diff --git a/CMSOdataset2018-3DsphrdInvCollHT1080-Bakker/isa/Appendix I 3D spheroid culture.pdf b/CMSOdataset2018-3DsphrdInvCollHT1080-Bakker/isa/Appendix I 3D spheroid culture.pdf new file mode 100644 index 0000000..b4ffea0 Binary files /dev/null and b/CMSOdataset2018-3DsphrdInvCollHT1080-Bakker/isa/Appendix I 3D spheroid culture.pdf differ diff --git a/CMSOdataset2018-3DsphrdInvCollHT1080-Bakker/isa/Appendix II Microscopy.pdf b/CMSOdataset2018-3DsphrdInvCollHT1080-Bakker/isa/Appendix II Microscopy.pdf new file mode 100644 index 0000000..f4940f2 Binary files /dev/null and b/CMSOdataset2018-3DsphrdInvCollHT1080-Bakker/isa/Appendix II Microscopy.pdf differ diff --git a/CMSOdataset2018-3DsphrdInvCollHT1080-Bakker/isa/Appendix III Image analysis (Extended).pdf b/CMSOdataset2018-3DsphrdInvCollHT1080-Bakker/isa/Appendix III Image analysis (Extended).pdf new file mode 100644 index 0000000..328d10a Binary files /dev/null and b/CMSOdataset2018-3DsphrdInvCollHT1080-Bakker/isa/Appendix III Image 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0000000..51e6214 --- /dev/null +++ b/CMSOdataset2018-3DsphrdInvCollHT1080-Bakker/isa/i_Investigation.txt @@ -0,0 +1,116 @@ +ONTOLOGY SOURCE REFERENCE +Term Source Name MESH UBERON CLO PLOSTHES +Term Source File http://data.bioontology.org/ontologies/MESH http://data.bioontology.org/ontologies/UBERON http://data.bioontology.org/ontologies/CLO http://data.bioontology.org/ontologies/PLOSTHES +Term Source Version 11 244 53 7 +Term Source Description Medical Subject Headings Uber Anatomy Ontology Cell Line Ontology PLOS Thesaurus +INVESTIGATION +Investigation Identifier 2018_3DsphInvasion +Investigation Title 2018_3DsphInvasion_HT1080_Collagen +Investigation Description 3D multicellular spheroid invasion assay and analysis, following the standardized Multimot protocol from workpackage 6, applied to the HT1080 fibrosarcoma cell line. The invasion phenotype was modulated by the collagen matrix density, by using two different concentrations of collagen solution. +Investigation Submission Date 21-9-2018 +Investigation Public Release Date 4-4-2019 +Comment[Investigation Conclusions] Data can be uploaded but not all fields can be changed. +Comment[Created with configuration] +Comment[Last Opened With Configuration] +Comment[ISA-Tab Files Version] +Comment[Created With Configuration] +INVESTIGATION PUBLICATIONS +Investigation PubMed ID +Investigation Publication DOI +Investigation Publication Author List +Investigation Publication Title +Investigation Publication Status +Investigation Publication Status Term Accession Number +Investigation Publication Status Term Source REF +INVESTIGATION CONTACTS +Investigation Person Last Name Bakker +Investigation Person First Name Gert-Jan +Investigation Person Mid Initials +Investigation Person Email gert-jan.bakker@radboudumc.nl +Investigation Person Phone +Investigation Person Fax +Investigation Person Address +Investigation Person Affiliation Radboudumc +Investigation Person Roles Work package 6 +Investigation Person Roles Term Accession Number +Investigation Person Roles Term Source REF +STUDY +Study Identifier 2018_3DsphInvasion_HT1080_Collagen +Study Title Standardized 3D culture and analysis of HT1080 fibrosarcoma spheroid invasion assay. +Study Description 3D multicellular spheroid invasion assay and analysis, following the standardized Multimot protocol from workpackage 6, applied to the HT1080 fibrosarcoma cell line. The invasion phenotype was modulated by the collagen matrix density, by using two different concentrations of collagen solution. The low concentration resulted in a more single cell invasion phenotype, while the high concentration induced a more collective invasion phenotype. +Study Submission Date 21-9-2018 +Study Public Release Date 4-4-2019 +Study File Name s_2018_3DsphInvasion_HT1080_Collagen.txt +Comment[Funding Organization Name] EU, Horizon 2020 +Comment[Funding Organization Identifier] http://dx.doi.org/10.13039/100010661,Horizon 2020 Framework Programme +Comment[Grant Identifier] MULTIMOT, PHC-32-2014 +Comment[Grant Name] Capture, dissemination and analysis of multiscale cell migration data for biological and clinical applications (MULTIMOT). +Comment[Basic Approach] "FBbi:single-spot confocal microscopy;RH-MESH:Microscopy, Confocal;RH-MESH:Cell Culture Techniques;CCONT:cell culture;BIOMODELS:spheroid;DCM:Segmentation" +Comment[Study