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ht29 ahr reporter assay ht29 lucia ahr cells  (InvivoGen)


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    InvivoGen ht29 ahr reporter assay ht29 lucia ahr cells
    Ht29 Ahr Reporter Assay Ht29 Lucia Ahr Cells, supplied by InvivoGen, used in various techniques. Bioz Stars score: 99/100, based on 50 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/ht-29/HT29-Lucia+AhR+Cells/us12371408-811-3-13
    Average 99 stars, based on 50 article reviews
    ht29 ahr reporter assay ht29 lucia ahr cells - by Bioz Stars, 2026-11
    99/100 stars

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    Recombinant:

    Article Title: Genomic and phenotypic comparisons reveal lineage-specific traits of the probiotic Saccharomyces boulardii .
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples S. boulardii CNCM I-745 Biocodex (Precosa) CNCM I-745 S. boulardii DBVPG 6763 Gnosis (Sachhaflor) DBVPG 6763 S. boulardii ATCC MYA-796 ATCC MYA-796 S. boulardii CNCM I-3799 NOW Foods CNCM I-3799 S. boulardii CNCM I-1079 Lallemand CNCM I-1079 S. cerevisiae baker’s (SE) KronJäst N/A S. cerevisiae baker’s (DK) Lallemand N/A S. cerevisiae CEN.PK113-5D Euroscarf CEN.PK113-5D Chemicals, peptides, and recombinant proteins DNA/RNA Shield Zymo Research Cat. No. R1100 Artificial gastric fluid Biochemazone Cat. No. BZ175 Artificial intestinal fluid Biochemazone Cat. No. BZ176 Artificial colonic fluid Biochemazone Cat. No. BZ177 Yeast Live/Dead kit Biotium Cat. No. 31064 D-(+)-Glucose monohydrate Sigma-Aldrich Cat. No. 16301 Ethanol absolute VWR Cat. No. 20821.310 Sodium acetate Sigma-Aldrich Cat. No. S8750 Sodium L-lactate Sigma-Aldrich Cat. No. 71718 Sodium succinate dibasic Sigma-Aldrich Cat. No. 14160 McCoy’s 5A medium Thermo Fisher Cat. No. 16600082 Fetal bovine serum Thermo Fisher Cat. No. A5670701 Penicillin–streptomycin Thermo Fisher Cat. No. 15140148 RPMI-1640 medium Thermo Fisher Cat. No. 12027599 PMA Sigma-Aldrich Cat. No. P8139 Zeocin InvivoGen Cat. No. 11006-33-0 Puromycin Thermo Fisher Cat. No. A1113803 2-Mercaptoethanol Thermo Fisher Cat. No. 21985023 LPS (E. coli O111:B4) Sigma-Aldrich Cat. No. L2630 TNFα R&D Systems Cat. No. 10291-TA FICZ Sigma-Aldrich Cat. No. 172922-91-7 Critical commercial assays QUANTI-Luc reagent InvivoGen Cat. No. rep-qlc4r2 Bright-Glo Luciferase assay Promega Cat. No. E2610 IL-8 ELISA kit R&D Systems Cat. No. DY208 TNFα ELISA kit Abcam Cat. No. ab181421 Yeast Live-or-DyeTM Live/Dead kit Biotium Cat. No. 31064 Deposited data PRJNA1312645 whole genome sequencing dataset NCBI https://www.ncbi.nlm.nih.gov/sra/PRJNA1312645 Experimental models: Cell lines HT-29 cells ATCC Cat. No. HTB-38 HT29-Lucia AhR cells InvivoGen Cat. No. ht2l-ahr THP-1 cells ATCC Cat. No. TIB-202 THP-1 NF-κB reporter cells ATCC Cat. No. TIB-202-NFkB-LUC2 Caco-2 cells ATCC Cat. No. HTB-37 (Continued on next page) e1 iScience 29, 115706, May 15, 2026 ..

    Luciferase:

