Recombinant:Article Title: Single-cell morphodynamical trajectories enable prediction of gene expression accompanying cell state change.
Article Snippet: .. Cells were maintained in DMEM/ F12 supplemented with insulin, sodium selenite, hydrocortisone, β-estrogen, and transferrin, and maintained in 5% C02 at 37◦C.111 REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Recombinant Human EGF Protein, CF R&D Systems Cat#236-EG Recombinant Human Oncostatin M (HEK-293-expressed) Protein R&D Systems Cat#8475-OM Recombinant Human TGF-beta 1 Protein R&D Systems Cat240-B Recombinant Human HGF Protein R&D Systems Cat#294-HG Recombinant Human BMP2 Protein R&D Systems Cat#355-BM Recombinant Human IFNу Protein R&D Systems Cat#258-IF Recombinant Human EGF Protein Peprotech Cat#AF-100-15-500UG Recombinant Human IGF Protein Peprotech Cat#100-11-500UG Recombinant Human HGF Protein Peprotech Cat#100-39H-25UG MEKi/PD0325901 Selleckchem Cat# S1036 AKTi/MK2206 Selleckchem Cat# S1078 Deposited data mcf10a maging, image analysis, sequencing data This paper https://doi.org/10.5281/zenodo.11455833 RNAseq data from combination ligand treatments Mclean et al.74 GEO: GSE282654 RNAseq and protein expression data Gross et al.65 https://synapse.org/LINCS_MCF10A Live-cell imaging from combination ligand treatments Mclean et al.74 https://doi.org/10.5281/zenodo.14261795 Experimental models: Cell lines Human: MCF10A line Gift from Gordon Mills (OHSU) N/A Human: HMT-3522 T4-2 line Gift from Mina Bissell (LBNL) N/A Recombinant DNA Plasmid: pLJM1-ERKTR-mVenus-puro Gillies et al.107 https://doi.org/10.1016/j.cels.2017.10.019 Software and algorithms DESeq2 v1.24.0 Soneson et al.108 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html Label-free fluorescence prediction: pytorch_fnet Ounkomol et al.77 https://github.com/AllenCellModeling/pytorch_fnet btrack v0.4.2 Ulicna et al.78 https://github.com/quantumjot/btrack pyemma v2.5.12 Scherer et al.76 https://github.com/markovmodel/PyEMMA GSEApy Fang et al.109 https://github.com/zqfang/GSEApy CellPose v2.0 Stringer et al.110 https://github.com/MouseLand/cellpose Celltraj Copperman et al.30 https://doi.org/10.5281/zenodo.17806558 MMIST This paper https://doi.org/10.5281/zenodo.18624747 ll OPEN ACCESS Article e1 Cell Systems 17, 101567, May 20, 2026 .. Companion RNAseq and live-cell imaging data used in this paper are described in full in Gross et al.65 In brief, MCF10A cells were cultured in growth media composed of DMEM/F12 (Invitrogen #11330-032), 5% horse serum (Sigma #H1138), 20 ng/ml EGF (R&D Systems #236-EG), 10 μg/ml insulin (Sigma #I9278), 100 ng/ml cholera toxin (Sigma #C8052), 0.5 μg/ml hydrocortisone (Sigma #H4001), and 1% Pen/Strep (Invitrogen #15070-063).
Sequencing:Article Title: Single-cell morphodynamical trajectories enable prediction of gene expression accompanying cell state change.