Conclusions] For HT1080 fibrasarcoma, the low collagen matrix density resulted in a more single cell invasion phenotype, while the high concentration induced a more collective invasion phenotype. Thereby, the results are in line with previous observations [A. Haeger et al., Biochimica et Biophysica Acta 1840 (2014) 2386–2395] +Comment[MIACME Version] 0.3 +Comment[MIACME Compliance] yes +Comment[License for the whole dataset] BY +Comment[Number of subjects] 1 cell line +Comment[Number of biological replicates] 3 +Comment[Number of technical replicates] 3 up to 5 +Comment[Number of raw images] 30 multidimensional datafiles of 30 spheroids, including isotype control +Comment[License for raw images] BY +Comment[Number of processed images] 24 multidimensional datafiles of 24 spheroids +Comment[License for processed images] BY +Comment[Extracted Features] Nucleus coordinates, nucleus volume, nucleus surface, segment related intensity parameters derived from different channels and cellular segments, number of migrated single cells, number of migrated cells, cell migration distance, nearest neigbor distance, local cell density. +Comment[License for the extracted features] BY +Comment[Extracted features curation process] BY +STUDY DESIGN DESCRIPTORS +Study Design Type +Study Design Type Term Accession Number +Study Design Type Term Source REF +STUDY PUBLICATIONS +Study PubMed ID 24721714 +Study Publication DOI 10.1016/j.bbagen.2014.03.020 +Study Publication Author List Haeger A, Krause M, Wolf K, Friedl P. +Study Publication Title Cell jamming: collective invasion of mesenchymal tumor cells imposed by tissue confinement. +Study Publication Status Published +Study Publication Status Term Accession Number +Study Publication Status Term Source REF +STUDY FACTORS +Study Factor Name Rattail collagen type I concentration (mg/ml) +Study Factor Type physical +Study Factor Type Term Accession Number +Study Factor Type Term Source REF +STUDY ASSAYS +Study Assay File Name a_2018_3dsphinvasion_ht1080_collagen_spheroid_invasion_assay_microscopy_imaging-N2.txt a_2018_3dsphinvasion_ht1080_collagen_spheroid_invasion_assay_microscopy_imaging-N3.txt a_2018_3dsphinvasion_ht1080_collagen_spheroid_invasion_assay_microscopy_imaging-N4.txt +Study Assay Measurement Type spheroid invasion assay spheroid invasion assay spheroid invasion assay +Study Assay Measurement Type Term Accession Number +Study Assay Measurement Type Term Source REF +Study Assay Technology Type microscopy imaging microscopy imaging microscopy imaging +Study Assay Technology Type Term Accession Number +Study Assay Technology Type Term Source REF +Study Assay Technology Platform +STUDY PROTOCOLS +Study Protocol Name Appendix II Microscopy.pdf Appendix III Image analysis (Extended).pdf Appendix I 3D spheroid culture.pdf imaging data transformation +Study Protocol Type imaging data transformation wet lab imaging data transformation +Study Protocol Type Term Accession Number +Study Protocol Type Term Source REF +Study Protocol Description Laser scanning confocal imaging of 3D samples Segmentation, classification and feature extraction. 3D cell culture, fixation and immunolabeling +Study Protocol URI https://github.com/Mverp/Cell3DMeasurements +Study Protocol Version 1 1 1 +Study Protocol Parameters Name "imaging sequence type;pixel size;observation period;imaging modality;channel definition;time series interval;objective lens;numerical aperture" "segmentation;segmentation; SWO" "3D spheroid culture; Co-culture; hanging drop assay; rattail collagen I; pharmacological inhibitor; PFA fixation; immunofluorescent labeling; YAP mAb; DAPI, phalloidin." "imaging sequence type;pixel size;observation period;imaging modality;channel definition;time series interval;objective lens;numerical aperture" +Study Protocol Parameters Name Term Accession Number ";;;;;;;" ";;" ";;;;;;;;" ";;;;;;;" +Study Protocol Parameters Name Term Source REF ";;;;;;;" ";;" ";;;;;;;;" ";;;;;;;" +Study Protocol Components Name "Nucleus localization; nucleus segmentation; cell segmentation; classification of migration modes; feature extraction." "Preparation of Methylcellulose; Cell culture; Generation of 3D spheroids; Spheroid embedding in 3D collagen; Fixation and immunofluorescent staining; Adaptations of the standardized protocols to other cell lines and organoid culture. " +Study Protocol Components Type +Study Protocol Components Type