    Article Title: Genomic and phenotypic comparisons reveal lineage-specific traits of the probiotic Saccharomyces boulardii .
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples S. boulardii CNCM I-745 Biocodex (Precosa) CNCM I-745 S. boulardii DBVPG 6763 Gnosis (Sachhaflor) DBVPG 6763 S. boulardii ATCC MYA-796 ATCC MYA-796 S. boulardii CNCM I-3799 NOW Foods CNCM I-3799 S. boulardii CNCM I-1079 Lallemand CNCM I-1079 S. cerevisiae baker’s (SE) KronJäst N/A S. cerevisiae baker’s (DK) Lallemand N/A S. cerevisiae CEN.PK113-5D Euroscarf CEN.PK113-5D Chemicals, peptides, and recombinant proteins DNA/RNA Shield Zymo Research Cat. No. R1100 Artificial gastric fluid Biochemazone Cat. No. BZ175 Artificial intestinal fluid Biochemazone Cat. No. BZ176 Artificial colonic fluid Biochemazone Cat. No. BZ177 Yeast Live/Dead kit Biotium Cat. No. 31064 D-(+)-Glucose monohydrate Sigma-Aldrich Cat. No. 16301 Ethanol absolute VWR Cat. No. 20821.310 Sodium acetate Sigma-Aldrich Cat. No. S8750 Sodium L-lactate Sigma-Aldrich Cat. No. 71718 Sodium succinate dibasic Sigma-Aldrich Cat. No. 14160 McCoy’s 5A medium Thermo Fisher Cat. No. 16600082 Fetal bovine serum Thermo Fisher Cat. No. A5670701 Penicillin–streptomycin Thermo Fisher Cat. No. 15140148 RPMI-1640 medium Thermo Fisher Cat. No. 12027599 PMA Sigma-Aldrich Cat. No. P8139 Zeocin InvivoGen Cat. No. 11006-33-0 Puromycin Thermo Fisher Cat. No. A1113803 2-Mercaptoethanol Thermo Fisher Cat. No. 21985023 LPS (E. coli O111:B4) Sigma-Aldrich Cat. No. L2630 TNFα R&D Systems Cat. No. 10291-TA FICZ Sigma-Aldrich Cat. No. 172922-91-7 Critical commercial assays QUANTI-Luc reagent InvivoGen Cat. No. rep-qlc4r2 Bright-Glo Luciferase assay Promega Cat. No. E2610 IL-8 ELISA kit R&D Systems Cat. No. DY208 TNFα ELISA kit Abcam Cat. No. ab181421 Yeast Live-or-DyeTM Live/Dead kit Biotium Cat. No. 31064 Deposited data PRJNA1312645 whole genome sequencing dataset NCBI https://www.ncbi.nlm.nih.gov/sra/PRJNA1312645 Experimental models: Cell lines HT-29 cells ATCC Cat. No. HTB-38 HT29-Lucia AhR cells InvivoGen Cat. No. ht2l-ahr THP-1 cells ATCC Cat. No. TIB-202 THP-1 NF-κB reporter cells ATCC Cat. No. TIB-202-NFkB-LUC2 Caco-2 cells ATCC Cat. No. HTB-37 (Continued on next page) e1 iScience 29, 115706, May 15, 2026 ..

    Article Title: Gut microbial metabolism of peanuts generates immunoregulatory metabolites
    Article Snippet: SEAP activity was quantified in cell culture supernatants using QUANTI-Blue (InvivoGen, Toulouse, France) according to the manufacturer's instructions. .. AhR activity was assessed in HT29-Lucia AhR Cells (InvivoGen, Toulouse, France), an epithelial cell-derived reporter cell line stably expressing an AhR-inducible Lucia luciferase reporter gene. .. Luciferase activity was quantified in cell culture supernatants using QUANTI-Luc (InvivoGen, Toulouse, France) according to the manufacturer's instructions.

    Article Title: Microbiota-derived tryptophan metabolites shape Th2 lymphocyte responses via the aryl hydrocarbon receptor and metabolic reprogramming.
    Article Snippet: Plasma cytokine levels in mice (IL-1β and IL-10) were measured using MSD (Meso Scale Discovery, Rockville, MD, USA). .. AHR and STAT6 reporter cell lines HT29-Lucia AHR Cells (InvivoGen) were used to evaluate AHR activation by monitoring the expression of an AHR-dependent Lucia luciferase reporter protein. ..

    Article Title: Multi-omics analysis of saccharomyces boulardii supplementation reveals coordinated microbiome, metabolic, and immune signaling changes accompanying tumor suppression.
    Article Snippet: .. Luciferase-labeled HT29-LuciaTM cells with AhR driven by the Cyp1a1 gene promoter (referred to as AhR reporter cells), were acquired from InvivoGen (catalog reference ht2l-ahr). .. MC38 cells were grown in RPMI 1640 Medium (Thermo Fisher Scientific, catalog number 11875093) and HT29-Lucia cells in McCoy’s 5 A (Modified) Medium (Thermo Fisher Scientific, catalog number 16600082).

    Enzyme-linked Immunosorbent Assay:

