Software:Article Title: Coordinated protein modules define DNA damage responses to carboplatin at single-cell resolution in human ovarian carcinoma models.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data CyTOF datasets This manuscript Zenodo: 15328365 Experimental models: Cell lines HeLa ATCC CCL-2 .. TYK-nu JCRB Cell Bank JCRB0098 UWB1.289 ATCC CRL-2945 UWB1.289+BRCA1 ATCC CRL-2946 JHOS2 RIKEN BRC Cell Bank RBRC-RCB1521 CIOV1, CIOV 2, and CIOV3 Brenton Lab, University of Cambridge, UK N/A Software and algorithms R and Python scripts This manuscript Zenodo: 15807914 CellEngine analysis software CellCarta https://cellengine.com/#/ R environment R-project https://www.r-project.org/ Premessa R package N/A https://github.com/ParkerICI/premessa tidyverse R package https://joss.theoj.org/ papers/10.21105/joss.01686 https://cran.r-project.org/web/packages/ tidyverse/index.html MASS R package N/A https://cran.r-project.org/web/ packages/MASS/index.html igraph R package N/A https://cran.r-project.org/web/packages/ igraph/index.html ComplexHeatmap R package Gu et al.80 https://www.bioconductor.org/packages/ release/bioc/html/ComplexHeatmap.html MATLAB – Normalizer Finck et al.81 https://github.com/nolanlab/bead-normalization/ MATLAB – Single Cell Debarcoder Zunder et al.82 https://github.com/nolanlab/single-cell-debarcoder Prism GraphPad Software https://www.graphpad.com/ Microsoft excel Microsoft https://www.microsoft.com/en-us/microsoft-365/excel BioRender BioRender https://www.biorender.com/ AmiGO 2 Gene Ontology analysis AmiGO 2 https://amigo.geneontology.org/amigo/landing Python environment Python https://www.python.org/ Scanpy Python package Wolf et al.83 https://scanpy.readthedocs.io/en/stable/ Scikit-learn Python package N/A https://github.com/scikit-learn/scikit-learn Monocle 3 single-cell analysis pipeline Cao et al.84 https://cole-trapnell-lab.github.io/monocle3/ Partition-based graph abstraction (PAGA) Wolf et al.63 https://github.com/theislab/paga Non-negative matrix factorization (NMF) Kotliar et al.64 N/A Other CyTOF2 mass cytometer Standard BioTools N/A 5 mL Falcon round-bottom polystyrene tubes with cell strainer cap Thermo Fisher Ca#08-771-23 BD LSRII Flow cytometer BD Biosciences N/A Keyence BZ-X800 microscope Keyence N/A Cell Reports Medicine 6, 102295, September 16, 2025 e2 Article ll OPEN ACCESS .. HeLa and OVCAR3 (American Type Culture Collection (ATCC)) and TYK-nu (National Institute of Biomedical Innovation, Japanese Collection of Research Bioresources Cell Bank (JCRB)) cell lines were cultured in Dulbecco’s Modified Eagle Medium (DMEM) (Gibco), McCoy’s 5A modified medium (Gibco) and Eagle’s minimal essential medium (EMEM) (ATCC) respectively supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Hyclone), 1% Penicillin-Streptomycin (Gibco) and 2 mM L-glutamine (Gibco).