Term Accession Number +Study Protocol Components Type Term Source REF +STUDY CONTACTS +Study Person Last Name Bakker Vullings Erp +Study Person First Name Gert-Jan Manon Merijn +Study Person Mid Initials van +Study Person Email gert-jan.bakker@radboudumc.nl manon.vullings@radboudumc.nl merijn.vanerp@radboudumc.nl +Study Person Phone +31(0)24 36 14296 +Study Person Fax +Study Person Address +Study Person Affiliation Radboud University Medical Center Radboud University Medical Center Radboud University Medical Center +Study Person Roles Coordination, reporting, data analysis excecution assay, imaging programming and development analysis pipeline +Study Person Roles Term Accession Number +Study Person Roles Term Source REF +Comment[Study Person Identifier] GJB MV MVE diff --git a/CMSOdataset2018-3DsphrdInvCollHT1080-Bakker/isa/s_2018_3DsphInvasion_HT1080_Collagen.txt b/CMSOdataset2018-3DsphrdInvCollHT1080-Bakker/isa/s_2018_3DsphInvasion_HT1080_Collagen.txt new file mode 100644 index 0000000..cc2d69f --- /dev/null +++ b/CMSOdataset2018-3DsphrdInvCollHT1080-Bakker/isa/s_2018_3DsphInvasion_HT1080_Collagen.txt @@ -0,0 +1,29 @@ +Source Name Sample Name Characteristics[cell model] Term Source REF Term Accession Number Characteristics[cell type] Term Source REF Term Accession Number Characteristics[organism] Term Source REF Term Accession Number Characteristics[specific cell description] Characteristics[cell provider] Characteristics[tissue] Term Source REF Term Accession Number Characteristics[cellular component] Term Source REF Term Accession Number Characteristics[life cycle stage] Characteristics[genotype] Protocol REF Parameter Value[(micro)environment] Characteristics[Cell culture type] Term Source REF Term Accession Number Characteristics[Cell culture dimension] Term Source REF Term Accession Number Parameter Value[cell culture vessel] Characteristics[Labeling type] Term Source REF Term Accession Number Characteristics[Immunofluorescent label 1] Term Source REF Term Accession Number Characteristics[Fluorescent reagent 1] Term Source REF Term Accession Number Characteristics[Fluorescent reagent 2] Term Source REF Term Accession Number Parameter Value[cell culture medium] Parameter Value[cell culture serum] Parameter Value[cell culture serum concentration] Unit Term Source REF Term Accession Number Parameter Value[cell culture antibiotics] Parameter Value[cell culture temperature] Unit Term Source REF Term Accession Number Parameter Value[cell culture CO2 partial pressure] Unit Term Source REF Term Accession Number Factor Value[Rattail collagen type I concentration (mg/ml)] Unit Term Source REF Term Accession Number +a_2018_3dsphinvasion_ht1080_collagen_spheroid_invasion_assay_microscopy_imaging-N2 B2_20x_medium_YAP_second image HT-1080 cell CLO http://purl.obolibrary.org/obo/CLO_0004276 fibrosarcoma CLO http://purl.obolibrary.org/obo/DOID_3355 human Human fibrosarcoma, cell line with a mesenchymal phenotype, established with 2D cell culture. ATCC fibroblast of dermis UBERON http://purl.obolibrary.org/obo/CL_0002551 YAP immortalized cell skin fibroblasts Appendix I 3D spheroid culture.pdf gel collagen spheroid 3D coated microplate Fluorescent Antibody Technique, Indirect MESH http://purl.bioontology.org/ontology/MESH/D019084 YAP mAb DAPI MESH http://purl.bioontology.org/ontology/MESH/C007293 Phalloidine MESH http://purl.bioontology.org/ontology/MESH/D010590 DMEM high glucose fetal calf serum 10 % vol Penicillin / streptavidin 37 Degrees Celcius 10 % 2.5 mg/ml +a_2018_3dsphinvasion_ht1080_collagen_spheroid_invasion_assay_microscopy_imaging-N2 B5_20x_medium_IgG_good settings HT-1080 cell CLO http://purl.obolibrary.org/obo/CLO_0004276 fibrosarcoma CLO http://purl.obolibrary.org/obo/DOID_3355 human Human fibrosarcoma, cell line with a mesenchymal phenotype, established with 2D cell culture. ATCC fibroblast of dermis UBERON http://purl.obolibrary.org/obo/CL_0002551 YAP immortalized cell skin fibroblasts Appendix I 3D spheroid culture.pdf gel collagen spheroid 3D coated microplate Fluorescent Antibody Technique, Indirect MESH http://purl.bioontology.org/ontology/MESH/D019084 IgG1 isotype control DAPI MESH http://purl.bioontology.org/ontology/MESH/C007293 Phalloidine MESH http://purl.bioontology.org/ontology/MESH/D010590 DMEM high glucose fetal calf serum 10 % vol Penicillin / streptavidin 37 Degrees Celcius 10 % 2.5 mg/ml +a_2018_3dsphinvasion_ht1080_collagen_spheroid_invasion_assay_microscopy_imaging-N2 C4_20x_medium_YAP HT-1080 cell CLO http://purl.obolibrary.org/obo/CLO_0004276 fibrosarcoma CLO http://purl.obolibrary.org/obo/DOID_3355 human Human fibrosarcoma, cell line with a mesenchymal phenotype, established with 2D cell culture. ATCC fibroblast of dermis UBERON http://purl.obolibrary.org/obo/CL_0002551 YAP immortalized cell skin fibroblasts Appendix I 3D spheroid culture.pdf gel collagen spheroid 3D coated microplate Fluorescent Antibody Technique, Indirect MESH http://purl.bioontology.org/ontology/MESH/D019084 YAP mAb DAPI MESH http://purl.bioontology.org/ontology/MESH/C007293 Phalloidine MESH http://purl.bioontology.org/ontology/MESH/D010590 DMEM high glucose fetal calf serum 10 % vol Penicillin / streptavidin 37 Degrees Celcius 10 % 2.5 mg/ml +a_2018_3dsphinvasion_ht1080_collagen_spheroid_invasion_assay_microscopy_imaging-N2 C7_20x_medium_YAP HT-1080 cell CLO http://purl.obolibrary.org/obo/CLO_0004276 fibrosarcoma CLO http://purl.obolibrary.org/obo/DOID_3355 human Human fibrosarcoma, cell line with a mesenchymal phenotype, established with 2D cell culture. ATCC fibroblast of dermis UBERON http://purl.obolibrary.org/obo/CL_0002551 YAP immortalized cell skin fibroblasts Appendix I 3D spheroid culture.pdf gel collagen spheroid 3D coated microplate Fluorescent Antibody Technique, Indirect MESH http://purl.bioontology.org/ontology/MESH/D019084 YAP mAb DAPI MESH http://purl.bioontology.org/ontology/MESH/C007293 Phalloidine MESH http://purl.bioontology.org/ontology/MESH/D010590 DMEM high glucose fetal calf serum 10 % vol Penicillin / streptavidin 37 Degrees Celcius 10 % 2.5 mg/ml +a_2018_3dsphinvasion_ht1080_collagen_spheroid_invasion_assay_microscopy_imaging-N2 E2_20x_medium_YAP HT-1080 cell CLO http://purl.obolibrary.org/obo/CLO_0004276 fibrosarcoma CLO http://purl.obolibrary.org/obo/DOID_3355 human Human fibrosarcoma, cell line with a mesenchymal phenotype, established with 2D cell culture. ATCC fibroblast of dermis UBERON http://purl.obolibrary.org/obo/CL_0002551 YAP immortalized cell skin fibroblasts Appendix I 3D spheroid culture.pdf gel collagen spheroid 3D coated microplate Fluorescent Antibody Technique, Indirect MESH http://purl.bioontology.org/ontology/MESH/D019084 YAP mAb DAPI MESH http://purl.bioontology.org/ontology/MESH/C007293 Phalloidine MESH http://purl.bioontology.org/ontology/MESH/D010590 DMEM high glucose fetal calf serum 10 % vol Penicillin / streptavidin 37 Degrees Celcius 10 % 6.0 mg/ml +a_2018_3dsphinvasion_ht1080_collagen_spheroid_invasion_assay_microscopy_imaging-N2 F7_20x_medium_YAP HT-1080 cell CLO http://purl.obolibrary.org/obo/CLO_0004276 fibrosarcoma CLO http://purl.obolibrary.org/obo/DOID_3355 human Human fibrosarcoma, cell line with a mesenchymal phenotype, established with 2D cell culture. ATCC fibroblast of dermis UBERON http://purl.obolibrary.org/obo/CL_0002551 YAP immortalized cell skin fibroblasts Appendix I 3D spheroid culture.pdf gel collagen spheroid 3D coated microplate Fluorescent Antibody Technique, Indirect MESH http://purl.bioontology.org/ontology/MESH/D019084 YAP mAb DAPI MESH http://purl.bioontology.org/ontology/MESH/C007293 Phalloidine MESH http://purl.bioontology.org/ontology/MESH/D010590 DMEM high glucose fetal calf serum 10 % vol Penicillin / streptavidin 37 Degrees Celcius 10 % 6.0 mg/ml +a_2018_3dsphinvasion_ht1080_collagen_spheroid_invasion_assay_microscopy_imaging-N2 G6_20x_medium_IgG HT-1080 cell CLO http://purl.obolibrary.org/obo/CLO_0004276 fibrosarcoma CLO http://purl.obolibrary.org/obo/DOID_3355 human Human fibrosarcoma, cell line with a mesenchymal phenotype, established with 2D cell culture. ATCC fibroblast of dermis UBERON http://purl.obolibrary.org/obo/CL_0002551 YAP immortalized cell skin fibroblasts Appendix I 3D spheroid culture.pdf gel collagen spheroid 3D coated microplate Fluorescent Antibody Technique, Indirect MESH http://purl.bioontology.org/ontology/MESH/D019084 IgG1 isotype control DAPI MESH http://purl.bioontology.org/ontology/MESH/C007293 Phalloidine MESH http://purl.bioontology.org/ontology/MESH/D010590 DMEM high glucose fetal calf serum 10 % vol Penicillin / streptavidin 37 Degrees Celcius 10 % 6.0 mg/ml +a_2018_3dsphinvasion_ht1080_collagen_spheroid_invasion_assay_microscopy_imaging-N2 G9_20x_medium_YAP HT-1080 cell CLO http://purl.obolibrary.org/obo/CLO_0004276 fibrosarcoma CLO