Article Snippet: .. Cells were maintained in DMEM/ F12 supplemented with insulin, sodium selenite, hydrocortisone, β-estrogen, and transferrin, and maintained in 5% C02 at 37◦C.111 REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Recombinant Human EGF Protein, CF R&D Systems Cat#236-EG Recombinant Human Oncostatin M (HEK-293-expressed) Protein R&D Systems Cat#8475-OM Recombinant Human TGF-beta 1 Protein R&D Systems Cat240-B Recombinant Human HGF Protein R&D Systems Cat#294-HG Recombinant Human BMP2 Protein R&D Systems Cat#355-BM Recombinant Human IFNу Protein R&D Systems Cat#258-IF Recombinant Human EGF Protein Peprotech Cat#AF-100-15-500UG Recombinant Human IGF Protein Peprotech Cat#100-11-500UG Recombinant Human HGF Protein Peprotech Cat#100-39H-25UG MEKi/PD0325901 Selleckchem Cat# S1036 AKTi/MK2206 Selleckchem Cat# S1078 Deposited data mcf10a maging, image analysis, sequencing data This paper https://doi.org/10.5281/zenodo.11455833 RNAseq data from combination ligand treatments Mclean et al.74 GEO: GSE282654 RNAseq and protein expression data Gross et al.65 https://synapse.org/LINCS_MCF10A Live-cell imaging from combination ligand treatments Mclean et al.74 https://doi.org/10.5281/zenodo.14261795 Experimental models: Cell lines Human: MCF10A line Gift from Gordon Mills (OHSU) N/A Human: HMT-3522 T4-2 line Gift from Mina Bissell (LBNL) N/A Recombinant DNA Plasmid: pLJM1-ERKTR-mVenus-puro Gillies et al.107 https://doi.org/10.1016/j.cels.2017.10.019 Software and algorithms DESeq2 v1.24.0 Soneson et al.108 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html Label-free fluorescence prediction: pytorch_fnet Ounkomol et al.77 https://github.com/AllenCellModeling/pytorch_fnet btrack v0.4.2 Ulicna et al.78 https://github.com/quantumjot/btrack pyemma v2.5.12 Scherer et al.76 https://github.com/markovmodel/PyEMMA GSEApy Fang et al.109 https://github.com/zqfang/GSEApy CellPose v2.0 Stringer et al.110 https://github.com/MouseLand/cellpose Celltraj Copperman et al.30 https://doi.org/10.5281/zenodo.17806558 MMIST This paper https://doi.org/10.5281/zenodo.18624747 ll OPEN ACCESS Article e1 Cell Systems 17, 101567, May 20, 2026 .. Companion RNAseq and live-cell imaging data used in this paper are described in full in Gross et al.65 In brief, MCF10A cells were cultured in growth media composed of DMEM/F12 (Invitrogen #11330-032), 5% horse serum (Sigma #H1138), 20 ng/ml EGF (R&D Systems #236-EG), 10 μg/ml insulin (Sigma #I9278), 100 ng/ml cholera toxin (Sigma #C8052), 0.5 μg/ml hydrocortisone (Sigma #H4001), and 1% Pen/Strep (Invitrogen #15070-063).
RNA sequencing:Article Title: Single-cell morphodynamical trajectories enable prediction of gene expression accompanying cell state change.
Article Snippet: .. Cells were maintained in DMEM/ F12 supplemented with insulin, sodium selenite, hydrocortisone, β-estrogen, and transferrin, and maintained in 5% C02 at 37◦C.111 REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Recombinant Human EGF Protein, CF R&D Systems Cat#236-EG Recombinant Human Oncostatin M (HEK-293-expressed) Protein R&D Systems Cat#8475-OM Recombinant Human TGF-beta 1 Protein R&D Systems Cat240-B Recombinant Human HGF Protein R&D Systems Cat#294-HG Recombinant Human BMP2 Protein R&D Systems Cat#355-BM Recombinant Human IFNу Protein R&D Systems Cat#258-IF Recombinant Human EGF Protein Peprotech Cat#AF-100-15-500UG Recombinant Human IGF Protein Peprotech Cat#100-11-500UG Recombinant Human HGF Protein Peprotech Cat#100-39H-25UG MEKi/PD0325901 Selleckchem Cat# S1036 AKTi/MK2206 Selleckchem Cat# S1078 Deposited data mcf10a maging, image analysis, sequencing data This paper https://doi.org/10.5281/zenodo.11455833 RNAseq data from combination ligand treatments Mclean et al.74 GEO: GSE282654 RNAseq and protein expression data Gross et al.65 https://synapse.org/LINCS_MCF10A Live-cell imaging from combination ligand treatments Mclean et al.74 https://doi.org/10.5281/zenodo.14261795 Experimental models: Cell lines Human: MCF10A line Gift from Gordon