From 9bd4a446da91917a50693180f734c4a3f99536bf Mon Sep 17 00:00:00 2001 From: Jente Houweling <“jente.houweling@rivm.nl”> Date: Mon, 29 Sep 2025 11:58:56 +0200 Subject: [PATCH] - Created JSON files for Deiodinase, Metabolism, Receptor Activation, and TH Transport assays with detailed assay information including organism, chemicals, experimental design, and endpoints. - Added corresponding TSV files for each assay, including submission details, study information, authors, and experimental design parameters. --- .../Template__Deiodinase_assay_.json | 222 ++++++++++ .../Template__Metabolism_Assay_.json | 189 ++++++++ .../Template__Receptor_activation_.json | 117 +++++ .../Template__TH_Transport_Assay_.json | 405 ++++++++++++++++++ .../tsv/Template__Deiodinase_assay_.tsv | 74 ++++ .../tsv/Template__Metabolism_Assay_.tsv | 67 +++ .../tsv/Template__Receptor_activation_.tsv | 62 +++ .../tsv/Template__TH_Transport_Assay_.tsv | 75 ++++ 8 files changed, 1211 insertions(+) create mode 100644 biostudies/enriched /Template__Deiodinase_assay_.json create mode 100644 biostudies/enriched /Template__Metabolism_Assay_.json create mode 100644 biostudies/enriched /Template__Receptor_activation_.json create mode 100644 biostudies/enriched /Template__TH_Transport_Assay_.json create mode 100644 biostudies/enriched /tsv/Template__Deiodinase_assay_.tsv create mode 100644 biostudies/enriched /tsv/Template__Metabolism_Assay_.tsv create mode 100644 biostudies/enriched /tsv/Template__Receptor_activation_.tsv create mode 100644 biostudies/enriched /tsv/Template__TH_Transport_Assay_.tsv diff --git a/biostudies/enriched /Template__Deiodinase_assay_.json b/biostudies/enriched /Template__Deiodinase_assay_.json new file mode 100644 index 0000000..40aacf4 --- /dev/null +++ b/biostudies/enriched /Template__Deiodinase_assay_.json @@ -0,0 +1,222 @@ +{ + "assays": [ + { + "title": "Assay", + "description": null, + "organism": { + "name": "Homo sapiens" + }, + "organ": "brain", + "tissue": "neural tissue", + "bioassay": { + "name": "Deiodination" + }, + "files": [], + "cell_lines": [ + { + "name": "SK-N-AS", + "rrid": "CVCL_1700", + "supplier": "ATCC" + }, + { + "name": "MO3.13", + "rrid": "CVCL_D357", + "supplier": "Cedarlane Laboratories" + } + ], + "chemicals": [ + { + "name": "Amiodarone", + "cas": "19774-82-4", + "smiles": "CCCCC1=C(C2=CC=CC=C2O1)C(=O)C3=CC(=C(C(=C3)I)OCCN(CC)CC)I.Cl", + "concentrations": [ + { + "value": 10, + "unit": "µM", + "ucum": "umol/L" + } + ] + }, + { + "name": "BSP (sulfobromophthalein sodium)", + "cas": "123359-42-2", + "smiles": "[Na+].[Na+].[H]O[H].Oc1ccc(cc1S([O-])(=O)=O)C2(OC(=O)c3c(Br)c(Br)c(Br)c(Br)c23)c4ccc(O)c(c4)S([O-])(=O)=O", + "concentrations": [ + { + "value": 300, + "unit": "µm", + "ucum": "umol/L" + } + ] + }, + { + "name": "Cefuroxime", + "cas": "55268-75-2", + "smiles": "O=C(O)COC1=CC(C)=C(CC2=CC(C#CC3=CC=C([N+]([O-])=O)C=C3)=C(O)C(C(C)C)=C2)C(C)=C1", + "concentrations": [ + { + "value": 100, + "unit": "µM", + "ucum": "umol/L" + } + ] + }, + { + "name": "Chlorpyrifos", + "cas": "2921-88-2", + "smiles": "CCOP(=S)(OCC)Oc1nc(Cl)c(Cl)cc1Cl", + "concentrations": [ + { + "value": 20, + "unit": "µM", + "ucum": "umol/L" + } + ] + }, + { + "name": "Iopanoic