http://purl.obolibrary.org/obo/DOID_3355 human Human fibrosarcoma, cell line with a mesenchymal phenotype, established with 2D cell culture. ATCC fibroblast of dermis UBERON http://purl.obolibrary.org/obo/CL_0002551 YAP immortalized cell skin fibroblasts Appendix I 3D spheroid culture.pdf gel collagen spheroid 3D coated microplate Fluorescent Antibody Technique, Indirect MESH http://purl.bioontology.org/ontology/MESH/D019084 YAP mAb DAPI MESH http://purl.bioontology.org/ontology/MESH/C007293 Phalloidine MESH http://purl.bioontology.org/ontology/MESH/D010590 DMEM high glucose fetal calf serum 10 % vol Penicillin / streptavidin 37 Degrees Celcius 10 % 6.0 mg/ml +a_2018_3dsphinvasion_ht1080_collagen_spheroid_invasion_assay_microscopy_imaging-N3 B2_medium_20x_goodsettings_YAP HT-1080 cell CLO http://purl.obolibrary.org/obo/CLO_0004276 fibrosarcoma CLO http://purl.obolibrary.org/obo/DOID_3355 human Human fibrosarcoma, cell line with a mesenchymal phenotype, established with 2D cell culture. ATCC fibroblast of dermis UBERON http://purl.obolibrary.org/obo/CL_0002551 YAP immortalized cell skin fibroblasts Appendix I 3D spheroid culture.pdf gel collagen spheroid 3D coated microplate Fluorescent Antibody Technique, Indirect MESH http://purl.bioontology.org/ontology/MESH/D019084 YAP mAb DAPI MESH http://purl.bioontology.org/ontology/MESH/C007293 Phalloidine MESH http://purl.bioontology.org/ontology/MESH/D010590 DMEM high glucose fetal calf serum 10 % vol Penicillin / streptavidin 37 Degrees Celcius 10 % 2.5 mg/ml +a_2018_3dsphinvasion_ht1080_collagen_spheroid_invasion_assay_microscopy_imaging-N3 B5_medium_20x_YAP HT-1080 cell CLO http://purl.obolibrary.org/obo/CLO_0004276 fibrosarcoma CLO http://purl.obolibrary.org/obo/DOID_3355 human Human fibrosarcoma, cell line with a mesenchymal phenotype, established with 2D cell culture. ATCC fibroblast of dermis UBERON http://purl.obolibrary.org/obo/CL_0002551 YAP immortalized cell skin fibroblasts Appendix I 3D spheroid culture.pdf gel collagen spheroid 3D coated microplate Fluorescent Antibody Technique, Indirect MESH http://purl.bioontology.org/ontology/MESH/D019084 YAP mAb DAPI MESH http://purl.bioontology.org/ontology/MESH/C007293 Phalloidine MESH http://purl.bioontology.org/ontology/MESH/D010590 DMEM high glucose fetal calf serum 10 % vol Penicillin / streptavidin 37 Degrees Celcius 10 % 2.5 mg/ml +a_2018_3dsphinvasion_ht1080_collagen_spheroid_invasion_assay_microscopy_imaging-N3 C5_medium_20x_IgG HT-1080 cell CLO http://purl.obolibrary.org/obo/CLO_0004276 fibrosarcoma CLO http://purl.obolibrary.org/obo/DOID_3355 human Human fibrosarcoma, cell line with a mesenchymal phenotype, established with 2D cell culture. ATCC fibroblast of dermis UBERON http://purl.obolibrary.org/obo/CL_0002551 YAP immortalized cell skin fibroblasts Appendix I 3D spheroid culture.pdf gel collagen spheroid 3D coated microplate Fluorescent Antibody Technique, Indirect MESH http://purl.bioontology.org/ontology/MESH/D019084 IgG1 isotype control DAPI MESH http://purl.bioontology.org/ontology/MESH/C007293 Phalloidine MESH http://purl.bioontology.org/ontology/MESH/D010590 DMEM high glucose fetal calf serum 10 % vol Penicillin / streptavidin 37 Degrees Celcius 10 % 2.5 mg/ml +a_2018_3dsphinvasion_ht1080_collagen_spheroid_invasion_assay_microscopy_imaging-N3 D5_medium_20x_YAP HT-1080 cell CLO http://purl.obolibrary.org/obo/CLO_0004276 fibrosarcoma CLO http://purl.obolibrary.org/obo/DOID_3355 human Human fibrosarcoma, cell line with a mesenchymal phenotype, established with 2D cell culture. ATCC fibroblast of dermis UBERON http://purl.obolibrary.org/obo/CL_0002551 YAP immortalized cell skin fibroblasts Appendix I 3D spheroid culture.pdf gel collagen spheroid 3D coated microplate Fluorescent Antibody Technique, Indirect MESH http://purl.bioontology.org/ontology/MESH/D019084 YAP mAb DAPI MESH http://purl.bioontology.org/ontology/MESH/C007293 Phalloidine MESH http://purl.bioontology.org/ontology/MESH/D010590 DMEM high glucose fetal calf serum 10 % vol Penicillin / streptavidin 37 Degrees Celcius 10 % 2.5 mg/ml +a_2018_3dsphinvasion_ht1080_collagen_spheroid_invasion_assay_microscopy_imaging-N3 E5_medium_20x_YAP HT-1080 cell CLO http://purl.obolibrary.org/obo/CLO_0004276 fibrosarcoma CLO http://purl.obolibrary.org/obo/DOID_3355 human Human fibrosarcoma, cell line with a mesenchymal phenotype, established with 2D cell culture. ATCC fibroblast of