Mills (OHSU) N/A Human: HMT-3522 T4-2 line Gift from Mina Bissell (LBNL) N/A Recombinant DNA Plasmid: pLJM1-ERKTR-mVenus-puro Gillies et al.107 https://doi.org/10.1016/j.cels.2017.10.019 Software and algorithms DESeq2 v1.24.0 Soneson et al.108 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html Label-free fluorescence prediction: pytorch_fnet Ounkomol et al.77 https://github.com/AllenCellModeling/pytorch_fnet btrack v0.4.2 Ulicna et al.78 https://github.com/quantumjot/btrack pyemma v2.5.12 Scherer et al.76 https://github.com/markovmodel/PyEMMA GSEApy Fang et al.109 https://github.com/zqfang/GSEApy CellPose v2.0 Stringer et al.110 https://github.com/MouseLand/cellpose Celltraj Copperman et al.30 https://doi.org/10.5281/zenodo.17806558 MMIST This paper https://doi.org/10.5281/zenodo.18624747 ll OPEN ACCESS Article e1 Cell Systems 17, 101567, May 20, 2026 .. Companion RNAseq and live-cell imaging data used in this paper are described in full in Gross et al.65 In brief, MCF10A cells were cultured in growth media composed of DMEM/F12 (Invitrogen #11330-032), 5% horse serum (Sigma #H1138), 20 ng/ml EGF (R&D Systems #236-EG), 10 μg/ml insulin (Sigma #I9278), 100 ng/ml cholera toxin (Sigma #C8052), 0.5 μg/ml hydrocortisone (Sigma #H4001), and 1% Pen/Strep (Invitrogen #15070-063).
Expressing:Article Title: Single-cell morphodynamical trajectories enable prediction of gene expression accompanying cell state change.
Article Snippet: .. Cells were maintained in DMEM/ F12 supplemented with insulin, sodium selenite, hydrocortisone, β-estrogen, and transferrin, and maintained in 5% C02 at 37◦C.111 REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Recombinant Human EGF Protein, CF R&D Systems Cat#236-EG Recombinant Human Oncostatin M (HEK-293-expressed) Protein R&D Systems Cat#8475-OM Recombinant Human TGF-beta 1 Protein R&D Systems Cat240-B Recombinant Human HGF Protein R&D Systems Cat#294-HG Recombinant Human BMP2 Protein R&D Systems Cat#355-BM Recombinant Human IFNу Protein R&D Systems Cat#258-IF Recombinant Human EGF Protein Peprotech Cat#AF-100-15-500UG Recombinant Human IGF Protein Peprotech Cat#100-11-500UG Recombinant Human HGF Protein Peprotech Cat#100-39H-25UG MEKi/PD0325901 Selleckchem Cat# S1036 AKTi/MK2206 Selleckchem Cat# S1078 Deposited data mcf10a maging, image analysis, sequencing data This paper https://doi.org/10.5281/zenodo.11455833 RNAseq data from combination ligand treatments Mclean et al.74 GEO: GSE282654 RNAseq and protein expression data Gross et al.65 https://synapse.org/LINCS_MCF10A Live-cell imaging from combination ligand treatments Mclean et al.74 https://doi.org/10.5281/zenodo.14261795 Experimental models: Cell lines Human: MCF10A line Gift from Gordon Mills (OHSU) N/A Human: HMT-3522 T4-2 line Gift from Mina Bissell (LBNL) N/A Recombinant DNA Plasmid: pLJM1-ERKTR-mVenus-puro Gillies et al.107 https://doi.org/10.1016/j.cels.2017.10.019 Software and algorithms DESeq2 v1.24.0 Soneson et al.108 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html Label-free fluorescence prediction: pytorch_fnet Ounkomol et al.77 https://github.com/AllenCellModeling/pytorch_fnet btrack v0.4.2 Ulicna et al.78 https://github.com/quantumjot/btrack pyemma v2.5.12 Scherer et al.76 https://github.com/markovmodel/PyEMMA GSEApy Fang et al.109 https://github.com/zqfang/GSEApy CellPose v2.0 Stringer et al.110 https://github.com/MouseLand/cellpose Celltraj Copperman et al.30 https://doi.org/10.5281/zenodo.17806558 MMIST This paper https://doi.org/10.5281/zenodo.18624747 ll OPEN ACCESS Article e1 Cell Systems 17, 101567, May 20, 2026 .. Companion RNAseq and live-cell imaging data used in this paper are described in full in Gross et al.65 In brief, MCF10A cells were cultured in growth media composed of DMEM/F12 (Invitrogen #11330-032), 5% horse serum (Sigma #H1138), 20 ng/ml EGF (R&D Systems #236-EG), 10 μg/ml insulin (Sigma #I9278), 100 ng/ml cholera toxin (Sigma #C8052), 0.5 μg/ml hydrocortisone (Sigma #H4001), and 1% Pen/Strep (Invitrogen #15070-063).
