We grew Candida albicans strains of the SC5314 background, with four genotypes, in RPMI-1640 at 37°C with shaking for 4 hours, a strongly hypha-inducing condition (`treatment` reads RPMI, 4hrs for every sample). The genotype is recorded in the `group` column, which holds our groups (`genotype` repeats it): WT is the wild type, ndt80dd the ndt80Δ/Δ deletion mutant, ndt80ddUME6OE the ndt80Δ/Δ mutant with UME6 overexpressed from the RBT5 promoter, and UME6OE the wild-type background with UME6 overexpressed from the RBT5 promoter. Each genotype was grown as three cultures, 12 samples in all, and all were collected after 4 hours, so there is a single time point.

Each sample is one culture of one strain (one biological replicate), made into its own library and sequenced once, so there are no technical replicates. The sample names give the strain code of each genotype (MC22 for WT, KG11 for ndt80dd, KG16 for ndt80ddUME6OE, KG21 for UME6OE) and a culture number _1 to _3, which matches bio rep_1 to bio rep_3 in `original_sample_id`; the numbers only count the cultures within each strain, and nothing records that cultures with the same number were grown or processed together. No batch is recorded, and we know of no other variable that matters; the remaining columns are GEO annotations that are constant or repeat the genotype.

The data are bulk poly(A) RNA-seq, given as raw integer read counts per gene for 6,193 protein-coding genes of the SC5314 Assembly 22 haplotype A annotation; the counting tool is not recorded.

Our question is which genes are differentially expressed in the ndt80dd mutant compared with the WT strain under this hypha-inducing condition. All 12 samples are part of this question: the ndt80ddUME6OE and UME6OE strains come from the same experiment, even though they are not among the groups being compared.