acid", + "cas": "96-83-3", + "smiles": "O=C(O)C(CC)CC1=C(I)C(N)=C(I)C=C1I", + "concentrations": [ + { + "value": 100, + "unit": "µM", + "ucum": "umol/L" + } + ] + }, + { + "name": "Mono-buthyl phtalate (MBP)", + "cas": "131-70-4", + "smiles": "CCCCOC(=O)c1ccccc1C(O)=O", + "concentrations": [ + { + "value": 100, + "unit": "µm", + "ucum": "umol/L" + } + ] + }, + { + "name": "NH-3", + "cas": "447415-26-1", + "smiles": "O=C(O)COC1=CC(C)=C(CC2=CC(C#CC3=CC=C([N+]([O-])=O)C=C3)=C(O)C(C(C)C)=C2)C(C)=C1", + "concentrations": [ + { + "value": 1000, + "unit": "nM", + "ucum": "nmol/L" + } + ] + }, + { + "name": "PBDE-99", + "cas": "60348-60-9", + "smiles": "C1=CC(=C(C=C1Br)Br)OC2=CC(=C(C=C2Br)Br)Br", + "concentrations": [ + { + "value": 1000, + "unit": "nM", + "ucum": "nmol/L" + } + ] + }, + { + "name": "Silychristin", + "cas": "33889-69-9", + "smiles": "COc1cc(ccc1O)[C@@H]2Oc3c(O)cc(cc3[C@H]2CO)[C@H]4Oc5cc(O)cc(O)c5C(=O)[C@@H]4O", + "concentrations": [ + { + "value": 10, + "unit": "µM", + "ucum": "umol/L" + } + ] + }, + { + "name": "TBBPA", + "cas": "79-94-7", + "smiles": "CC(C)(c1cc(Br)c(O)c(Br)c1)c2cc(Br)c(O)c(Br)c2", + "concentrations": [ + { + "value": 10, + "unit": "µM", + "ucum": "umol/L" + } + ] + }, + { + "name": "Lesinurad", + "cas": "878672-00-5", + "smiles": "BrC1=NN=C(SCC(O)=O)N1C2=C3C(C=CC=C3)=C(C4CC4)C=C2", + "concentrations": [ + { + "value": 100, + "unit": "µM", + "ucum": "umol/L" + } + ] + }, + { + "name": "Xanthohumol ", + "cas": "6754-58-1", + "smiles": "COc1cc(O)c(C\\C=C(/C)C)c(O)c1C(=O)\\C=C\\c2ccc(O)cc2", + "concentrations": [ + { + "value": 3, + "unit": "µM", + "ucum": "umol/L" + } + ] + } + ], + "experimental_design": { + "timepoints": [ + { + "value": 2, + "unit": "hours", + "ucum": "h" + } + ], + "replicates": 2, + "number_of_samples": null, + "instruments": [ + { + "name": "Waters Acquitytm Premier UPLC + RAMONA star (Elisia Raytest)", + "manufacturer": null + } + ], + "measured_entity": { + "name": "AUC (Area under curve)", + "unit": "AUC (Area under curve)" + }, + "endpoints": [ + { + "name": "T3 conversion to T2 and T1", + "unit": "fmol/min/mg protein", + "ucum": null + }, + { + "name": "fmol/min/mg protein", + "unit": "fmol/min/mg protein", + "ucum": null + } + ], + "substrates": [ + "1 nM T3" + ] + }, + "mie": [ + { + "target": "D3" + }, + { + "target": "None" + } + ] + } + ], + "registries": { + "organizations": {} + } +} \ No newline at end of file diff --git a/biostudies/enriched /Template__Metabolism_Assay_.json b/biostudies/enriched /Template__Metabolism_Assay_.json new file mode 100644 index 0000000..f1c7239 --- /dev/null +++ b/biostudies/enriched /Template__Metabolism_Assay_.json @@ -0,0 +1,189 @@ +{ + "assays": [ + { + "title": "Assay", + "description": null, + "organism": { + "name": "Homo sapiens" + }, + "organ": "brain", + "tissue": "neural tissue", + "files": [], + "cell_lines": [ + { + "name": "SK-N-AS", + "rrid": "CVCL_1700", + "supplier": "ATCC" + }, + { + "name": "MO3.13", + "rrid": "CVCL_D357", + "supplier": "Cedarlane Laboratories" + } + ], + "chemicals": [ + { + "name": "BSP (sulfobromophthalein sodium)", + "cas": "123359-42-2", + "smiles": "[Na+].[Na+].