    Article Title: Genomic and phenotypic comparisons reveal lineage-specific traits of the probiotic Saccharomyces boulardii .
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples S. boulardii CNCM I-745 Biocodex (Precosa) CNCM I-745 S. boulardii DBVPG 6763 Gnosis (Sachhaflor) DBVPG 6763 S. boulardii ATCC MYA-796 ATCC MYA-796 S. boulardii CNCM I-3799 NOW Foods CNCM I-3799 S. boulardii CNCM I-1079 Lallemand CNCM I-1079 S. cerevisiae baker’s (SE) KronJäst N/A S. cerevisiae baker’s (DK) Lallemand N/A S. cerevisiae CEN.PK113-5D Euroscarf CEN.PK113-5D Chemicals, peptides, and recombinant proteins DNA/RNA Shield Zymo Research Cat. No. R1100 Artificial gastric fluid Biochemazone Cat. No. BZ175 Artificial intestinal fluid Biochemazone Cat. No. BZ176 Artificial colonic fluid Biochemazone Cat. No. BZ177 Yeast Live/Dead kit Biotium Cat. No. 31064 D-(+)-Glucose monohydrate Sigma-Aldrich Cat. No. 16301 Ethanol absolute VWR Cat. No. 20821.310 Sodium acetate Sigma-Aldrich Cat. No. S8750 Sodium L-lactate Sigma-Aldrich Cat. No. 71718 Sodium succinate dibasic Sigma-Aldrich Cat. No. 14160 McCoy’s 5A medium Thermo Fisher Cat. No. 16600082 Fetal bovine serum Thermo Fisher Cat. No. A5670701 Penicillin–streptomycin Thermo Fisher Cat. No. 15140148 RPMI-1640 medium Thermo Fisher Cat. No. 12027599 PMA Sigma-Aldrich Cat. No. P8139 Zeocin InvivoGen Cat. No. 11006-33-0 Puromycin Thermo Fisher Cat. No. A1113803 2-Mercaptoethanol Thermo Fisher Cat. No. 21985023 LPS (E. coli O111:B4) Sigma-Aldrich Cat. No. L2630 TNFα R&D Systems Cat. No. 10291-TA FICZ Sigma-Aldrich Cat. No. 172922-91-7 Critical commercial assays QUANTI-Luc reagent InvivoGen Cat. No. rep-qlc4r2 Bright-Glo Luciferase assay Promega Cat. No. E2610 IL-8 ELISA kit R&D Systems Cat. No. DY208 TNFα ELISA kit Abcam Cat. No. ab181421 Yeast Live-or-DyeTM Live/Dead kit Biotium Cat. No. 31064 Deposited data PRJNA1312645 whole genome sequencing dataset NCBI https://www.ncbi.nlm.nih.gov/sra/PRJNA1312645 Experimental models: Cell lines HT-29 cells ATCC Cat. No. HTB-38 HT29-Lucia AhR cells InvivoGen Cat. No. ht2l-ahr THP-1 cells ATCC Cat. No. TIB-202 THP-1 NF-κB reporter cells ATCC Cat. No. TIB-202-NFkB-LUC2 Caco-2 cells ATCC Cat. No. HTB-37 (Continued on next page) e1 iScience 29, 115706, May 15, 2026 ..

    Sequencing:

    Article Title: Genomic and phenotypic comparisons reveal lineage-specific traits of the probiotic Saccharomyces boulardii .
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples S. boulardii CNCM I-745 Biocodex (Precosa) CNCM I-745 S. boulardii DBVPG 6763 Gnosis (Sachhaflor) DBVPG 6763 S. boulardii ATCC MYA-796 ATCC MYA-796 S. boulardii CNCM I-3799 NOW Foods CNCM I-3799 S. boulardii CNCM I-1079 Lallemand CNCM I-1079 S. cerevisiae baker’s (SE) KronJäst N/A S. cerevisiae baker’s (DK) Lallemand N/A S. cerevisiae CEN.PK113-5D Euroscarf CEN.PK113-5D Chemicals, peptides, and recombinant proteins DNA/RNA Shield Zymo Research Cat. No. R1100 Artificial gastric fluid Biochemazone Cat. No. BZ175 Artificial intestinal fluid Biochemazone Cat. No. BZ176 Artificial colonic fluid Biochemazone Cat. No. BZ177 Yeast Live/Dead kit Biotium Cat. No. 31064 D-(+)-Glucose monohydrate Sigma-Aldrich Cat. No. 16301 Ethanol absolute VWR Cat. No. 20821.310 Sodium acetate Sigma-Aldrich Cat. No. S8750 Sodium L-lactate Sigma-Aldrich Cat. No. 71718 Sodium succinate dibasic Sigma-Aldrich Cat. No. 14160 McCoy’s 5A medium Thermo Fisher Cat. No. 16600082 Fetal bovine serum Thermo Fisher Cat. No. A5670701 Penicillin–streptomycin Thermo Fisher Cat. No. 15140148 RPMI-1640 medium Thermo Fisher Cat. No. 12027599 PMA Sigma-Aldrich Cat. No. P8139 Zeocin InvivoGen Cat. No. 11006-33-0 Puromycin Thermo Fisher Cat. No. A1113803 2-Mercaptoethanol Thermo Fisher Cat. No. 21985023 LPS (E. coli O111:B4) Sigma-Aldrich Cat. No. L2630 TNFα R&D Systems Cat. No. 10291-TA FICZ Sigma-Aldrich Cat. No. 172922-91-7 Critical commercial assays QUANTI-Luc reagent InvivoGen Cat. No. rep-qlc4r2 Bright-Glo Luciferase assay Promega Cat. No. E2610 IL-8 ELISA kit R&D Systems Cat. No. DY208 TNFα ELISA kit Abcam Cat. No. ab181421 Yeast Live-or-DyeTM Live/Dead kit Biotium Cat. No. 31064 Deposited data PRJNA1312645 whole genome sequencing dataset NCBI https://www.ncbi.nlm.nih.gov/sra/PRJNA1312645 Experimental models: Cell lines HT-29 cells ATCC Cat. No. HTB-38 HT29-Lucia AhR cells InvivoGen Cat. No. ht2l-ahr THP-1 cells ATCC Cat. No. TIB-202 THP-1 NF-κB reporter cells ATCC Cat. No. TIB-202-NFkB-LUC2 Caco-2 cells ATCC Cat. No. HTB-37 (Continued on next page) e1 iScience 29, 115706, May 15, 2026 ..