Live Cell Imaging:Article Title: Single-cell morphodynamical trajectories enable prediction of gene expression accompanying cell state change.
Article Snippet: .. Cells were maintained in DMEM/ F12 supplemented with insulin, sodium selenite, hydrocortisone, β-estrogen, and transferrin, and maintained in 5% C02 at 37◦C.111 REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Recombinant Human EGF Protein, CF R&D Systems Cat#236-EG Recombinant Human Oncostatin M (HEK-293-expressed) Protein R&D Systems Cat#8475-OM Recombinant Human TGF-beta 1 Protein R&D Systems Cat240-B Recombinant Human HGF Protein R&D Systems Cat#294-HG Recombinant Human BMP2 Protein R&D Systems Cat#355-BM Recombinant Human IFNу Protein R&D Systems Cat#258-IF Recombinant Human EGF Protein Peprotech Cat#AF-100-15-500UG Recombinant Human IGF Protein Peprotech Cat#100-11-500UG Recombinant Human HGF Protein Peprotech Cat#100-39H-25UG MEKi/PD0325901 Selleckchem Cat# S1036 AKTi/MK2206 Selleckchem Cat# S1078 Deposited data mcf10a maging, image analysis, sequencing data This paper https://doi.org/10.5281/zenodo.11455833 RNAseq data from combination ligand treatments Mclean et al.74 GEO: GSE282654 RNAseq and protein expression data Gross et al.65 https://synapse.org/LINCS_MCF10A Live-cell imaging from combination ligand treatments Mclean et al.74 https://doi.org/10.5281/zenodo.14261795 Experimental models: Cell lines Human: MCF10A line Gift from Gordon Mills (OHSU) N/A Human: HMT-3522 T4-2 line Gift from Mina Bissell (LBNL) N/A Recombinant DNA Plasmid: pLJM1-ERKTR-mVenus-puro Gillies et al.107 https://doi.org/10.1016/j.cels.2017.10.019 Software and algorithms DESeq2 v1.24.0 Soneson et al.108 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html Label-free fluorescence prediction: pytorch_fnet Ounkomol et al.77 https://github.com/AllenCellModeling/pytorch_fnet btrack v0.4.2 Ulicna et al.78 https://github.com/quantumjot/btrack pyemma v2.5.12 Scherer et al.76 https://github.com/markovmodel/PyEMMA GSEApy Fang et al.109 https://github.com/zqfang/GSEApy CellPose v2.0 Stringer et al.110 https://github.com/MouseLand/cellpose Celltraj Copperman et al.30 https://doi.org/10.5281/zenodo.17806558 MMIST This paper https://doi.org/10.5281/zenodo.18624747 ll OPEN ACCESS Article e1 Cell Systems 17, 101567, May 20, 2026 .. Companion RNAseq and live-cell imaging data used in this paper are described in full in Gross et al.65 In brief, MCF10A cells were cultured in growth media composed of DMEM/F12 (Invitrogen #11330-032), 5% horse serum (Sigma #H1138), 20 ng/ml EGF (R&D Systems #236-EG), 10 μg/ml insulin (Sigma #I9278), 100 ng/ml cholera toxin (Sigma #C8052), 0.5 μg/ml hydrocortisone (Sigma #H4001), and 1% Pen/Strep (Invitrogen #15070-063).
HMT Assay:Article Title: Single-cell morphodynamical trajectories enable prediction of gene expression accompanying cell state change.
