. albicans liquid cultures were grown in a shaking incubator at 37 oC, 200 rpm in YNB (Yeast Nitrogen Base without amino acids) supplemented with 2% glucose or 2% inulin overnight Fresh media was then inoculated at an OD600 of 0.1 and grown for 3 hrs at 37oC with 200RPM shaking. Cells were subsequently collected via centrifugation for RNA extractionNucleic Acid Extraction - The Ribopure RNA Purification Kit, Yeast (Invitrogen) was used to isolate RNA from C. albicans according to the manufacturer’s instructions. Briefly, approximately 3x108 freshly grown C. albicans cells were centrifuged and the supernatant was removed. The lysis buffer, SDS and phenol:chloroform:isoamyl alcohol from the kit were added to the pellet and mixed well. The mixture was added to a screwcap Nunc tube containing zirconia beads and the C. albicans cells sheared for 10 minutes at maximum speed using a bead beater (MP FastPrep 24). After centrifugation for 5 minutes, the supernatant was collected and added to a fresh tube. Binding buffer was added to each sample, followed by 100% ethanol. The mixture was added to a filter cartridge assembled in a collection tube and centrifuged for 1 minute. The supernatant was discarded and the filter cartridge was washed once with Wash Solution 1, and twice with Wash Solution 2/3. In each case, the flow-through was discarded. The filter cartridgewas dried for 1 minute by centrifugation and then the RNA was eluted in preheated elution solution. To remove DNA, DNase I buffer was added to the RNA sample together with DNase I, and incubated at 37°C for 30 minutes. The DNase I was then inactivated via the addition of a DNase Inactivation Reagent for 5 minutes. Finally, the sample was centrifuged to pellet the inactivation reagent, the RNA supernatant was transferred to a fresh tube, and the sample stored at -80OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Gene expression values were normalized using the FPKM (Fragments Per Kilobase of transcript per Million mapped reads) method. Read counts were first adjusted for sequencing depth by dividing by the total number of mapped fragments (in millions). Values were then scaled by transcript length (in kilobases) to account for gene size, allowing comparison of expression across genes and samples. FPKM values were calculated using StringTie to ensure consistent normalization and transcript-level quantificationMetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of total RNACandida albicansEmer HickeyAlistair BrownfalseRNA-seq of Candida albicans SC5314 grown on minimal media supplemented with glucose or inulin preparationsChanges in carbon source influence genome-wide gene expression in Candida albicans, thereby modulating key virulence traits such as adhesion, morphogenesis, and stress resistance. To investigate the biological consequences of alternative nutrient utilisation, this experiment examined how growth on inulin, a complex polysaccharide commonly encountered in host and dietary environments, alters the C. albicans transcriptome compared to growth on glucose, a readily metabolisable sugar.2026-04-29T00:00:00Z2026-04-29T09:09:58.997Z2025-09-12T12:56:19.623ZE-MTAB-15594ERP180021EFO_0002944EFO_0004170EFO_0009653EFO_0005518EFO_0003816EFO_0004184