Characterization of cell-free breast cancer patient-derived scaffolds using liquid chromatography-mass spectrometry/mass spectrometry data and RNA sequencing data
Patient-derived scaffolds (PDSs) generated from primary breast cancer tumors can be used to model the tumor microenvironment in vitro. Patient-derived scaffolds are generated by repeated detergent washing, removing all cells. Here, we analyzed the protein composition of 15 decellularized PDSs using...
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| Format: | Article |
| Language: | English |
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Elsevier
2020-08-01
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| Series: | Data in Brief |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S235234092030754X |
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doaj-a296415c8e3d41e384ef36b83bd5436b |
|---|---|
| record_format |
Article |
| collection |
DOAJ |
| language |
English |
| format |
Article |
| sources |
DOAJ |
| author |
Göran Landberg Emma Jonasson Anna Gustafsson Paul Fitzpatrick Pauline Isakson Joakim Karlsson Erik Larsson Andreas Svanström Svanheidur Rafnsdottir Emma Persson Daniel Andersson Jennifer Rosendahl Sarunas Petronis Parmida Ranji Pernilla Gregersson Ylva Magnusson Joakim Håkansson Anders Ståhlberg |
| spellingShingle |
Göran Landberg Emma Jonasson Anna Gustafsson Paul Fitzpatrick Pauline Isakson Joakim Karlsson Erik Larsson Andreas Svanström Svanheidur Rafnsdottir Emma Persson Daniel Andersson Jennifer Rosendahl Sarunas Petronis Parmida Ranji Pernilla Gregersson Ylva Magnusson Joakim Håkansson Anders Ståhlberg Characterization of cell-free breast cancer patient-derived scaffolds using liquid chromatography-mass spectrometry/mass spectrometry data and RNA sequencing data Data in Brief Breast cancer Patient-derived scaffolds Extracellular matrix Liquid chromatography-mass spectrometry/mass spectrometry RNA sequencing 3d cell culture |
| author_facet |
Göran Landberg Emma Jonasson Anna Gustafsson Paul Fitzpatrick Pauline Isakson Joakim Karlsson Erik Larsson Andreas Svanström Svanheidur Rafnsdottir Emma Persson Daniel Andersson Jennifer Rosendahl Sarunas Petronis Parmida Ranji Pernilla Gregersson Ylva Magnusson Joakim Håkansson Anders Ståhlberg |
| author_sort |
Göran Landberg |
| title |
Characterization of cell-free breast cancer patient-derived scaffolds using liquid chromatography-mass spectrometry/mass spectrometry data and RNA sequencing data |
| title_short |
Characterization of cell-free breast cancer patient-derived scaffolds using liquid chromatography-mass spectrometry/mass spectrometry data and RNA sequencing data |
| title_full |
Characterization of cell-free breast cancer patient-derived scaffolds using liquid chromatography-mass spectrometry/mass spectrometry data and RNA sequencing data |
| title_fullStr |
Characterization of cell-free breast cancer patient-derived scaffolds using liquid chromatography-mass spectrometry/mass spectrometry data and RNA sequencing data |
| title_full_unstemmed |
Characterization of cell-free breast cancer patient-derived scaffolds using liquid chromatography-mass spectrometry/mass spectrometry data and RNA sequencing data |
| title_sort |
characterization of cell-free breast cancer patient-derived scaffolds using liquid chromatography-mass spectrometry/mass spectrometry data and rna sequencing data |
| publisher |
Elsevier |
| series |
Data in Brief |
| issn |
2352-3409 |
| publishDate |
2020-08-01 |
| description |
Patient-derived scaffolds (PDSs) generated from primary breast cancer tumors can be used to model the tumor microenvironment in vitro. Patient-derived scaffolds are generated by repeated detergent washing, removing all cells. Here, we analyzed the protein composition of 15 decellularized PDSs using liquid chromatography-mass spectrometry/mass spectrometry. One hundred forty-three proteins were detected and their relative abundance was calculated using a reference sample generated from all PDSs. We performed heatmap analysis of all the detected proteins to display their expression patterns across different PDSs together with pathway enrichment analysis to reveal which processes that were connected to PDS protein composition. This protein dataset together with clinical information is useful to investigators studying the microenvironment of breast cancers. Further, after repopulating PDSs with either MCF7 or MDA-MB-231 cells, we quantified their gene expression profiles using RNA sequencing. These data were also compared to cells cultured in conventional 2D conditions, as well as to cells cultured as xenografts in immune-deficient mice. We investigated the overlap of genes regulated between these different culture conditions and performed pathway enrichment analysis of genes regulated by both PDS and xenograft cultures compared to 2D in both cell lines to describe common processes associated with both culture conditions. Apart from our described analyses of these systems, these data are useful when comparing different experimental model systems. Downstream data analyses and interpretations can be found in the research article “Patient-derived scaffolds uncover breast cancer promoting properties of the microenvironment” [1]. |
| topic |
Breast cancer Patient-derived scaffolds Extracellular matrix Liquid chromatography-mass spectrometry/mass spectrometry RNA sequencing 3d cell culture |
| url |
http://www.sciencedirect.com/science/article/pii/S235234092030754X |
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1724624630782623744 |