Single Cell:Article Title: Coordinated protein modules define DNA damage responses to carboplatin at single-cell resolution in human ovarian carcinoma models.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data CyTOF datasets This manuscript Zenodo: 15328365 Experimental models: Cell lines HeLa ATCC CCL-2 .. TYK-nu JCRB Cell Bank JCRB0098 UWB1.289 ATCC CRL-2945 UWB1.289+BRCA1 ATCC CRL-2946 JHOS2 RIKEN BRC Cell Bank RBRC-RCB1521 CIOV1, CIOV 2, and CIOV3 Brenton Lab, University of Cambridge, UK N/A Software and algorithms R and Python scripts This manuscript Zenodo: 15807914 CellEngine analysis software CellCarta https://cellengine.com/#/ R environment R-project https://www.r-project.org/ Premessa R package N/A https://github.com/ParkerICI/premessa tidyverse R package https://joss.theoj.org/ papers/10.21105/joss.01686 https://cran.r-project.org/web/packages/ tidyverse/index.html MASS R package N/A https://cran.r-project.org/web/ packages/MASS/index.html igraph R package N/A https://cran.r-project.org/web/packages/ igraph/index.html ComplexHeatmap R package Gu et al.80 https://www.bioconductor.org/packages/ release/bioc/html/ComplexHeatmap.html MATLAB – Normalizer Finck et al.81 https://github.com/nolanlab/bead-normalization/ MATLAB – Single Cell Debarcoder Zunder et al.82 https://github.com/nolanlab/single-cell-debarcoder Prism GraphPad Software https://www.graphpad.com/ Microsoft excel Microsoft https://www.microsoft.com/en-us/microsoft-365/excel BioRender BioRender https://www.biorender.com/ AmiGO 2 Gene Ontology analysis AmiGO 2 https://amigo.geneontology.org/amigo/landing Python environment Python https://www.python.org/ Scanpy Python package Wolf et al.83 https://scanpy.readthedocs.io/en/stable/ Scikit-learn Python package N/A https://github.com/scikit-learn/scikit-learn Monocle 3 single-cell analysis pipeline Cao et al.84 https://cole-trapnell-lab.github.io/monocle3/ Partition-based graph abstraction (PAGA) Wolf et al.63 https://github.com/theislab/paga Non-negative matrix factorization (NMF) Kotliar et al.64 N/A Other CyTOF2 mass cytometer Standard BioTools N/A 5 mL Falcon round-bottom polystyrene tubes with cell strainer cap Thermo Fisher Ca#08-771-23 BD LSRII Flow cytometer BD Biosciences N/A Keyence BZ-X800 microscope Keyence N/A Cell Reports Medicine 6, 102295, September 16, 2025 e2 Article ll OPEN ACCESS .. HeLa and OVCAR3 (American Type Culture Collection (ATCC)) and TYK-nu (National Institute of Biomedical Innovation, Japanese Collection of Research Bioresources Cell Bank (JCRB)) cell lines were cultured in Dulbecco’s Modified Eagle Medium (DMEM) (Gibco), McCoy’s 5A modified medium (Gibco) and Eagle’s minimal essential medium (EMEM) (ATCC) respectively supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Hyclone), 1% Penicillin-Streptomycin (Gibco) and 2 mM L-glutamine (Gibco).
Cytometry:Article Title: Coordinated protein modules define DNA damage responses to carboplatin at single-cell resolution in human ovarian carcinoma models.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data CyTOF datasets This manuscript Zenodo: 15328365 Experimental models: Cell lines HeLa ATCC CCL-2 .. TYK-nu JCRB Cell Bank JCRB0098 UWB1.289 ATCC CRL-2945 UWB1.289+BRCA1 ATCC CRL-2946 JHOS2 RIKEN BRC Cell Bank RBRC-RCB1521 CIOV1, CIOV 2, and CIOV3 Brenton Lab, University of Cambridge, UK N/A Software and algorithms R and Python scripts This manuscript Zenodo: 15807914 CellEngine analysis software CellCarta https://cellengine.com/#/ R environment R-project https://www.r-project.org/ Premessa R package N/A https://github.com/ParkerICI/premessa tidyverse R package https://joss.theoj.org/ papers/10.21105/joss.01686 https://cran.r-project.org/web/packages/ tidyverse/index.html MASS R package N/A https://cran.r-project.org/web/ packages/MASS/index.html igraph R package N/A https://cran.r-project.org/web/packages/ igraph/index.html ComplexHeatmap R package Gu et al.80 https://www.bioconductor.org/packages/ release/bioc/html/ComplexHeatmap.html MATLAB – Normalizer Finck et al.81 https://github.com/nolanlab/bead-normalization/ MATLAB – Single Cell Debarcoder Zunder et al.82 https://github.com/nolanlab/single-cell-debarcoder Prism GraphPad Software https://www.graphpad.com/ Microsoft excel Microsoft