Table 1:

Examples of reporters used in single-cell imaging

Reporter	Information provided	Example [organism] (Reference)
Molecule-specific
Fluorescently tagged	Organelle morphology, protein abundance and localization, metabolic state	Gap1-mNeon to assess nitrogen metabolism [Sc] (Arguello-Miranda et al., 2018)
tFT linked to protein or organelle localization sequence	Protein or organelle age and stability	tFT-PTS to determine age of peroxisomes [Sc] (Kumar et al., 2018)
Antibody system	Organelle morphology, protein abundance and localization	anti-LAMP1 antibody to assess lysosome morphology [Hs] (Liberali et al., 2014)
MS2 RNA stem loop + GFP-MS2 coat protein system	RNA localization, abundance	MS2 fused to TFF1 gene to assess RNA abundance [Hs] (Rodriguez et al., 2019)
Signalling
Relocation reporter	Activation of pathway	JNK-KTR to quantify activation of JNK pathway [Hs] (Lane et al., 2019; Regot et al., 2014)
TF binding elements or isolated promoter driving reporter expression	Activation of pathway	HSP70pr-CFP to quantify activation of heat shock pathway [Hs] (Gaglia et al., 2020)
Cell State
Cell cycle reporter	Cell cycle position	FUCCI system to assess G1, G1/S, S/G2, M/early G1 [Hs] (Sakaue-Sawano et al., 2008)
pH sensor	Ratiometric readout of intracellular pH	Ratiometric pHluorin to quantify cytosolic pH [Sc] (Mouton et al., 2020)
Flux sensor	Metabolic flux readout	CggR-based YFP system to quantify FBP as a measure of metabolic flux [Sc] (Monteiro et al., 2019)
Redox sensor	Ratiometric readout of metabolite levels	iNap-cpYFP to quantify intracellular NADPH/NADP+ levels [Hs] (Tao et al., 2017)
FRET-based sensor of metabolite	Intracellular concentration of metabolite	ZapCV2 to quantify Zn2+ in cytosol [Hs] (Lo et al., 2020)
Live cell stains	Abundance and morphology of organelles, cellular structures, metabolites, proteins	Fluorescently labelled WGA to quantify bud scars (determine replicative age) [Sc] (Mattiazzi Usaj et al., 2020)

Abbreviations: tFT, tandem fluorescent timer; PTS, peroxisome targeting sequence; JNK-KTR, c-Jun N-terminal kinase-kinase translocation reporter; TF, transcription factor; HSP, Heat Shock Protein; FUCCI, fluorescent ubiquitination-based cell cycle indicator; FBP, fructose-1,6-bisphosphate; iNap-cpYFP, indicator of NADPH fused to circularly permuted YFP; FRET, Förster resonance energy transfer; ZapCV2, Zap1 zinc finger binding domain connecting FRET pair CFP and circularly permuted Venus; WGA, wheat germ agglutinin; Hs, Homo sapiens; Sc, Saccharomyces cerevisiae