dermis UBERON http://purl.obolibrary.org/obo/CL_0002551 YAP immortalized cell skin fibroblasts Appendix I 3D spheroid culture.pdf gel collagen spheroid 3D coated microplate Fluorescent Antibody Technique, Indirect MESH http://purl.bioontology.org/ontology/MESH/D019084 YAP mAb DAPI MESH http://purl.bioontology.org/ontology/MESH/C007293 Phalloidine MESH http://purl.bioontology.org/ontology/MESH/D010590 DMEM high glucose fetal calf serum 10 % vol Penicillin / streptavidin 37 Degrees Celcius 10 % 6.0 mg/ml +a_2018_3dsphinvasion_ht1080_collagen_spheroid_invasion_assay_microscopy_imaging-N3 F2_medium_20x_YAP HT-1080 cell CLO http://purl.obolibrary.org/obo/CLO_0004276 fibrosarcoma CLO http://purl.obolibrary.org/obo/DOID_3355 human Human fibrosarcoma, cell line with a mesenchymal phenotype, established with 2D cell culture. ATCC fibroblast of dermis UBERON http://purl.obolibrary.org/obo/CL_0002551 YAP immortalized cell skin fibroblasts Appendix I 3D spheroid culture.pdf gel collagen spheroid 3D coated microplate Fluorescent Antibody Technique, Indirect MESH http://purl.bioontology.org/ontology/MESH/D019084 YAP mAb DAPI MESH http://purl.bioontology.org/ontology/MESH/C007293 Phalloidine MESH http://purl.bioontology.org/ontology/MESH/D010590 DMEM high glucose fetal calf serum 10 % vol Penicillin / streptavidin 37 Degrees Celcius 10 % 6.0 mg/ml +a_2018_3dsphinvasion_ht1080_collagen_spheroid_invasion_assay_microscopy_imaging-N3 F5_medium_20x_YAP HT-1080 cell CLO http://purl.obolibrary.org/obo/CLO_0004276 fibrosarcoma CLO http://purl.obolibrary.org/obo/DOID_3355 human Human fibrosarcoma, cell line with a mesenchymal phenotype, established with 2D cell culture. ATCC fibroblast of dermis UBERON http://purl.obolibrary.org/obo/CL_0002551 YAP immortalized cell skin fibroblasts Appendix I 3D spheroid culture.pdf gel collagen spheroid 3D coated microplate Fluorescent Antibody Technique, Indirect MESH http://purl.bioontology.org/ontology/MESH/D019084 YAP mAb DAPI MESH http://purl.bioontology.org/ontology/MESH/C007293 Phalloidine MESH http://purl.bioontology.org/ontology/MESH/D010590 DMEM high glucose fetal calf serum 10 % vol Penicillin / streptavidin 37 Degrees Celcius 10 % 6.0 mg/ml +a_2018_3dsphinvasion_ht1080_collagen_spheroid_invasion_assay_microscopy_imaging-N3 G2_medium_20x_YAP HT-1080 cell CLO http://purl.obolibrary.org/obo/CLO_0004276 fibrosarcoma CLO http://purl.obolibrary.org/obo/DOID_3355 human Human fibrosarcoma, cell line with a mesenchymal phenotype, established with 2D cell culture. ATCC fibroblast of dermis UBERON http://purl.obolibrary.org/obo/CL_0002551 YAP immortalized cell skin fibroblasts Appendix I 3D spheroid culture.pdf gel collagen spheroid 3D coated microplate Fluorescent Antibody Technique, Indirect MESH http://purl.bioontology.org/ontology/MESH/D019084 YAP mAb DAPI MESH http://purl.bioontology.org/ontology/MESH/C007293 Phalloidine MESH http://purl.bioontology.org/ontology/MESH/D010590 DMEM high glucose fetal calf serum 10 % vol Penicillin / streptavidin 37 Degrees Celcius 10 % 6.0 mg/ml +a_2018_3dsphinvasion_ht1080_collagen_spheroid_invasion_assay_microscopy_imaging-N3 G5_medium_20x_YAP HT-1080 cell CLO http://purl.obolibrary.org/obo/CLO_0004276 fibrosarcoma CLO http://purl.obolibrary.org/obo/DOID_3355 human Human fibrosarcoma, cell line with a mesenchymal phenotype, established with 2D cell culture. ATCC fibroblast of dermis UBERON http://purl.obolibrary.org/obo/CL_0002551 YAP immortalized cell skin fibroblasts Appendix I 3D spheroid culture.pdf gel collagen spheroid 3D coated microplate Fluorescent Antibody Technique, Indirect MESH http://purl.bioontology.org/ontology/MESH/D019084 YAP mAb DAPI MESH http://purl.bioontology.org/ontology/MESH/C007293 Phalloidine MESH http://purl.bioontology.org/ontology/MESH/D010590 DMEM high glucose fetal calf serum 10 % vol Penicillin / streptavidin 37 Degrees Celcius 10 % 6.0 mg/ml +a_2018_3dsphinvasion_ht1080_collagen_spheroid_invasion_assay_microscopy_imaging-N4 Medium_B2_20x_YAP HT-1080 cell CLO http://purl.obolibrary.org/obo/CLO_0004276 fibrosarcoma CLO http://purl.obolibrary.org/obo/DOID_3355 human Human fibrosarcoma, cell line with a mesenchymal phenotype, established with 2D cell culture. ATCC fibroblast of dermis UBERON http://purl.obolibrary.org/obo/CL_0002551 YAP immortalized cell skin fibroblasts Appendix I 3D spheroid culture.pdf gel collagen spheroid 3D coated microplate