https://www.microsoft.com/en-us/microsoft-365/excel BioRender BioRender https://www.biorender.com/ AmiGO 2 Gene Ontology analysis AmiGO 2 https://amigo.geneontology.org/amigo/landing Python environment Python https://www.python.org/ Scanpy Python package Wolf et al.83 https://scanpy.readthedocs.io/en/stable/ Scikit-learn Python package N/A https://github.com/scikit-learn/scikit-learn Monocle 3 single-cell analysis pipeline Cao et al.84 https://cole-trapnell-lab.github.io/monocle3/ Partition-based graph abstraction (PAGA) Wolf et al.63 https://github.com/theislab/paga Non-negative matrix factorization (NMF) Kotliar et al.64 N/A Other CyTOF2 mass cytometer Standard BioTools N/A 5 mL Falcon round-bottom polystyrene tubes with cell strainer cap Thermo Fisher Ca#08-771-23 BD LSRII Flow cytometer BD Biosciences N/A Keyence BZ-X800 microscope Keyence N/A Cell Reports Medicine 6, 102295, September 16, 2025 e2 Article ll OPEN ACCESS .. HeLa and OVCAR3 (American Type Culture Collection (ATCC)) and TYK-nu (National Institute of Biomedical Innovation, Japanese Collection of Research Bioresources Cell Bank (JCRB)) cell lines were cultured in Dulbecco’s Modified Eagle Medium (DMEM) (Gibco), McCoy’s 5A modified medium (Gibco) and Eagle’s minimal essential medium (EMEM) (ATCC) respectively supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Hyclone), 1% Penicillin-Streptomycin (Gibco) and 2 mM L-glutamine (Gibco).
Flow Cytometry:Article Title: Coordinated protein modules define DNA damage responses to carboplatin at single-cell resolution in human ovarian carcinoma models.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data CyTOF datasets This manuscript Zenodo: 15328365 Experimental models: Cell lines HeLa ATCC CCL-2 .. TYK-nu JCRB Cell Bank JCRB0098 UWB1.289 ATCC CRL-2945 UWB1.289+BRCA1 ATCC CRL-2946 JHOS2 RIKEN BRC Cell Bank RBRC-RCB1521 CIOV1, CIOV 2, and CIOV3 Brenton Lab, University of Cambridge, UK N/A Software and algorithms R and Python scripts This manuscript Zenodo: 15807914 CellEngine analysis software CellCarta https://cellengine.com/#/ R environment R-project https://www.r-project.org/ Premessa R package N/A https://github.com/ParkerICI/premessa tidyverse R package https://joss.theoj.org/ papers/10.21105/joss.01686 https://cran.r-project.org/web/packages/ tidyverse/index.html MASS R package N/A https://cran.r-project.org/web/ packages/MASS/index.html igraph R package N/A https://cran.r-project.org/web/packages/ igraph/index.html ComplexHeatmap R package Gu et al.80 https://www.bioconductor.org/packages/ release/bioc/html/ComplexHeatmap.html MATLAB – Normalizer Finck et al.81 https://github.com/nolanlab/bead-normalization/ MATLAB – Single Cell Debarcoder Zunder et al.82 https://github.com/nolanlab/single-cell-debarcoder Prism GraphPad Software https://www.graphpad.com/ Microsoft excel Microsoft https://www.microsoft.com/en-us/microsoft-365/excel BioRender BioRender https://www.biorender.com/ AmiGO 2 Gene Ontology analysis AmiGO 2 https://amigo.geneontology.org/amigo/landing Python environment Python https://www.python.org/ Scanpy Python package Wolf et al.83 https://scanpy.readthedocs.io/en/stable/ Scikit-learn Python package N/A https://github.com/scikit-learn/scikit-learn Monocle 3 single-cell analysis pipeline Cao et al.84 https://cole-trapnell-lab.github.io/monocle3/ Partition-based graph abstraction (PAGA) Wolf et al.63 https://github.com/theislab/paga Non-negative matrix factorization (NMF) Kotliar et al.64 N/A Other CyTOF2 mass cytometer Standard BioTools N/A 5 mL Falcon round-bottom polystyrene tubes with cell strainer cap Thermo Fisher Ca#08-771-23 BD LSRII Flow cytometer BD Biosciences N/A Keyence BZ-X800 microscope Keyence N/A Cell Reports Medicine 6, 102295, September 16, 2025 e2 Article ll OPEN ACCESS .. HeLa and OVCAR3 (American Type Culture Collection (ATCC)) and TYK-nu (National Institute of Biomedical Innovation, Japanese Collection of Research Bioresources Cell Bank (JCRB)) cell lines were cultured in Dulbecco’s Modified Eagle Medium (DMEM) (Gibco), McCoy’s 5A modified medium (Gibco) and Eagle’s minimal essential medium (EMEM) (ATCC) respectively supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Hyclone), 1% Penicillin-Streptomycin (Gibco) and 2 mM L-glutamine (Gibco).