    Activity Assay:

    Article Title: Gut microbial metabolism of peanuts generates immunoregulatory metabolites
    Article Snippet: SEAP activity was quantified in cell culture supernatants using QUANTI-Blue (InvivoGen, Toulouse, France) according to the manufacturer's instructions. .. AhR activity was assessed in HT29-Lucia AhR Cells (InvivoGen, Toulouse, France), an epithelial cell-derived reporter cell line stably expressing an AhR-inducible Lucia luciferase reporter gene. .. Luciferase activity was quantified in cell culture supernatants using QUANTI-Luc (InvivoGen, Toulouse, France) according to the manufacturer's instructions.

    Stable Transfection:

    Article Title: Gut microbial metabolism of peanuts generates immunoregulatory metabolites
    Article Snippet: SEAP activity was quantified in cell culture supernatants using QUANTI-Blue (InvivoGen, Toulouse, France) according to the manufacturer's instructions. .. AhR activity was assessed in HT29-Lucia AhR Cells (InvivoGen, Toulouse, France), an epithelial cell-derived reporter cell line stably expressing an AhR-inducible Lucia luciferase reporter gene. .. Luciferase activity was quantified in cell culture supernatants using QUANTI-Luc (InvivoGen, Toulouse, France) according to the manufacturer's instructions.

    Article Title: Screening psychobiotic bacteria in the human colonic microbiota under high perceived stress.
    Article Snippet: .. AR TIC LE IN PR ES S ARTICLE IN PRESS HT29-LuciaTM AhR reporter cells (Invivogen, Toulouse, France) derived from human colorectal adenocarcinoma and stably transfected to express the aryl hydrocarbon receptor (AhR) were cultured in DMEM supplemented with FBS (10%), PEEN (100 U/mL Penicillin G + 100 μg/mL Streptomycin) and the specific antibiotics NormocinTM and ZeocinTM (100 μg/mL each). .. Briefly, each reaction (20 μL) included Takyon NoRox SYBR 2X master mix (Eurogentec S.A., Seraing, Belgium), forward and reverse primers (Table 2), 2.5 μL of DNA template (10 ng), and molecular biology grade water.

    Expressing:

    Article Title: Gut microbial metabolism of peanuts generates immunoregulatory metabolites
    Article Snippet: SEAP activity was quantified in cell culture supernatants using QUANTI-Blue (InvivoGen, Toulouse, France) according to the manufacturer's instructions. .. AhR activity was assessed in HT29-Lucia AhR Cells (InvivoGen, Toulouse, France), an epithelial cell-derived reporter cell line stably expressing an AhR-inducible Lucia luciferase reporter gene. .. Luciferase activity was quantified in cell culture supernatants using QUANTI-Luc (InvivoGen, Toulouse, France) according to the manufacturer's instructions.

    Article Title: Microbiota-derived tryptophan metabolites shape Th2 lymphocyte responses via the aryl hydrocarbon receptor and metabolic reprogramming.
    Article Snippet: Plasma cytokine levels in mice (IL-1β and IL-10) were measured using MSD (Meso Scale Discovery, Rockville, MD, USA). .. AHR and STAT6 reporter cell lines HT29-Lucia AHR Cells (InvivoGen) were used to evaluate AHR activation by monitoring the expression of an AHR-dependent Lucia luciferase reporter protein. ..

    Activation Assay:

    Article Title: Microbiota-derived tryptophan metabolites shape Th2 lymphocyte responses via the aryl hydrocarbon receptor and metabolic reprogramming.
    Article Snippet: Plasma cytokine levels in mice (IL-1β and IL-10) were measured using MSD (Meso Scale Discovery, Rockville, MD, USA). .. AHR and STAT6 reporter cell lines HT29-Lucia AHR Cells (InvivoGen) were used to evaluate AHR activation by monitoring the expression of an AHR-dependent Lucia luciferase reporter protein. ..

    Derivative Assay:

    Article Title: Screening psychobiotic bacteria in the human colonic microbiota under high perceived stress.
    Article Snippet: .. AR TIC LE IN PR ES S ARTICLE IN PRESS HT29-LuciaTM AhR reporter cells (Invivogen, Toulouse, France) derived from human colorectal adenocarcinoma and stably transfected to express the aryl hydrocarbon receptor (AhR) were cultured in DMEM supplemented with FBS (10%), PEEN (100 U/mL Penicillin G + 100 μg/mL Streptomycin) and the specific antibiotics NormocinTM and ZeocinTM (100 μg/mL each). .. Briefly, each reaction (20 μL) included Takyon NoRox SYBR 2X master mix (Eurogentec S.A., Seraing, Belgium), forward and reverse primers (Table 2), 2.5 μL of DNA template (10 ng), and molecular biology grade water.