Article Snippet: .. Cells were maintained in DMEM/ F12 supplemented with insulin, sodium selenite, hydrocortisone, β-estrogen, and transferrin, and maintained in 5% C02 at 37◦C.111 REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Recombinant Human EGF Protein, CF R&D Systems Cat#236-EG Recombinant Human Oncostatin M (HEK-293-expressed) Protein R&D Systems Cat#8475-OM Recombinant Human TGF-beta 1 Protein R&D Systems Cat240-B Recombinant Human HGF Protein R&D Systems Cat#294-HG Recombinant Human BMP2 Protein R&D Systems Cat#355-BM Recombinant Human IFNу Protein R&D Systems Cat#258-IF Recombinant Human EGF Protein Peprotech Cat#AF-100-15-500UG Recombinant Human IGF Protein Peprotech Cat#100-11-500UG Recombinant Human HGF Protein Peprotech Cat#100-39H-25UG MEKi/PD0325901 Selleckchem Cat# S1036 AKTi/MK2206 Selleckchem Cat# S1078 Deposited data mcf10a maging, image analysis, sequencing data This paper https://doi.org/10.5281/zenodo.11455833 RNAseq data from combination ligand treatments Mclean et al.74 GEO: GSE282654 RNAseq and protein expression data Gross et al.65 https://synapse.org/LINCS_MCF10A Live-cell imaging from combination ligand treatments Mclean et al.74 https://doi.org/10.5281/zenodo.14261795 Experimental models: Cell lines Human: MCF10A line Gift from Gordon Mills (OHSU) N/A Human: HMT-3522 T4-2 line Gift from Mina Bissell (LBNL) N/A Recombinant DNA Plasmid: pLJM1-ERKTR-mVenus-puro Gillies et al.107 https://doi.org/10.1016/j.cels.2017.10.019 Software and algorithms DESeq2 v1.24.0 Soneson et al.108 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html Label-free fluorescence prediction: pytorch_fnet Ounkomol et al.77 https://github.com/AllenCellModeling/pytorch_fnet btrack v0.4.2 Ulicna et al.78 https://github.com/quantumjot/btrack pyemma v2.5.12 Scherer et al.76 https://github.com/markovmodel/PyEMMA GSEApy Fang et al.109 https://github.com/zqfang/GSEApy CellPose v2.0 Stringer et al.110 https://github.com/MouseLand/cellpose Celltraj Copperman et al.30 https://doi.org/10.5281/zenodo.17806558 MMIST This paper https://doi.org/10.5281/zenodo.18624747 ll OPEN ACCESS Article e1 Cell Systems 17, 101567, May 20, 2026 .. Companion RNAseq and live-cell imaging data used in this paper are described in full in Gross et al.65 In brief, MCF10A cells were cultured in growth media composed of DMEM/F12 (Invitrogen #11330-032), 5% horse serum (Sigma #H1138), 20 ng/ml EGF (R&D Systems #236-EG), 10 μg/ml insulin (Sigma #I9278), 100 ng/ml cholera toxin (Sigma #C8052), 0.5 μg/ml hydrocortisone (Sigma #H4001), and 1% Pen/Strep (Invitrogen #15070-063).
Plasmid Preparation:Article Title: Single-cell morphodynamical trajectories enable prediction of gene expression accompanying cell state change.
Article Snippet: .. Cells were maintained in DMEM/ F12 supplemented with insulin, sodium selenite, hydrocortisone, β-estrogen, and transferrin, and maintained in 5% C02 at 37◦C.111 REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Recombinant Human EGF Protein, CF R&D Systems Cat#236-EG Recombinant Human Oncostatin M (HEK-293-expressed) Protein R&D Systems Cat#8475-OM Recombinant Human TGF-beta 1 Protein R&D Systems Cat240-B Recombinant Human HGF Protein R&D Systems Cat#294-HG Recombinant Human BMP2 Protein R&D Systems Cat#355-BM Recombinant Human IFNу Protein R&D Systems Cat#258-IF Recombinant Human EGF Protein Peprotech Cat#AF-100-15-500UG Recombinant Human IGF Protein Peprotech Cat#100-11-500UG Recombinant Human HGF Protein Peprotech Cat#100-39H-25UG MEKi/PD0325901 Selleckchem Cat# S1036 AKTi/MK2206 Selleckchem Cat# S1078 Deposited data mcf10a maging, image analysis, sequencing data This paper https://doi.org/10.5281/zenodo.11455833 RNAseq data from combination ligand treatments Mclean et al.74 GEO: GSE282654 RNAseq and protein expression data Gross et al.65 https://synapse.org/LINCS_MCF10A Live-cell imaging from combination ligand treatments Mclean et al.74 https://doi.org/10.5281/zenodo.14261795 Experimental models: Cell lines Human: MCF10A line Gift from Gordon