Microscopy:Article Title: Coordinated protein modules define DNA damage responses to carboplatin at single-cell resolution in human ovarian carcinoma models.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data CyTOF datasets This manuscript Zenodo: 15328365 Experimental models: Cell lines HeLa ATCC CCL-2 .. TYK-nu JCRB Cell Bank JCRB0098 UWB1.289 ATCC CRL-2945 UWB1.289+BRCA1 ATCC CRL-2946 JHOS2 RIKEN BRC Cell Bank RBRC-RCB1521 CIOV1, CIOV 2, and CIOV3 Brenton Lab, University of Cambridge, UK N/A Software and algorithms R and Python scripts This manuscript Zenodo: 15807914 CellEngine analysis software CellCarta https://cellengine.com/#/ R environment R-project https://www.r-project.org/ Premessa R package N/A https://github.com/ParkerICI/premessa tidyverse R package https://joss.theoj.org/ papers/10.21105/joss.01686 https://cran.r-project.org/web/packages/ tidyverse/index.html MASS R package N/A https://cran.r-project.org/web/ packages/MASS/index.html igraph R package N/A https://cran.r-project.org/web/packages/ igraph/index.html ComplexHeatmap R package Gu et al.80 https://www.bioconductor.org/packages/ release/bioc/html/ComplexHeatmap.html MATLAB – Normalizer Finck et al.81 https://github.com/nolanlab/bead-normalization/ MATLAB – Single Cell Debarcoder Zunder et al.82 https://github.com/nolanlab/single-cell-debarcoder Prism GraphPad Software https://www.graphpad.com/ Microsoft excel Microsoft https://www.microsoft.com/en-us/microsoft-365/excel BioRender BioRender https://www.biorender.com/ AmiGO 2 Gene Ontology analysis AmiGO 2 https://amigo.geneontology.org/amigo/landing Python environment Python https://www.python.org/ Scanpy Python package Wolf et al.83 https://scanpy.readthedocs.io/en/stable/ Scikit-learn Python package N/A https://github.com/scikit-learn/scikit-learn Monocle 3 single-cell analysis pipeline Cao et al.84 https://cole-trapnell-lab.github.io/monocle3/ Partition-based graph abstraction (PAGA) Wolf et al.63 https://github.com/theislab/paga Non-negative matrix factorization (NMF) Kotliar et al.64 N/A Other CyTOF2 mass cytometer Standard BioTools N/A 5 mL Falcon round-bottom polystyrene tubes with cell strainer cap Thermo Fisher Ca#08-771-23 BD LSRII Flow cytometer BD Biosciences N/A Keyence BZ-X800 microscope Keyence N/A Cell Reports Medicine 6, 102295, September 16, 2025 e2 Article ll OPEN ACCESS .. HeLa and OVCAR3 (American Type Culture Collection (ATCC)) and TYK-nu (National Institute of Biomedical Innovation, Japanese Collection of Research Bioresources Cell Bank (JCRB)) cell lines were cultured in Dulbecco’s Modified Eagle Medium (DMEM) (Gibco), McCoy’s 5A modified medium (Gibco) and Eagle’s minimal essential medium (EMEM) (ATCC) respectively supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Hyclone), 1% Penicillin-Streptomycin (Gibco) and 2 mM L-glutamine (Gibco).
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