    Transfection:

    Article Title: Screening psychobiotic bacteria in the human colonic microbiota under high perceived stress.
    Article Snippet: .. AR TIC LE IN PR ES S ARTICLE IN PRESS HT29-LuciaTM AhR reporter cells (Invivogen, Toulouse, France) derived from human colorectal adenocarcinoma and stably transfected to express the aryl hydrocarbon receptor (AhR) were cultured in DMEM supplemented with FBS (10%), PEEN (100 U/mL Penicillin G + 100 μg/mL Streptomycin) and the specific antibiotics NormocinTM and ZeocinTM (100 μg/mL each). .. Briefly, each reaction (20 μL) included Takyon NoRox SYBR 2X master mix (Eurogentec S.A., Seraing, Belgium), forward and reverse primers (Table 2), 2.5 μL of DNA template (10 ng), and molecular biology grade water.

    Cell Culture:

    Article Title: Screening psychobiotic bacteria in the human colonic microbiota under high perceived stress.
    Article Snippet: .. AR TIC LE IN PR ES S ARTICLE IN PRESS HT29-LuciaTM AhR reporter cells (Invivogen, Toulouse, France) derived from human colorectal adenocarcinoma and stably transfected to express the aryl hydrocarbon receptor (AhR) were cultured in DMEM supplemented with FBS (10%), PEEN (100 U/mL Penicillin G + 100 μg/mL Streptomycin) and the specific antibiotics NormocinTM and ZeocinTM (100 μg/mL each). .. Briefly, each reaction (20 μL) included Takyon NoRox SYBR 2X master mix (Eurogentec S.A., Seraing, Belgium), forward and reverse primers (Table 2), 2.5 μL of DNA template (10 ng), and molecular biology grade water.

    Incubation:

    Article Title: Mucin degradation by Akkermansia muciniphila promotes Alistipes -dependent tryptophan metabolism and Th17-driven autoimmunity
    Article Snippet: .. HT29-Lucia AhR (InvivoGen, cat#: ht2l-ahr) reporter cells (2.8×10 5 cells/ml) were incubated with fecal suspensions at 37°C, 5% CO 2 for 48 hr. .. The supernatant was harvested and mixed with 50 μl of QUANTI-Luc Gold (InvivoGen, cat#: qlcg2).



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    a Composite image of an HCT116 spheroid at 30 µm depth, showing nuclei (Hoechst, blue), RNA and cytoplasm (SYTO 14, green), and cytoskeleton, plasma membrane, and Golgi (phalloidin and wheat germ agglutinin, WGA; red). Scale bar is 50 µm, and spheroids were imaged at 30 × (0.227 µm/pixel). Inset: magnified view showing individual cells (scale bar, 10 µm). b Individual channels from the same acquisition: Hoechst (nuclei, blue), concanavalin A (endoplasmic reticulum, cyan), SYTO 14 (cytoplasm and RNA, green), phalloidin and WGA (cytoskeleton, plasma membrane, and Golgi, red), and MitoTracker (mitochondria, gray). c An example of nuclei (left) and cell segmentation (right) by Cellpose. Objects are outlined in white. Scale bar is 50 µm. a – d Number of 2D segmentation object instances per spheroid at each z -section for HCT116 (gray) and HT29 (black). Right: total instances summed across the full z -stack per spheroid. e Detections per cell across the z -stack (duplicate estimate), reflecting how many times the same cell is counted across optical sections. Each datapoint is one well at one section; n = 58 HCT116 and 56 HT29 DMSO wells. Box plots: center line, median; box bounds, 25th and 75th percentiles; whiskers, most extreme value within 1.5 × the interquartile range; outliers not shown. f Representative 3D distribution of detected cell positions in an HCT116 spheroid exposed to 0.1% DMSO. g Principal Component Analysis (PCA) of single-cell morphological profiles normalized per-plate (left) versus per-section (right). Both panels use identical PCA loadings (computed on the per-plate-normalized DMSO data; PC1 and PC2 explain 23.64% and 13.19% of total variance, respectively) to facilitate direct comparison. Section dependence was assessed by two-sided Pearson correlation of PC2 against optical section, with η² from a one-way ANOVA as a descriptive effect size ( n = 348 well–section observations, 29 wells, no correction for multiple comparisons). Section-dependent effects are present before normalization (PC2: r = 0.79, η² = 68%, p = 1.1 × 10⁻ 76 ), but much less after (PC2: r = −0.00, η² = 1%, p = 0.96). Spheroid optical section (0–11) is color-coded in ( f , g ). Images in a – c are 16-bit, with display ranges of 190-1328 (Hoechst), 299-4332 (SYTO14), and 347-5876 (Phalloidin and WGA) out of 65535. Rolling-ball background subtraction (radius 50 pixels) was applied in an and b but not in c . Source data are provided as a Source Data file.