[H]O[H].Oc1ccc(cc1S([O-])(=O)=O)C2(OC(=O)c3c(Br)c(Br)c(Br)c(Br)c23)c4ccc(O)c(c4)S([O-])(=O)=O", + "concentrations": [ + { + "value": 300, + "unit": "µm", + "ucum": "umol/L" + } + ] + }, + { + "name": "Chlorpyrifos", + "cas": "2921-88-2", + "smiles": "CCOP(=S)(OCC)Oc1nc(Cl)c(Cl)cc1Cl", + "concentrations": [ + { + "value": 0.1, + "unit": "µM", + "ucum": "umol/L" + }, + { + "value": 1, + "unit": "µM", + "ucum": "umol/L" + }, + { + "value": 10, + "unit": "µM", + "ucum": "umol/L" + }, + { + "value": 20, + "unit": "µM", + "ucum": "umol/L" + } + ] + }, + { + "name": "Iopanoic acid", + "cas": "96-83-3", + "smiles": "O=C(O)C(CC)CC1=C(I)C(N)=C(I)C=C1I", + "concentrations": [ + { + "value": 3, + "unit": "µM", + "ucum": "umol/L" + }, + { + "value": 10, + "unit": "µM", + "ucum": "umol/L" + }, + { + "value": 30, + "unit": "µM", + "ucum": "umol/L" + }, + { + "value": 100, + "unit": "µM", + "ucum": "umol/L" + } + ] + }, + { + "name": "Silychristin", + "cas": "33889-69-9", + "smiles": "COc1cc(ccc1O)[C@@H]2Oc3c(O)cc(cc3[C@H]2CO)[C@H]4Oc5cc(O)cc(O)c5C(=O)[C@@H]4O", + "concentrations": [ + { + "value": 10, + "unit": "µM", + "ucum": "umol/L" + } + ] + }, + { + "name": "TBBPA", + "cas": "79-94-7", + "smiles": "CC(C)(c1cc(Br)c(O)c(Br)c1)c2cc(Br)c(O)c(Br)c2", + "concentrations": [ + { + "value": 10, + "unit": "µM", + "ucum": "umol/L" + } + ] + }, + { + "name": "Xanthohumol ", + "cas": "6754-58-1", + "smiles": "COc1cc(O)c(C\\C=C(/C)C)c(O)c1C(=O)\\C=C\\c2ccc(O)cc2", + "concentrations": [ + { + "value": 0.1, + "unit": "µM", + "ucum": "umol/L" + }, + { + "value": 0.3, + "unit": "µM", + "ucum": "umol/L" + }, + { + "value": 1, + "unit": "µM", + "ucum": "umol/L" + }, + { + "value": 3, + "unit": "µM", + "ucum": "umol/L" + } + ] + } + ], + "experimental_design": { + "timepoints": [ + { + "value": 24, + "unit": "hours", + "ucum": "h" + } + ], + "replicates": 2, + "number_of_samples": null, + "instruments": [ + { + "name": "Waters Acquitytm Premier UPLC + RAMONA star (Elisia Raytest)", + "manufacturer": null + } + ], + "measured_entity": { + "name": "AUC (Area under curve)", + "unit": "AUC (Area under curve)" + }, + "endpoints": [ + { + "name": "Conversion of T3 into metabolites T2 and T1", + "unit": "%", + "ucum": "%" + }, + { + "name": "%", + "unit": "%", + "ucum": "%" + } + ], + "substrates": [ + "1 nM T3" + ] + }, + "mie": [ + { + "target": "D3" + } + ] + } + ], + "registries": { + "organizations": {} + } +} \ No newline at end of file diff --git a/biostudies/enriched /Template__Receptor_activation_.json b/biostudies/enriched /Template__Receptor_activation_.json new file mode 100644 index 0000000..4ca1a78 --- /dev/null +++ b/biostudies/enriched /Template__Receptor_activation_.json @@ -0,0 +1,117 @@ +{ + "assays": [ + { + "title": "Assay", + "description": null, + "organism": { + "name": "Homo sapiens" + }, + "organ": "brain", + "tissue": "neural tissue", + "bioassay": { + "name": "Genetic transcription" + }, + "files": [], + "cell_lines": [ + { + "name": "SK-N-AS", + "rrid": "CVCL_1700", + "supplier": "ATCC" + } + ], + "chemicals": [ + { + "name": "NH-3", + "cas": "447415-26-1", + "smiles": "O=C(O)COC1=CC(C)=C(CC2=CC(C#CC3=CC=C([N+]([O-])=O)C=C3)=C(O)C(C(C)C)=C2)C(C)=C1", + "concentrations": [ + { + "value": 1000, + "unit": "nM", + "ucum": "nmol/L" + } + ] + }, + { + "name": "Silychristin", + "cas": "33889-69-9", + "smiles": "COc1cc(ccc1O)[C@@H]2Oc3c(O)cc(cc3[C@H]2CO)[C@H]4Oc5cc(O)cc(O)c5C(=O)[C@@H]4O", + "concentrations": [ + { + "value": 10, + "unit": "µM", + "ucum": "umol/L" + } + ] + }, + { + "name": "TBBPA", + "cas": "79-94-7", + "smiles": "CC(C)(c1cc(Br)c(O)c(Br)c1)c2cc(Br)c(O)c(Br)c2", + "concentrations": [ + { + "value": 10, + "unit": "µM", + "ucum": "umol/L" + } + ] + } + ], + "experimental_design": { + "timepoints": [ + { + "value": 6, + "unit": "hours", + "ucum": "h" + } + ], + "replicates": 3, + "number_of_samples": null, + "instruments": [ + { + "name": "QuantStudio 7 Flex ", + "manufacturer": null + } + ], + "measured_entity": { + "name": "∆∆CT", + "unit": "∆∆CT" + }, + "endpoints": [ + { + "name": "KLF9 expression", + "unit": "Fold change", + "ucum": null + }, + { + "name": "Fold change", + "unit": "Fold change", + "ucum": null + }, + { + "name": null, + "unit": null, + "ucum": null + }, + { + "name": null, + "unit": null, + "ucum": null + } + ], + "substrates": [ + null, + null + ] + }, + "mie": [ + { + "target": "TRa" + } + ] + } + ], + "registries": { + "organizations": {} + } +} \ No newline at end of file diff --git a/biostudies/enriched /Template__TH_Transport_Assay_.json b/biostudies/enriched /Template__TH_Transport_Assay_.json new file mode 100644 index 0000000..5057d46 --- /dev/null +++ b/biostudies/enriched /Template__TH_Transport_Assay_.json @@ -0,0 +1,405 @@ +{ + "assays": [ + { + "title": "Assay", + "description": null, + "organism": { + "name": "Homo sapiens" + }, + "organ": "brain", + "tissue": "neural tissue", + "bioassay": { + "name": "transporter inhibition assay" + }, + "files": [], + "cell_lines": [ + { + "name": "SK-N-AS", + "rrid": "CVCL_1700", + "supplier": "ATCC" + }, + { + "name": "H4", + "rrid": "CVCL_1239", + "supplier": "ATCC" + }, + { + "name": "MO3.13", + "rrid": "CVCL_D357", + "supplier": "Cedarlane Laboratories" + } + ], + "chemicals": [ + { + "name": "Amiodarone", + "cas": "19774-82-4", + "smiles": "CCCCC1=C(C2=CC=CC=C2O1)C(=O)C3=CC(=C(C(=C3)I)OCCN(CC)CC)I.Cl", + "concentrations": [ + { + "value": 0.5, + "unit": "µM", + "ucum": "umol/L" + }, + { + "value": 1, + "unit": "µM", + "ucum": "umol/L" + }, + { + "value": 5, + "unit": "µM", + "ucum": "umol/L" + }, + { + "value": 10, + "unit": "µM", + "ucum": "umol/L" + } + ] + }, + { + "name": "BSP (sulfobromophthalein sodium)", + "cas": "123359-42-2", + "smiles": "[Na+].[Na+].[H]O[H].Oc1ccc(cc1S([O-])(=O)=O)C2(OC(=O)c3c(Br)c(Br)c(Br)c(Br)c23)c4ccc(O)c(c4)S([O-])(=O)=O", + "concentrations": [ + { + "value": 10, + "unit": "µm", + "ucum": "umol/L" + }, + { + "value": 30, + "unit": "µm", + "ucum": "umol/L" + }, + { + "value": 100, + "unit": "µm", + "ucum": "umol/L" + }, + { + "value": 300, + "unit": "µm", + "ucum": "umol/L" + } + ] + }, + { + "name": "Cefuroxime", + "cas": "55268-75-2", + "smiles": "O=C(O)COC1=CC(C)=C(CC2=CC(C#CC3=CC=C([N+]([O-])=O)C=C3)=C(O)C(C(C)C)=C2)C(C)=C1", + "concentrations": [ + { + "value": 0.1, + "unit": "µM", + "ucum": "umol/L" + }, + { + "value": 1, + "unit": "µM", + "ucum": "umol/L" + }, + { + "value": 10, + "unit": "µM", + "ucum": "umol/L" + }, + { + "value": 100, + "unit": "µM", + "ucum": "umol/L" + } + ] + }, + { + "name": "Chlorpyrifos", + "cas": "2921-88-2", + "smiles": "CCOP(=S)(OCC)Oc1nc(Cl)c(Cl)cc1Cl", + "concentrations": [ + { + "value": 0.1, + "unit": "µM", + "ucum": "umol/L" + }, + { + "value": 1, + "unit": "µM", + "ucum": "umol/L" + }, + { + "value": 10, + "unit": "µM", + "ucum": "umol/L" + }, + { + "value": 20, + "unit": "µM", + "ucum": "umol/L" + } + ] + }, + { + "name": "Iopanoic acid", + "cas": "96-83-3", + "smiles": "O=C(O)C(CC)CC1=C(I)C(N)=C(I)C=C1I", + "concentrations": [ + { + "value": 3, + "unit": "µM", + "ucum": "umol/L" + }, + { + "value": 10, + "unit": "µM", + "ucum": "umol/L" + }, + { + "value": 30, + "unit": "µM", + "ucum": "umol/L" + }, + { + "value": 100, + "unit": "µM", + "ucum": "umol/L" + } + ] + }, + { + "name": "Mono-buthyl phtalate (MBP)", + "cas": "131-70-4", + "smiles": "CCCCOC(=O)c1ccccc1C(O)=O", + "concentrations": [ + { + "value": 0.1, + "unit": "µm", + "ucum": "umol/L" + }, + { + "value": 1, + "unit": "µm", + "ucum": "umol/L" + }, + { + "value": 10, + "unit": "µm", + "ucum": "umol/L" + }, + { + "value": 100, + "unit": "µm", + "ucum": "umol/L" + } + ] + }, + { + "name": "NH-3", + "cas": "447415-26-1", + "smiles": "O=C(O)COC1=CC(C)=C(CC2=CC(C#CC3=CC=C([N+]([O-])=O)C=C3)=C(O)C(C(C)C)=C2)C(C)=C1", + "concentrations": [ + { + "value": 1, + "unit": "nM", + "ucum": "nmol/L" + }, + { + "value": 10, + "unit": "nM", + "ucum": "nmol/L" + }, + { + "value": 100, + "unit": "nM", + "ucum": "nmol/L" + }, + { + "value": 1000, + "unit": "nM", + "ucum": "nmol/L" + } + ] + }, + { + "name": "PBDE-99", + "cas": "60348-60-9", + "smiles": "C1=CC(=C(C=C1Br)Br)OC2=CC(=C(C=C2Br)Br)Br", + "concentrations": [ + { + "value": 30, + "unit": "nM", + "ucum": "nmol/L" + }, + { + "value": 100, + "unit": "nM", + "ucum": "nmol/L" + }, + { + "value": 300, + "unit": "nM", + "ucum": "nmol/L" + }, + { + "value": 1000, + "unit": "nM", + "ucum": "nmol/L" + } + ] + }, + { + "name": "Silychristin", + "cas": "33889-69-9", + "smiles": "COc1cc(ccc1O)[C@@H]2Oc3c(O)cc(cc3[C@H]2CO)[C@H]4Oc5cc(O)cc(O)c5C(=O)[C@@H]4O", + "concentrations": [ + { + "value": 10, + "unit": "µM", + "ucum": "umol/L" + } + ] + }, + { + "name": "TBBPA", + "cas": "79-94-7", + "smiles": "CC(C)(c1cc(Br)c(O)c(Br)c1)c2cc(Br)c(O)c(Br)c2", + "concentrations": [ + { + "value": 0.3, + "unit": "µM", + "ucum": "umol/L" + }, + { + "value": 1, + "unit": "µM", + "ucum": "umol/L" + }, + { + "value": 3, + "unit": "µM", + "ucum": "umol/L" + }, + { + "value": 10, + "unit": "µM", + "ucum": "umol/L" + } + ] + }, + { + "name": "Lesinurad", + "cas": "878672-00-5", + "smiles": "BrC1=NN=C(SCC(O)=O)N1C2=C3C(C=CC=C3)=C(C4CC4)C=C2", + "concentrations": [ + { + "value": 100, + "unit": "µM", + "ucum": "umol/L" + } + ] + }, + { + "name": "Xanthohumol ", + "cas": "6754-58-1", + "smiles": "COc1cc(O)c(C\\C=C(/C)C)c(O)c1C(=O)\\C=C\\c2ccc(O)cc2", + "concentrations": [ + { + "value": 0.1, + "unit": "µM", + "ucum": "umol/L" + }, + { + "value": 0.3, + "unit": "µM", + "ucum": "umol/L" + }, + { + "value": 1, + "unit": "µM", + "ucum": "umol/L" + }, + { + "value": 3, + "unit": "µM", + "ucum": "umol/L" + } + ] + } + ], + "experimental_design": { + "timepoints": [ + { + "value": 10, + "unit": "minutes", + "ucum": "min" + } + ], + "replicates": 2, + "number_of_samples": null, + "instruments": [ + { + "name": "Gamma Counter", + "manufacturer": null + } + ], + "measured_entity": { + "name": "counts per minute", + "unit": "counts per minute", + "ucum": "cpm" + }, + "endpoints": [ + { + "name": "T3 uptake", + "unit": "%", + "ucum": "%" + }, + { + "name": "%", + "unit": "%", + "ucum": "%" + }, + { + "name": "T4 uptake", + "unit": "%", + "ucum": "%" + }, + { + "name": "%", + "unit": "%", + "ucum": "%" + } + ], + "substrates": [ + "T3", + "T4" + ] + }, + "mie": [ + { + "target": "MCT8" + }, + { + "target": "AOP wiki ID: 2258", + "aop_refs": [ + "AOP:2258" + ] + }, + { + "target": "OATP1C1" + }, + { + "target": "Other Transporters" + } + ], + "aop_links": [ + { + "id": "AOP:2258", + "source": "AOP-Wiki", + "url": "https://aopwiki.org/aops/2258" + } + ] + } + ], + "registries": { + "organizations": {} + } +} \ No newline at end of file diff --git a/biostudies/enriched /tsv/Template__Deiodinase_assay_.tsv b/biostudies/enriched /tsv/Template__Deiodinase_assay_.tsv new file mode 100644 index 0000000..d57c6d8 --- /dev/null +++ b/biostudies/enriched /tsv/Template__Deiodinase_assay_.tsv @@ -0,0 +1,74 @@ +Submission S-VHPS13 +Title Deiodinase Activity Assessment for Thyroid-Mediated Neurotoxicity Screening +ReleaseDate 2026-06-01 +AttachTo VHP4Safety + +Study +Title Deiodinase Activity Assessment for Thyroid-Mediated Neurotoxicity Screening +ReleaseDate 2026-06-01 +Description +Organism Homo sapiens (human) +License CC BY 4.0 +[URL] https://creativecommons.org/licenses/by/4.0/legalcode +Bioassay Deiodination +[Ontology] BAO +Organ Brain +Tissue Neural tissue +Adverse outcome Pathway [Placeholder] +[URL] https://aopwiki.org/aops/ +AOP event D3 +[URL] https://aopwiki.org/events/ + +Link https://docs.vhp4safety.nl/en/latest/ +Description Documentation page VHP4Safety + +Link https://platform.vhp4safety.nl/ +Description VHP4Safety platform + +Link https://www.ebi.ac.uk/biostudies/vhp4safety/studies/S-VHPS5 +Description Associated study + +author +Name Nathalie Dierichs +E-mail nathalie.dierichs@rivm.nl +Email nathalie.dierichs@rivm.nl +Role Data producer + o1 +ORCID 0009-0000-5074-6239 + +author +Name Jente Houweling +E-mail jente.houweling@rivm.nl +ORCID 0009-0005-3680-0645 +Email jente.houweling@rivm.nl +Role Data steward + o1 + +organisation o1 +Name Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands + +Funding +Agency NWA +grant_id 1292.19.272 + +Cell lines[] Cell line RRID Supplier + SK-N-AS CVCL_1700 ATCC + MO3.13 CVCL_D357 Cedarlane Laboratories + +Chemicals[] Chemical CAS CompoundWikiID + Amiodarone 19774-82-4 Q17 + BSP (sulfobromophthalein sodium) 123359-42-2 + Cefuroxime 55268-75-2 Q4751 + Chlorpyrifos 2921-88-2 Q4722 + Iopanoic acid 96-83-3 Q1879 + Mono-buthyl phtalate (MBP) 131-70-4 + NH-3 447415-26-1 Q1882 + PBDE-99 60348-60-9 Q4757 + Silychristin 33889-69-9 Q5049 + TBBPA 79-94-7 Q82 + Lesinurad 878672-00-5 Q1880 + Xanthohumol 6754-58-1 Q4753 + +Experimental design[] Time point Time point_unit Replicates Detection instrument Instrument manufacturer Measured entity Measured entity_unit Substrate Endpoint Endpoint_unit + 2 hours 2 Waters Acquitytm Premier UPLC + RAMONA star (Elisia Raytest) AUC (Area under curve) AUC (Area under curve) 1 nM T3 T3 conversion to T2 and T1 fmol/min/mg protein + diff --git