Mills (OHSU) N/A Human: HMT-3522 T4-2 line Gift from Mina Bissell (LBNL) N/A Recombinant DNA Plasmid: pLJM1-ERKTR-mVenus-puro Gillies et al.107 https://doi.org/10.1016/j.cels.2017.10.019 Software and algorithms DESeq2 v1.24.0 Soneson et al.108 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html Label-free fluorescence prediction: pytorch_fnet Ounkomol et al.77 https://github.com/AllenCellModeling/pytorch_fnet btrack v0.4.2 Ulicna et al.78 https://github.com/quantumjot/btrack pyemma v2.5.12 Scherer et al.76 https://github.com/markovmodel/PyEMMA GSEApy Fang et al.109 https://github.com/zqfang/GSEApy CellPose v2.0 Stringer et al.110 https://github.com/MouseLand/cellpose Celltraj Copperman et al.30 https://doi.org/10.5281/zenodo.17806558 MMIST This paper https://doi.org/10.5281/zenodo.18624747 ll OPEN ACCESS Article e1 Cell Systems 17, 101567, May 20, 2026 .. Companion RNAseq and live-cell imaging data used in this paper are described in full in Gross et al.65 In brief, MCF10A cells were cultured in growth media composed of DMEM/F12 (Invitrogen #11330-032), 5% horse serum (Sigma #H1138), 20 ng/ml EGF (R&D Systems #236-EG), 10 μg/ml insulin (Sigma #I9278), 100 ng/ml cholera toxin (Sigma #C8052), 0.5 μg/ml hydrocortisone (Sigma #H4001), and 1% Pen/Strep (Invitrogen #15070-063).
Software:Article Title: Single-cell morphodynamical trajectories enable prediction of gene expression accompanying cell state change.
Article Snippet: .. Cells were maintained in DMEM/ F12 supplemented with insulin, sodium selenite, hydrocortisone, β-estrogen, and transferrin, and maintained in 5% C02 at 37◦C.111 REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Recombinant Human EGF Protein, CF R&D Systems Cat#236-EG Recombinant Human Oncostatin M (HEK-293-expressed) Protein R&D Systems Cat#8475-OM Recombinant Human TGF-beta 1 Protein R&D Systems Cat240-B Recombinant Human HGF Protein R&D Systems Cat#294-HG Recombinant Human BMP2 Protein R&D Systems Cat#355-BM Recombinant Human IFNу Protein R&D Systems Cat#258-IF Recombinant Human EGF Protein Peprotech Cat#AF-100-15-500UG Recombinant Human IGF Protein Peprotech Cat#100-11-500UG Recombinant Human HGF Protein Peprotech Cat#100-39H-25UG MEKi/PD0325901 Selleckchem Cat# S1036 AKTi/MK2206 Selleckchem Cat# S1078 Deposited data mcf10a maging, image analysis, sequencing data This paper https://doi.org/10.5281/zenodo.11455833 RNAseq data from combination ligand treatments Mclean et al.74 GEO: GSE282654 RNAseq and protein expression data Gross et al.65 https://synapse.org/LINCS_MCF10A Live-cell imaging from combination ligand treatments Mclean et al.74 https://doi.org/10.5281/zenodo.14261795 Experimental models: Cell lines Human: MCF10A line Gift from Gordon Mills (OHSU) N/A Human: HMT-3522 T4-2 line Gift from Mina Bissell (LBNL) N/A Recombinant DNA Plasmid: pLJM1-ERKTR-mVenus-puro Gillies et al.107 https://doi.org/10.1016/j.cels.2017.10.019 Software and algorithms DESeq2 v1.24.0 Soneson et al.108 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html Label-free fluorescence prediction: pytorch_fnet Ounkomol et al.77 https://github.com/AllenCellModeling/pytorch_fnet btrack v0.4.2 Ulicna et al.78 https://github.com/quantumjot/btrack pyemma v2.5.12 Scherer et al.76 https://github.com/markovmodel/PyEMMA GSEApy Fang et al.109 https://github.com/zqfang/GSEApy CellPose v2.0 Stringer et al.110 https://github.com/MouseLand/cellpose Celltraj Copperman et al.30 https://doi.org/10.5281/zenodo.17806558 MMIST This paper https://doi.org/10.5281/zenodo.18624747 ll OPEN ACCESS Article e1 Cell Systems 17, 101567, May 20, 2026 .. Companion RNAseq and live-cell imaging data used in this paper are described in full in Gross et al.65 In brief, MCF10A cells were cultured in growth media composed of DMEM/F12 (Invitrogen #11330-032), 5% horse serum (Sigma #H1138), 20 ng/ml EGF (R&D Systems #236-EG), 10 μg/ml insulin (Sigma #I9278), 100 ng/ml cholera toxin (Sigma #C8052), 0.5 μg/ml hydrocortisone (Sigma #H4001), and 1% Pen/Strep (Invitrogen #15070-063).