    Journal: Nature Communications

    Article Title: High-content morphological profiling by Cell Painting in 3D spheroids

    doi: 10.1038/s41467-026-78596-5

    Figure Lengend Snippet: a Composite image of an HCT116 spheroid at 30 µm depth, showing nuclei (Hoechst, blue), RNA and cytoplasm (SYTO 14, green), and cytoskeleton, plasma membrane, and Golgi (phalloidin and wheat germ agglutinin, WGA; red). Scale bar is 50 µm, and spheroids were imaged at 30 × (0.227 µm/pixel). Inset: magnified view showing individual cells (scale bar, 10 µm). b Individual channels from the same acquisition: Hoechst (nuclei, blue), concanavalin A (endoplasmic reticulum, cyan), SYTO 14 (cytoplasm and RNA, green), phalloidin and WGA (cytoskeleton, plasma membrane, and Golgi, red), and MitoTracker (mitochondria, gray). c An example of nuclei (left) and cell segmentation (right) by Cellpose. Objects are outlined in white. Scale bar is 50 µm. a – d Number of 2D segmentation object instances per spheroid at each z -section for HCT116 (gray) and HT29 (black). Right: total instances summed across the full z -stack per spheroid. e Detections per cell across the z -stack (duplicate estimate), reflecting how many times the same cell is counted across optical sections. Each datapoint is one well at one section; n = 58 HCT116 and 56 HT29 DMSO wells. Box plots: center line, median; box bounds, 25th and 75th percentiles; whiskers, most extreme value within 1.5 × the interquartile range; outliers not shown. f Representative 3D distribution of detected cell positions in an HCT116 spheroid exposed to 0.1% DMSO. g Principal Component Analysis (PCA) of single-cell morphological profiles normalized per-plate (left) versus per-section (right). Both panels use identical PCA loadings (computed on the per-plate-normalized DMSO data; PC1 and PC2 explain 23.64% and 13.19% of total variance, respectively) to facilitate direct comparison. Section dependence was assessed by two-sided Pearson correlation of PC2 against optical section, with η² from a one-way ANOVA as a descriptive effect size ( n = 348 well–section observations, 29 wells, no correction for multiple comparisons). Section-dependent effects are present before normalization (PC2: r = 0.79, η² = 68%, p = 1.1 × 10⁻ 76 ), but much less after (PC2: r = −0.00, η² = 1%, p = 0.96). Spheroid optical section (0–11) is color-coded in ( f , g ). Images in a – c are 16-bit, with display ranges of 190-1328 (Hoechst), 299-4332 (SYTO14), and 347-5876 (Phalloidin and WGA) out of 65535. Rolling-ball background subtraction (radius 50 pixels) was applied in an and b but not in c . Source data are provided as a Source Data file.

    Article Snippet: Two human colorectal cancer cell lines were used: HCT116 (RRID:CVCL_0291; colorectal carcinoma, adult male donor; originally ATCC CCL-247) and HT29 (RRID:CVCL_0320; colorectal adenocarcinoma, female donor; originally ATCC HTB-38).

    Techniques: Clinical Proteomics, Membrane, Spheroids, Analysis, Single Cell, Comparison, Reference Subtraction

    a Representative examples of HCT116 (top) and HT29 (bottom) max intensity projections (MIPs) for the compounds SN-38 (0.03 µM), binimetinib (10 µM), abemaciclib (3.0 µM), and DMSO (0.1%), as well as for ( b ) a single section at 30 µm depth. SYTO 14 (RNA) is shown in green, Hoechst (nuclei) is shown in blue, and phalloidin/WGA (cytoskeleton and golgi) are shown in red. Scale bars are 50 µm; images were acquired at 30 × (0.227 µm/pixel). Images are 16-bit, with display ranges of 190-1328 (Hoechst), 299-4332 (SYTO14), and 347-5876 (Phalloidin and WGA) out of 65535. No rolling-ball background subtraction was applied. c , d Grit scores measuring phenotypic effect are shown for MIP-based ( c ) and aggregated ( d ) profiles. Each bar is one compound–dose perturbation, 4 wells; error bars, mean ± 1 s.d. The dashed horizontal line marks the grit > 1.96 threshold. e , f Null and median pairwise replicate correlations distributions across dose steps for both HCT116 and HT29 cell lines. Null distributions are in grays and replicate in blues. Box plots (both series): center line, median; box bounds, 25th and 75th percentiles; whiskers, most extreme value within 1.5 × the interquartile range; outliers not shown. Each point is one compound–dose perturbation (4 wells); n = 41–52 per box, 208 per null. c – h pre-filter, treatment wells only. g , h Comparison of median pairwise replicate correlations of MIP-based and scAgg profiles in both HCT116 and HT29 cell lines. Data points are compound–dose perturbations ( n = 383; 196 HCT116, 187 HT29), color-coded for ( g ) dose, or ( h ) pathway. Source data are provided as a Source Data file.

    Journal: Nature Communications

    Article Title: High-content morphological profiling by Cell Painting in 3D spheroids