Fluorescent Antibody Technique, Indirect MESH http://purl.bioontology.org/ontology/MESH/D019084 YAP mAb DAPI MESH http://purl.bioontology.org/ontology/MESH/C007293 Phalloidine MESH http://purl.bioontology.org/ontology/MESH/D010590 DMEM high glucose fetal calf serum 10 % vol Penicillin / streptavidin 37 Degrees Celcius 10 % 2.5 mg/ml +a_2018_3dsphinvasion_ht1080_collagen_spheroid_invasion_assay_microscopy_imaging-N4 Medium_B5_20x_YAP HT-1080 cell CLO http://purl.obolibrary.org/obo/CLO_0004276 fibrosarcoma CLO http://purl.obolibrary.org/obo/DOID_3355 human Human fibrosarcoma, cell line with a mesenchymal phenotype, established with 2D cell culture. ATCC fibroblast of dermis UBERON http://purl.obolibrary.org/obo/CL_0002551 YAP immortalized cell skin fibroblasts Appendix I 3D spheroid culture.pdf gel collagen spheroid 3D coated microplate Fluorescent Antibody Technique, Indirect MESH http://purl.bioontology.org/ontology/MESH/D019084 YAP mAb DAPI MESH http://purl.bioontology.org/ontology/MESH/C007293 Phalloidine MESH http://purl.bioontology.org/ontology/MESH/D010590 DMEM high glucose fetal calf serum 10 % vol Penicillin / streptavidin 37 Degrees Celcius 10 % 2.5 mg/ml +a_2018_3dsphinvasion_ht1080_collagen_spheroid_invasion_assay_microscopy_imaging-N4 Medium_C2_20x_YAP HT-1080 cell CLO http://purl.obolibrary.org/obo/CLO_0004276 fibrosarcoma CLO http://purl.obolibrary.org/obo/DOID_3355 human Human fibrosarcoma, cell line with a mesenchymal phenotype, established with 2D cell culture. ATCC fibroblast of dermis UBERON http://purl.obolibrary.org/obo/CL_0002551 YAP immortalized cell skin fibroblasts Appendix I 3D spheroid culture.pdf gel collagen spheroid 3D coated microplate Fluorescent Antibody Technique, Indirect MESH http://purl.bioontology.org/ontology/MESH/D019084 YAP mAb DAPI MESH http://purl.bioontology.org/ontology/MESH/C007293 Phalloidine MESH http://purl.bioontology.org/ontology/MESH/D010590 DMEM high glucose fetal calf serum 10 % vol Penicillin / streptavidin 37 Degrees Celcius 10 % 2.5 mg/ml +a_2018_3dsphinvasion_ht1080_collagen_spheroid_invasion_assay_microscopy_imaging-N4 Medium_C5_20x_YAP HT-1080 cell CLO http://purl.obolibrary.org/obo/CLO_0004276 fibrosarcoma CLO http://purl.obolibrary.org/obo/DOID_3355 human Human fibrosarcoma, cell line with a mesenchymal phenotype, established with 2D cell culture. ATCC fibroblast of dermis UBERON http://purl.obolibrary.org/obo/CL_0002551 YAP immortalized cell skin fibroblasts Appendix I 3D spheroid culture.pdf gel collagen spheroid 3D coated microplate Fluorescent Antibody Technique, Indirect MESH http://purl.bioontology.org/ontology/MESH/D019084 YAP mAb DAPI MESH http://purl.bioontology.org/ontology/MESH/C007293 Phalloidine MESH http://purl.bioontology.org/ontology/MESH/D010590 DMEM high glucose fetal calf serum 10 % vol Penicillin / streptavidin 37 Degrees Celcius 10 % 2.5 mg/ml +a_2018_3dsphinvasion_ht1080_collagen_spheroid_invasion_assay_microscopy_imaging-N4 Medium_D2_20x_YAP HT-1080 cell CLO http://purl.obolibrary.org/obo/CLO_0004276 fibrosarcoma CLO http://purl.obolibrary.org/obo/DOID_3355 human Human fibrosarcoma, cell line with a mesenchymal phenotype, established with 2D cell culture. ATCC fibroblast of dermis UBERON http://purl.obolibrary.org/obo/CL_0002551 YAP immortalized cell skin fibroblasts Appendix I 3D spheroid culture.pdf gel collagen spheroid 3D coated microplate Fluorescent Antibody Technique, Indirect MESH http://purl.bioontology.org/ontology/MESH/D019084 YAP mAb DAPI MESH http://purl.bioontology.org/ontology/MESH/C007293 Phalloidine MESH http://purl.bioontology.org/ontology/MESH/D010590 DMEM high glucose fetal calf serum 10 % vol Penicillin / streptavidin 37 Degrees Celcius 10 % 2.5 mg/ml +a_2018_3dsphinvasion_ht1080_collagen_spheroid_invasion_assay_microscopy_imaging-N4 Medium_D5_20x_IgG HT-1080 cell CLO http://purl.obolibrary.org/obo/CLO_0004276 fibrosarcoma CLO http://purl.obolibrary.org/obo/DOID_3355 human Human fibrosarcoma, cell line with a mesenchymal phenotype, established with 2D cell culture. ATCC fibroblast of dermis UBERON http://purl.obolibrary.org/obo/CL_0002551 YAP immortalized cell skin fibroblasts Appendix I 3D spheroid culture.pdf gel collagen spheroid 3D coated microplate Fluorescent Antibody Technique, Indirect MESH http://purl.bioontology.org/ontology/MESH/D019084 IgG1 isotype control DAPI MESH http://purl.bioontology.org/ontology/MESH/C007293 Phalloidine