smFISH + 4i experiment – single-cell feature values and summaries

Data from the smFISH + 4i experiment in the paper "Cellular state landscape and herpes simplex virus type 1 infection progression are connected" by Pietilä et al., 2023:
- Single-cell feature values: HeLa_smFISH_4i_cellular_features.csv.gz (Figure 1e, 2b, 2c, 2d, 2e, 3, 5b, 5c, 6a, 7a, 7c, 7d, 7e, 7f, 8, and Supplementary 3e, 3f, 4b, 6, 7, 9a, and 9d) and HeLa_smFISH_4i_viral_features.csv (Figure 3)
- Single-cell spot count of HSV-1 UL19 and UL29 transcripts in HeLa cells: HeLa_smFISH_4i_UL19_spotCounts.csv (Figure 1c left UL19) and HeLa_smFISH_4i_UL29_spotCounts.csv (Figure 1c left UL29)
- Summary of HSV-1 UL19 or UL29-expressing HeLa cells: HeLa_smFISH_4i_UL19_UL29_expressingCells.csv (Supplementary Figure 1a left)
- Summary of ICP5 virion-containing HeLa cells: HeLa_smFISH_4i_virions_percentage.csv (Supplementary Figure 3b)
- Summary of infected HeLa cells: HeLa_smFISH_4i_infectedCells.csv (Supplementary Figure 3c)

HeLa cells were mock infected or infected with HSV-1 and fixed at different time points (indicated by "timePoint"). After fixation, the transcripts were detected by single-molecule RNA fluorescence in situ hybridization (smFISH) and viral and cellular markers by iterative indirect immunofluorescence imaging (4i). Single-cell feature extraction, and classification of cells were applied as described in the paper. Two or four replicates were used for mock and HSV-1 infection, respectively (indicated by “well_name”). Single-cell intensities are provided as corrected and background-subtracted or corrected, background-subtracted, and normalised mean and sum intensity values for the nucleus, cytoplasm, and whole-cell, as appropriate. Single-cell textures are provided as corrected and normalised texture values for the nucleus, cytoplasm, and whole-cell. Other single-cell features are provided with or without normalisation. Data cleanup, correction, background subtraction, and normalisation were performed as described in the paper.