smFISH of UL19, UL29, EEA1, ERBBB2, RELA and HPRT-1 – single-cell feature values

Data in the paper "Cellular state landscape and herpes simplex virus type 1 infection progression are connected" by Pietilä et al., 2023:
- HSV-1 transcript counts: HeLa_UL19_spotCounts_MOIs.csv (Figure 1c right UL19, Supplementary Figure 1b) and HeLa_UL29_spotCounts_MOIs.csv (Figure 1c right UL29, Supplementary Figure 1b)
- Summary of HSV-1 UL19 or UL29-expressing HeLa cells: HeLa_HSV1_MOIs_infectedCells.csv (Supplementary Figure 1a right)
- Cellular transcript counts: HeLa_EEA1_spotCounts.csv, HeLa_ERBB2_spotCounts.csv, HeLa_HPRT1_spotCounts.csv, and HeLa_RELA_spotCounts.csv (Supplementary Figure 1b)
- Single-cell feature values: HeLa_smFISH_IF_mlr.csv (Supplementary Figure 1c)

HeLa cells were mock- or HSV-1-infected (indicated by "condition"). After fixation, HSV-1 UL19 and UL29 and cellular HPRT-1, EEA1, ERBB2, and RELA transcripts were detected by single-molecule RNA fluorescence in situ hybridization (smFISH). Transcript quantification, single-cell feature extraction, and classification of cells were applied as described in the paper. Five replicates were used (indicated by “well_name”). Single-cell intensities are provided as background-subtracted, corrected, and normalised mean and sum intensity values for the whole-cell, nucleus, and cytoplasm, as appropriate. Other single-cell features are provided as normalised values. Data cleanup, correction, background subtraction, and normalisation were performed as described in the paper.