Fluorescence:Article Title: Single-cell morphodynamical trajectories enable prediction of gene expression accompanying cell state change.
Article Snippet: .. Cells were maintained in DMEM/ F12 supplemented with insulin, sodium selenite, hydrocortisone, β-estrogen, and transferrin, and maintained in 5% C02 at 37◦C.111 REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Recombinant Human EGF Protein, CF R&D Systems Cat#236-EG Recombinant Human Oncostatin M (HEK-293-expressed) Protein R&D Systems Cat#8475-OM Recombinant Human TGF-beta 1 Protein R&D Systems Cat240-B Recombinant Human HGF Protein R&D Systems Cat#294-HG Recombinant Human BMP2 Protein R&D Systems Cat#355-BM Recombinant Human IFNу Protein R&D Systems Cat#258-IF Recombinant Human EGF Protein Peprotech Cat#AF-100-15-500UG Recombinant Human IGF Protein Peprotech Cat#100-11-500UG Recombinant Human HGF Protein Peprotech Cat#100-39H-25UG MEKi/PD0325901 Selleckchem Cat# S1036 AKTi/MK2206 Selleckchem Cat# S1078 Deposited data mcf10a maging, image analysis, sequencing data This paper https://doi.org/10.5281/zenodo.11455833 RNAseq data from combination ligand treatments Mclean et al.74 GEO: GSE282654 RNAseq and protein expression data Gross et al.65 https://synapse.org/LINCS_MCF10A Live-cell imaging from combination ligand treatments Mclean et al.74 https://doi.org/10.5281/zenodo.14261795 Experimental models: Cell lines Human: MCF10A line Gift from Gordon Mills (OHSU) N/A Human: HMT-3522 T4-2 line Gift from Mina Bissell (LBNL) N/A Recombinant DNA Plasmid: pLJM1-ERKTR-mVenus-puro Gillies et al.107 https://doi.org/10.1016/j.cels.2017.10.019 Software and algorithms DESeq2 v1.24.0 Soneson et al.108 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html Label-free fluorescence prediction: pytorch_fnet Ounkomol et al.77 https://github.com/AllenCellModeling/pytorch_fnet btrack v0.4.2 Ulicna et al.78 https://github.com/quantumjot/btrack pyemma v2.5.12 Scherer et al.76 https://github.com/markovmodel/PyEMMA GSEApy Fang et al.109 https://github.com/zqfang/GSEApy CellPose v2.0 Stringer et al.110 https://github.com/MouseLand/cellpose Celltraj Copperman et al.30 https://doi.org/10.5281/zenodo.17806558 MMIST This paper https://doi.org/10.5281/zenodo.18624747 ll OPEN ACCESS Article e1 Cell Systems 17, 101567, May 20, 2026 .. Companion RNAseq and live-cell imaging data used in this paper are described in full in Gross et al.65 In brief, MCF10A cells were cultured in growth media composed of DMEM/F12 (Invitrogen #11330-032), 5% horse serum (Sigma #H1138), 20 ng/ml EGF (R&D Systems #236-EG), 10 μg/ml insulin (Sigma #I9278), 100 ng/ml cholera toxin (Sigma #C8052), 0.5 μg/ml hydrocortisone (Sigma #H4001), and 1% Pen/Strep (Invitrogen #15070-063).
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