Computational protocol: Pho4 mediates phosphate acquisition in Candida albicans and is vital for stress resistance and metal homeostasis

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Protocol publication

[…] Samples were processed through the Ion Torrent Proton sequencer at the Centre for Genome-Enabled Biology and Medicine, University of Aberdeen, Genomics Facility. Raw fastq files were successively processed in the following order through Fastqc (version 10.1), Trimgalore (version 3.1), Samtools (version 1.19), STAR aligner (version 2.4), and Htseq (version 5.4). Genome alignment was conducted against the C_albicans_SC5314_version_A21-s02-m09-r08 chromosomes file provided by the Candida Genome Database (www.candidagenome.org/). Gene expression analysis was performed using Partek Genomics Suite software, version 6.6. GO term analysis was performed in parallel through the Candida Genome Database GO Term Finder and the Cytoscape, version 3, Clue GO plug-in (). Network construction was performed with Cytoscape, version 3, freeware, Venn diagrams through Venny (version 2.0.2) online freeware, and heat maps with TM4 MultiExperiment Viewer (version 4.9). Statistical comparison among GO term enrichment percentages was performed with GraphPad Prism (version 6). […]

Pipeline specifications

Software tools FastQC, Trim Galore!, SAMtools, HTSeq, Partek Genomics Suite, GO::TermFinder, VENNY, TM4
Databases CGD
Application RNA-seq analysis
Organisms Homo sapiens, Candida albicans, Saccharomyces cerevisiae, Fungi
Diseases Infection, Drug-Related Side Effects and Adverse Reactions
Chemicals Copper, Manganese, Phosphates, Superoxides