    doi: 10.1038/s41467-026-78596-5

    Figure Lengend Snippet: a Representative examples of HCT116 (top) and HT29 (bottom) max intensity projections (MIPs) for the compounds SN-38 (0.03 µM), binimetinib (10 µM), abemaciclib (3.0 µM), and DMSO (0.1%), as well as for ( b ) a single section at 30 µm depth. SYTO 14 (RNA) is shown in green, Hoechst (nuclei) is shown in blue, and phalloidin/WGA (cytoskeleton and golgi) are shown in red. Scale bars are 50 µm; images were acquired at 30 × (0.227 µm/pixel). Images are 16-bit, with display ranges of 190-1328 (Hoechst), 299-4332 (SYTO14), and 347-5876 (Phalloidin and WGA) out of 65535. No rolling-ball background subtraction was applied. c , d Grit scores measuring phenotypic effect are shown for MIP-based ( c ) and aggregated ( d ) profiles. Each bar is one compound–dose perturbation, 4 wells; error bars, mean ± 1 s.d. The dashed horizontal line marks the grit > 1.96 threshold. e , f Null and median pairwise replicate correlations distributions across dose steps for both HCT116 and HT29 cell lines. Null distributions are in grays and replicate in blues. Box plots (both series): center line, median; box bounds, 25th and 75th percentiles; whiskers, most extreme value within 1.5 × the interquartile range; outliers not shown. Each point is one compound–dose perturbation (4 wells); n = 41–52 per box, 208 per null. c – h pre-filter, treatment wells only. g , h Comparison of median pairwise replicate correlations of MIP-based and scAgg profiles in both HCT116 and HT29 cell lines. Data points are compound–dose perturbations ( n = 383; 196 HCT116, 187 HT29), color-coded for ( g ) dose, or ( h ) pathway. Source data are provided as a Source Data file.

    Article Snippet: Two human colorectal cancer cell lines were used: HCT116 (RRID:CVCL_0291; colorectal carcinoma, adult male donor; originally ATCC CCL-247) and HT29 (RRID:CVCL_0320; colorectal adenocarcinoma, female donor; originally ATCC HTB-38).

    Techniques: Reference Subtraction, Comparison

    a A quantification of the number of drugs with grit > 1.96 for cell lines HCT116 and HT29. Color-coded are the drugs unique to each culture format, as well as the non-unique drugs. The total amount of drugs is 52. b Semi-supervised UMAPs of 2D morphological profiles. c Heatmap displaying hierarchical clusters of cosine similarities for 2D profiles. d Comparison of cosine scores between pairs of compounds in 2D and 3D. The x-axis shows the difference in similarity scores (3D – 2D), while the y-axis shows the highest similarity score across both modalities for each pair. Pairs whose absolute between-format difference (3D – 2D) fell in the top 5% (95th percentile) across all matched pairs were flagged as divergent; among these, pairs with a cosine score of at least 0.5 in either 2D or 3D were labeled. e Representative images of cells in 2D (top) and 3D (bottom) exposed to olaparib (3 µM), 5-fluorouracil (5-FU) (10 µM), and the negative control DMSO (0.1%). SYTO 14 is green, phalloidin/WGA is red, and Hoechst is blue. 2D images were acquired at 20 × (0.34 µm/pixel) and 3D images at 30 × (0.227 µm/pixel) from a 30 µm depth. Images are 16-bit, with display ranges of 190-1328 (Hoechst), 299-4332 (SYTO14), and 347-5876 (Phalloidin and WGA) out of 65535. No rolling-ball background subtraction was applied. f Preprocessed morphological profiles are shown for 2D (top) and 3D (bottom) exposed to 5-FU (10 µM) and olaparib (3 µM). Scale bars are 50 µm. Source data are provided as a Source Data file.

    Journal: Nature Communications

    Article Title: High-content morphological profiling by Cell Painting in 3D spheroids

    doi: 10.1038/s41467-026-78596-5

    Figure Lengend Snippet: a A quantification of the number of drugs with grit > 1.96 for cell lines HCT116 and HT29. Color-coded are the drugs unique to each culture format, as well as the non-unique drugs. The total amount of drugs is 52. b Semi-supervised UMAPs of 2D morphological profiles. c Heatmap displaying hierarchical clusters of cosine similarities for 2D profiles. d Comparison of cosine scores between pairs of compounds in 2D and 3D. The x-axis shows the difference in similarity scores (3D – 2D), while the y-axis shows the highest similarity score across both modalities for each pair. Pairs whose absolute between-format difference (3D – 2D) fell in the top 5% (95th percentile) across all matched pairs were flagged as divergent; among these, pairs with a cosine score of at least 0.5 in either 2D or 3D were labeled. e Representative images of cells in 2D (top) and 3D (bottom) exposed to olaparib (3 µM), 5-fluorouracil (5-FU) (10 µM), and the negative control DMSO (0.1%). SYTO 14 is green, phalloidin/WGA is red, and Hoechst is blue. 2D images were acquired at 20 × (0.34 µm/pixel) and 3D images at 30 × (0.227 µm/pixel) from a 30 µm depth. Images are 16-bit, with display ranges of 190-1328 (Hoechst), 299-4332 (SYTO14), and 347-5876 (Phalloidin and WGA) out of 65535. No rolling-ball background subtraction was applied. f Preprocessed morphological profiles are shown for 2D (top) and 3D (bottom) exposed to 5-FU (10 µM) and olaparib (3 µM). Scale bars are 50 µm. Source data are provided as a Source Data file.

    Article Snippet: Two human colorectal cancer cell lines were used: HCT116 (RRID:CVCL_0291; colorectal carcinoma, adult male donor; originally ATCC CCL-247) and HT29 (RRID:CVCL_0320; colorectal adenocarcinoma, female donor; originally ATCC HTB-38).

