Extended Data Fig. 1: Overall experimental design of the current study.

a, Schematic representation of the experimental design. Each Candida species was co-cultivated with host cells. Controls included samples at 0 and 24 h for both host and yeasts alone. At the indicated time points of infection, fungal and host RNAs were independently extracted and subsequently combined (pooled) at a 2:3 fungus-to-host ratio into one sample for library preparation and sequencing. Sequencing data were mapped to a concatenated host and fungal reference genome. b, Schematic representation of the entire study including all samples. Each symbol corresponds to a sequenced sample (or technical replicates of the same sample). Host samples are depicted with circles; Candida samples are depicted with squares; the strategy for combining (pooling) human and fungal RNAs in the same sequencing library is shown with ovals surrounding the corresponding samples; technical replicates (that is the same sequencing library sequenced several times) are surrounded with dashed rectangles. Control samples are depicted in yellow; interacting host and fungal samples are depicted in blue; host samples interacting with non-viable fungal cells are depicted in purple. Each row indicates the samples for each human-yeast interaction experiment.