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doaj-a296415c8e3d41e384ef36b83bd5436b2020-11-25T03:18:58ZengElsevierData in Brief2352-34092020-08-0131105860Characterization of cell-free breast cancer patient-derived scaffolds using liquid chromatography-mass spectrometry/mass spectrometry data and RNA sequencing dataGöran Landberg0Emma Jonasson1Anna Gustafsson2Paul Fitzpatrick3Pauline Isakson4Joakim Karlsson5Erik Larsson6Andreas Svanström7Svanheidur Rafnsdottir8Emma Persson9Daniel Andersson10Jennifer Rosendahl11Sarunas Petronis12Parmida Ranji13Pernilla Gregersson14Ylva Magnusson15Joakim Håkansson16Anders Ståhlberg17Department of Laboratory medicine, Institute of Biomedicine, Sahlgrenska Academy, Sahlgrenska Cancer Center, University of Gothenburg, SE-41390 Gothenburg, Sweden; Corresponding author.Department of Laboratory medicine, Institute of Biomedicine, Sahlgrenska Academy, Sahlgrenska Cancer Center, University of Gothenburg, SE-41390 Gothenburg, SwedenDepartment of Laboratory medicine, Institute of Biomedicine, Sahlgrenska Academy, Sahlgrenska Cancer Center, University of Gothenburg, SE-41390 Gothenburg, SwedenDepartment of Laboratory medicine, Institute of Biomedicine, Sahlgrenska Academy, Sahlgrenska Cancer Center, University of Gothenburg, SE-41390 Gothenburg, SwedenDepartment of Laboratory medicine, Institute of Biomedicine, Sahlgrenska Academy, Sahlgrenska Cancer Center, University of Gothenburg, SE-41390 Gothenburg, SwedenDepartment of Medical Biochemistry and Cell biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-41390 Gothenburg, SwedenDepartment of Medical Biochemistry and Cell biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-41390 Gothenburg, SwedenDepartment of Laboratory medicine, Institute of Biomedicine, Sahlgrenska Academy, Sahlgrenska Cancer Center, University of Gothenburg, SE-41390 Gothenburg, SwedenDepartment of Laboratory medicine, Institute of Biomedicine, Sahlgrenska Academy, Sahlgrenska Cancer Center, University of Gothenburg, SE-41390 Gothenburg, SwedenDepartment of Laboratory medicine, Institute of Biomedicine, Sahlgrenska Academy, Sahlgrenska Cancer Center, University of Gothenburg, SE-41390 Gothenburg, SwedenDepartment of Laboratory medicine, Institute of Biomedicine, Sahlgrenska Academy, Sahlgrenska Cancer Center, University of Gothenburg, SE-41390 Gothenburg, SwedenRISE, Research Institutes of Sweden, Bioscience and Materials – Medical Device Technology, SE- 50115 Borås, SwedenRISE, Research Institutes of Sweden, Bioscience and Materials – Medical Device Technology, SE- 50115 Borås, SwedenDepartment of Laboratory medicine, Institute of Biomedicine, Sahlgrenska Academy, Sahlgrenska Cancer Center, University of Gothenburg, SE-41390 Gothenburg, SwedenDepartment of Laboratory medicine, Institute of Biomedicine, Sahlgrenska Academy, Sahlgrenska Cancer Center, University of Gothenburg, SE-41390 Gothenburg, SwedenDepartment of Laboratory medicine, Institute of Biomedicine, Sahlgrenska Academy, Sahlgrenska Cancer Center, University of Gothenburg, SE-41390 Gothenburg, SwedenRISE, Research Institutes of Sweden, Bioscience and Materials – Medical Device Technology, SE- 50115 Borås, SwedenDepartment of Laboratory medicine, Institute of Biomedicine, Sahlgrenska Academy, Sahlgrenska Cancer Center, University of Gothenburg, SE-41390 Gothenburg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-41390 Gothenburg, Sweden; Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, SE-41390 Gothenburg, Sweden; Corresponding author at: Department of Laboratory medicine, Institute of Biomedicine, Sahlgrenska Academy, Sahlgrenska Cancer Center, University of Gothenburg, SE-41390 Gothenburg, SwedenPatient-derived scaffolds (PDSs) generated from primary breast cancer tumors can be used to model the tumor microenvironment in vitro. Patient-derived scaffolds are generated by repeated detergent washing, removing all cells. Here, we analyzed the protein composition of 15 decellularized PDSs using liquid chromatography-mass spectrometry/mass spectrometry. One hundred forty-three proteins were detected and their relative abundance was calculated using a reference sample generated from all PDSs. We performed heatmap analysis of all the detected proteins to display their expression patterns across different PDSs together with pathway enrichment analysis to reveal which processes that were connected to PDS protein composition. This protein dataset together with clinical information is useful to investigators studying the microenvironment of breast cancers. Further, after repopulating PDSs with either MCF7 or MDA-MB-231 cells, we quantified their gene expression profiles using RNA sequencing. These data were also compared to cells cultured in conventional 2D conditions, as well as to cells cultured as xenografts in immune-deficient mice. We investigated the overlap of genes regulated between these different culture conditions and performed pathway enrichment analysis of genes regulated by both PDS and xenograft cultures compared to 2D in both cell lines to describe common processes associated with both culture conditions. Apart from our described analyses of these systems, these data are useful when comparing different experimental model systems. Downstream data analyses and interpretations can be found in the research article “Patient-derived scaffolds uncover breast cancer promoting properties of the microenvironment” [1].http://www.sciencedirect.com/science/article/pii/S235234092030754XBreast cancerPatient-derived scaffoldsExtracellular matrixLiquid chromatography-mass spectrometry/mass spectrometryRNA sequencing3d cell culture |