    Techniques: Comparison, Labeling, Negative Control, Reference Subtraction

    a Microscopy images of spheroids exposed to 5-FU (10 µM; n = 13; green), olaparib (3 µM; n = 13; purple), and etoposide (2.5 µM; n = 8; orange), plus a DMSO control (0.1%; n = 13; gray). Stained for EdU (red), Hoechst (blue), and γH2AX (green); 12-bit; channels background-subtracted in Fiji across the whole image (rolling ball = 50, 50, 5); display ranges Hoechst 0–2500, γH2AX 11–160, EdU unscaled (0–4095). Scale bars, 50 µm. Images were acquired at 30 × (0.227 µm/pixel) from a 30 µm depth. b Quantification of DNA damage (γH2AX foci/nucleus), S-phase entry (fraction of EdU-positive nuclei), and spheroid size (nuclei/spheroid) across the four conditions (n as in ( a ); unit of study, individual spheroid in a separate well); error bars, mean ± SEM. Significance by Kruskal–Wallis followed, where significant, by two-sided Mann–Whitney U; comparisons against DMSO were Bonferroni-corrected, the 5-FU versus olaparib comparison was not. Exact P values versus DMSO for 5-FU, olaparib and etoposide respectively, and for 5-FU versus olaparib: γH2AX foci, 0.0122, 6.2 × 10⁻⁵, 2.9 × 10⁻⁵ and 2.7 × 10⁻⁴; EdU-positive fraction, 4.9 × 10⁻⁵, 6.2 × 10⁻⁵, 4.8 × 10⁻⁴ and 5.9 × 10⁻⁴; nuclei per spheroid, 0.0088, 0.0359, 2.9 × 10⁻⁵ and 0.412 (not significant). c Hallmark gene-set enrichment analysis (GSEA): NES for 5-FU (x-axis) versus olaparib (y-axis), colored by agent as in ( a ) or black where significant for both (FDR < 0.1). d Per-gene log2FC for the 15 strongest effectors per signature (top to bottom: p53 Hallmark, E2F Hallmark, p53-apoptosis Reactome); colored as in ( a ), opacity indicating significance (FDR < 0.1). e Pairwise cosine-similarity maps of the 10 drugs most similar to 5-FU (10 µM) in HCT116 (left; subset of Fig. ) and HT29 (right); 5-FU boxed. Source data are provided as a Source Data file.

    Journal: Nature Communications

    Article Title: High-content morphological profiling by Cell Painting in 3D spheroids

    doi: 10.1038/s41467-026-78596-5

    Figure Lengend Snippet: a Microscopy images of spheroids exposed to 5-FU (10 µM; n = 13; green), olaparib (3 µM; n = 13; purple), and etoposide (2.5 µM; n = 8; orange), plus a DMSO control (0.1%; n = 13; gray). Stained for EdU (red), Hoechst (blue), and γH2AX (green); 12-bit; channels background-subtracted in Fiji across the whole image (rolling ball = 50, 50, 5); display ranges Hoechst 0–2500, γH2AX 11–160, EdU unscaled (0–4095). Scale bars, 50 µm. Images were acquired at 30 × (0.227 µm/pixel) from a 30 µm depth. b Quantification of DNA damage (γH2AX foci/nucleus), S-phase entry (fraction of EdU-positive nuclei), and spheroid size (nuclei/spheroid) across the four conditions (n as in ( a ); unit of study, individual spheroid in a separate well); error bars, mean ± SEM. Significance by Kruskal–Wallis followed, where significant, by two-sided Mann–Whitney U; comparisons against DMSO were Bonferroni-corrected, the 5-FU versus olaparib comparison was not. Exact P values versus DMSO for 5-FU, olaparib and etoposide respectively, and for 5-FU versus olaparib: γH2AX foci, 0.0122, 6.2 × 10⁻⁵, 2.9 × 10⁻⁵ and 2.7 × 10⁻⁴; EdU-positive fraction, 4.9 × 10⁻⁵, 6.2 × 10⁻⁵, 4.8 × 10⁻⁴ and 5.9 × 10⁻⁴; nuclei per spheroid, 0.0088, 0.0359, 2.9 × 10⁻⁵ and 0.412 (not significant). c Hallmark gene-set enrichment analysis (GSEA): NES for 5-FU (x-axis) versus olaparib (y-axis), colored by agent as in ( a ) or black where significant for both (FDR < 0.1). d Per-gene log2FC for the 15 strongest effectors per signature (top to bottom: p53 Hallmark, E2F Hallmark, p53-apoptosis Reactome); colored as in ( a ), opacity indicating significance (FDR < 0.1). e Pairwise cosine-similarity maps of the 10 drugs most similar to 5-FU (10 µM) in HCT116 (left; subset of Fig. ) and HT29 (right); 5-FU boxed. Source data are provided as a Source Data file.

    Article Snippet: Two human colorectal cancer cell lines were used: HCT116 (RRID:CVCL_0291; colorectal carcinoma, adult male donor; originally ATCC CCL-247) and HT29 (RRID:CVCL_0320; colorectal adenocarcinoma, female donor; originally ATCC HTB-38).

    Techniques: Microscopy, Spheroids, Control, Staining, MANN-WHITNEY, Comparison, Analysis