MESH http://purl.bioontology.org/ontology/MESH/D010590 DMEM high glucose fetal calf serum 10 % vol Penicillin / streptavidin 37 Degrees Celcius 10 % 2.5 mg/ml +a_2018_3dsphinvasion_ht1080_collagen_spheroid_invasion_assay_microscopy_imaging-N4 Medium_E2_20x_YAP 10 HT-1080 cell CLO http://purl.obolibrary.org/obo/CLO_0004276 fibrosarcoma CLO http://purl.obolibrary.org/obo/DOID_3355 human Human fibrosarcoma, cell line with a mesenchymal phenotype, established with 2D cell culture. ATCC fibroblast of dermis UBERON http://purl.obolibrary.org/obo/CL_0002551 YAP immortalized cell skin fibroblasts Appendix I 3D spheroid culture.pdf gel collagen spheroid 3D coated microplate Fluorescent Antibody Technique, Indirect MESH http://purl.bioontology.org/ontology/MESH/D019084 YAP mAb DAPI MESH http://purl.bioontology.org/ontology/MESH/C007293 Phalloidine MESH http://purl.bioontology.org/ontology/MESH/D010590 DMEM high glucose fetal calf serum 10 % vol Penicillin / streptavidin 37 Degrees Celcius 10 % 6.0 mg/ml +a_2018_3dsphinvasion_ht1080_collagen_spheroid_invasion_assay_microscopy_imaging-N4 Medium_E5_20x_YAP 10 HT-1080 cell CLO http://purl.obolibrary.org/obo/CLO_0004276 fibrosarcoma CLO http://purl.obolibrary.org/obo/DOID_3355 human Human fibrosarcoma, cell line with a mesenchymal phenotype, established with 2D cell culture. ATCC fibroblast of dermis UBERON http://purl.obolibrary.org/obo/CL_0002551 YAP immortalized cell skin fibroblasts Appendix I 3D spheroid culture.pdf gel collagen spheroid 3D coated microplate Fluorescent Antibody Technique, Indirect MESH http://purl.bioontology.org/ontology/MESH/D019084 YAP mAb DAPI MESH http://purl.bioontology.org/ontology/MESH/C007293 Phalloidine MESH http://purl.bioontology.org/ontology/MESH/D010590 DMEM high glucose fetal calf serum 10 % vol Penicillin / streptavidin 37 Degrees Celcius 10 % 6.0 mg/ml +a_2018_3dsphinvasion_ht1080_collagen_spheroid_invasion_assay_microscopy_imaging-N4 Medium_F2_20x_YAP 10 HT-1080 cell CLO http://purl.obolibrary.org/obo/CLO_0004276 fibrosarcoma CLO http://purl.obolibrary.org/obo/DOID_3355 human Human fibrosarcoma, cell line with a mesenchymal phenotype, established with 2D cell culture. ATCC fibroblast of dermis UBERON http://purl.obolibrary.org/obo/CL_0002551 YAP immortalized cell skin fibroblasts Appendix I 3D spheroid culture.pdf gel collagen spheroid 3D coated microplate Fluorescent Antibody Technique, Indirect MESH http://purl.bioontology.org/ontology/MESH/D019084 YAP mAb DAPI MESH http://purl.bioontology.org/ontology/MESH/C007293 Phalloidine MESH http://purl.bioontology.org/ontology/MESH/D010590 DMEM high glucose fetal calf serum 10 % vol Penicillin / streptavidin 37 Degrees Celcius 10 % 6.0 mg/ml +a_2018_3dsphinvasion_ht1080_collagen_spheroid_invasion_assay_microscopy_imaging-N4 Medium_G2_20x_YAP 10 HT-1080 cell CLO http://purl.obolibrary.org/obo/CLO_0004276 fibrosarcoma CLO http://purl.obolibrary.org/obo/DOID_3355 human Human fibrosarcoma, cell line with a mesenchymal phenotype, established with 2D cell culture. ATCC fibroblast of dermis UBERON http://purl.obolibrary.org/obo/CL_0002551 YAP immortalized cell skin fibroblasts Appendix I 3D spheroid culture.pdf gel collagen spheroid 3D coated microplate Fluorescent Antibody Technique, Indirect MESH http://purl.bioontology.org/ontology/MESH/D019084 YAP mAb DAPI MESH http://purl.bioontology.org/ontology/MESH/C007293 Phalloidine MESH http://purl.bioontology.org/ontology/MESH/D010590 DMEM high glucose fetal calf serum 10 % vol Penicillin / streptavidin 37 Degrees Celcius 10 % 6.0 mg/ml +a_2018_3dsphinvasion_ht1080_collagen_spheroid_invasion_assay_microscopy_imaging-N4 Medium_G5_20x_YAP 10 HT-1080 cell CLO http://purl.obolibrary.org/obo/CLO_0004276 fibrosarcoma CLO http://purl.obolibrary.org/obo/DOID_3355 human Human fibrosarcoma, cell line with a mesenchymal phenotype, established with 2D cell culture. ATCC fibroblast of dermis UBERON http://purl.obolibrary.org/obo/CL_0002551 YAP immortalized cell skin fibroblasts Appendix I 3D spheroid culture.pdf gel collagen spheroid 3D coated microplate Fluorescent Antibody Technique, Indirect MESH http://purl.bioontology.org/ontology/MESH/D019084 YAP mAb DAPI MESH http://purl.bioontology.org/ontology/MESH/C007293 Phalloidine MESH http://purl.bioontology.org/ontology/MESH/D010590 DMEM high glucose fetal calf serum 10 % vol Penicillin / streptavidin 37 Degrees Celcius 10 % 6.0 mg/ml