Single-molecule Fluorescent In Situ Hybridization (smFISH) for RNA detection in the fungal pathogen Candida albicans small example dataset

This small example dataset is connected to the protocol article titled:

Single-molecule Fluorescent In Situ Hybridization (smFISH) for RNA detection in the fungal pathogen Candida albicans

Abstract:

Candida albicans is the most prevalent human fungal pathogen. Its pathogenicity is linked to the ability of C. albicans to reversibly change morphology and to grow as yeast, pseudohyphal or hyphal cells in response to environmental stimuli. Understanding the molecular regulation controlling those morphological switches remains a challenge that, if solved, could help fight C. albicans infections.

While numerous studies investigated gene expression changes occurring during C. albicans morphological switches using bulk approaches (e.g., RNA sequencing), here we describe a single-cell and single-molecule RNA imaging and analysis protocol to measure absolute mRNA counts in morphologically intact cells. To detect endogenous mRNAs in single fixed cells, we optimized a single molecule fluorescent in situ hybridization (smFISH) protocol for C. albicans, which allows one to quantify the differential expression of mRNAs in yeast, pseudohyphae or hyphal cells. We quantified the expression of two mRNAs, cell cycle-controlled mRNA (CLB2) and a transcription regulator (EFG1), which show differential expression in the different morphological cell types and in different nutrient conditions. In this protocol we described in detail the major steps of this approach: growth and fixation, hybridization, imaging, cell-segmentation and mRNA spot analysis. Raw data is provided with the protocol to favour reproducibility. This approach could benefit the molecular characterization of C. albicans and other filamentous fungi, pathogenic or non-pathogenic.

Data description:

This dataset consists of a FISH experiment spanning two different mRNAs, EFG1 and CLB2, and one nutrient condition, SPIDER37, in Candida albicans. For culturing, the C. albicans wildtype strain SC5314 was inoculated at 30 degrees overnight (~15 hours) in 10 mL of TSB medium in a 30-degree (celsius) shaking incubator. Next, samples were diluted to a density of 10^5 cells/ mL and inoculated for 6 hours in 30 mL Spider medium at 37 degrees in falcon tubes on an orbital microplate shaker. Then, samples were fixated by adding PFA to a final concentration of 4% to the medium. For hybridization, both mRNAs were hybridized independently by specific DNA oligo labelled with a Quasar670 dye to enable the visualisation of single mRNA molecules. As both genes are labelled by the same dye, these oligos were not co-applied to the same sample but to independent samples.

Microscopy

For smFISH imaging we use an Olympus BX-63 epifluorescence microscope equipped with Ultrasonic stage and UPlanApo 100x 1.35NA oil-immersion objective (Olympus). Lumencore SOLA FISH light source, a Hamamatsu ORCA-Fusion sCMOS camera (6.5 µm-pixel size) mounted using U-CMT C-Mount Adapter, and zero-pixel shift filter sets: F36-500 DAPI HC Brightline Bandpass Filter, F36-502 FITC HC BrightLine Filter, F36-542 Cy3 HC BrightLine Filter, and F36-523 Cy5 HC BrightLine Filter. Images are acquired across 61-81 optical sections (depending on the sample thickness) with a z-step size of 0.2 μm. The CellSens software (Olympus) is used for instrument control and image acquisition. For the DAPI  channel 10-50 ms of exposure was used. Whilst, for the CY5 channel, used imaging the FISH probes, 750 ms was applied.