a/biostudies/enriched /tsv/Template__Metabolism_Assay_.tsv b/biostudies/enriched /tsv/Template__Metabolism_Assay_.tsv new file mode 100644 index 0000000..88cade5 --- /dev/null +++ b/biostudies/enriched /tsv/Template__Metabolism_Assay_.tsv @@ -0,0 +1,67 @@ +Submission S-VHPS14 +Title Whole-cell Metabolism Assay: Measurement of thyroid hormone biotransformation in neuronal cell culture +ReleaseDate 2026-06-01 +AttachTo VHP4Safety + +Study +Title Whole-cell Metabolism Assay: Measurement of thyroid hormone biotransformation in neuronal cell culture +ReleaseDate 2026-06-01 +Description +Organism Homo sapiens (human) +License CC BY 4.0 +[URL] https://creativecommons.org/licenses/by/4.0/legalcode +Bioassay +Organ Brain +Tissue Neural tissue +Adverse outcome Pathway placeholder +[URL] https://aopwiki.org/aops/ +AOP event D3 +[URL] https://aopwiki.org/events/ + +Link https://docs.vhp4safety.nl/en/latest/ +Description Documentation page VHP4Safety + +Link https://platform.vhp4safety.nl/ +Description VHP4Safety platform + +Link https://www.ebi.ac.uk/biostudies/vhp4safety/studies/S-VHPS5 +Description Associated study + +author +Name Nathalie Dierichs +E-mail nathalie.dierichs@rivm.nl +Email nathalie.dierichs@rivm.nl +Role Data producer + o1 +ORCID 0009-0000-5074-6239 + +author +Name Jente Houweling +E-mail jente.houweling@rivm.nl +ORCID 0009-0005-3680-0645 +Email jente.houweling@rivm.nl +Role Data steward + o1 + +organisation o1 +Name Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands + +Funding +Agency NWA +grant_id 1292.19.272 + +Cell lines[] Cell line RRID Supplier + SK-N-AS CVCL_1700 ATCC + MO3.13 CVCL_D357 Cedarlane Laboratories + +Chemicals[] Chemical CAS CompoundWikiID + BSP (sulfobromophthalein sodium) 123359-42-2 + Chlorpyrifos 2921-88-2 Q4722 + Iopanoic acid 96-83-3 Q1879 + Silychristin 33889-69-9 Q5049 + TBBPA 79-94-7 Q82 + Xanthohumol 6754-58-1 Q4753 + +Experimental design[] Time point Time point_unit Replicates Detection instrument Instrument manufacturer Measured entity Measured entity_unit Substrate Endpoint Endpoint_unit + 24 hours 2 Waters Acquitytm Premier UPLC + RAMONA star (Elisia Raytest) AUC (Area under curve) AUC (Area under curve) 1 nM T3 Conversion of T3 into metabolites T2 and T1 % + diff --git a/biostudies/enriched /tsv/Template__Receptor_activation_.tsv b/biostudies/enriched /tsv/Template__Receptor_activation_.tsv new file mode 100644 index 0000000..cfd04fb --- /dev/null +++ b/biostudies/enriched /tsv/Template__Receptor_activation_.tsv @@ -0,0 +1,62 @@ +Submission S-VHPS15 +Title Thyroid Hormone Receptor Activation Assay: Measurement of transcriptional response to T3 in neuronal cell cultures +ReleaseDate 2026-06-01 +AttachTo VHP4Safety + +Study +Title Thyroid Hormone Receptor Activation Assay: Measurement of transcriptional response to T3 in neuronal cell cultures +ReleaseDate 2026-06-01 +Description Part of the development of an in vitro testing battery aimed at evaluating thyroid hormone (TH)-mediated developmental neurotoxicity. +Organism Homo sapiens (human) +License CC BY 4.0 +[URL] https://creativecommons.org/licenses/by/4.0/legalcode +Bioassay Genetic transcription +[Ontology] BAO +[TermId] BAO_0002488 +Organ Brain +Tissue Neural tissue +Adverse outcome Pathway [Placeholder] +[URL] https://aopwiki.org/aops/ +AOP event Tr alpha +[URL] https://aopwiki.org/events/ + +Link https://docs.vhp4safety.nl/en/latest/ +Description Documentation page VHP4Safety + +Link https://platform.vhp4safety.nl/ +Description VHP4Safety platform + +author +Name Nathalie Dierichs +E-mail nathalie.dierichs@rivm.nl +Email nathalie.dierichs@rivm.nl +Role Data producer + o1 +ORCID 0009-0000-5074-6239 + +author +Name Jente Houweling +E-mail jente.houweling@rivm.nl +ORCID 0009-0005-3680-0645 +Email jente.houweling@rivm.nl +Role Data steward + o1 + +organisation o1 +Name Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands + +Funding +Agency NWA +grant_id 1292.19.272 + +Cell lines[] Cell line RRID Supplier + SK-N-AS CVCL_1700 ATCC + +Chemicals[] Chemical CAS CompoundWikiID + NH-3 447415-26-1 Q1882 + Silychristin 33889-69-9 Q5049 + TBBPA 79-94-7 Q82 + +Experimental design[] Time point Time point_unit Replicates Detection instrument Instrument manufacturer Measured entity Measured entity_unit Substrate Endpoint Endpoint_unit + 6 hours 3 QuantStudio 7 Flex ∆∆CT ∆∆CT KLF9 expression Fold change + diff --git a/biostudies/enriched /tsv/Template__TH_Transport_Assay_.tsv b/biostudies/enriched /tsv/Template__TH_Transport_Assay_.tsv new file mode 100644 index 0000000..8fa3a3f --- /dev/null +++ b/biostudies/enriched /tsv/Template__TH_Transport_Assay_.tsv @@ -0,0 +1,75 @@ +Submission S-VHPS9 +Title In Vitro Thyroid Hormone Uptake Assay for Transporter Inhibition in Neural Cells Using Gamma Counter Detection +ReleaseDate 2026-06-01 +AttachTo VHP4Safety + +Study +Title In Vitro Thyroid Hormone Uptake Assay for Transporter Inhibition in Neural Cells Using Gamma Counter Detection +ReleaseDate 2026-06-01 +Description +Organism Homo sapiens (human) +License CC BY 4.0 +[URL] https://creativecommons.org/licenses/by/4.0/legalcode +Bioassay Transporter inhibition assay +[Ontology] BAO +[TermId] BAO_0010188 +Organ Brain +Tissue Neural tissue +Adverse outcome Pathway [placeholder] +[URL] https://aopwiki.org/aops/ +AOP event MCT8 +[URL] https://aopwiki.org/events/2258 +AOP event OATP1C1 +[URL] https://aopwiki.org/events/ + +Link https://docs.vhp4safety.nl/en/latest/ +Description Documentation page VHP4Safety + +Link https://platform.vhp4safety.nl/ +Description VHP4Safety platform + +author +Name Nathalie Dierichs +E-mail nathalie.dierichs@rivm.nl +Email nathalie.dierichs@rivm.nl +Role Data producer + o1 +ORCID 0009-0000-5074-6239 + +author +Name Jente Houweling +E-mail jente.houweling@rivm.nl +ORCID 0009-0005-3680-0645 +Email jente.houweling@rivm.nl +Role Data steward + o1 + +organisation o1 +Name Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands + +Funding +Agency NWA +grant_id 1292.19.272 + +Cell lines[] Cell line RRID Supplier + SK-N-AS CVCL_1700 ATCC + H4 CVCL_1239 ATCC + MO3.13 CVCL_D357 Cedarlane Laboratories + +Chemicals[] Chemical CAS CompoundWikiID + Amiodarone 19774-82-4 Q17 + BSP (sulfobromophthalein sodium) 123359-42-2 + Cefuroxime 55268-75-2 Q4751 + Chlorpyrifos 2921-88-2 Q4722 + Iopanoic acid 96-83-3 Q1879 + Mono-buthyl phtalate (MBP) 131-70-4 + NH-3 447415-26-1 Q1882 + PBDE-99 60348-60-9 Q4757 + Silychristin 33889-69-9 Q5049 + TBBPA 79-94-7 Q82 + Lesinurad 878672-00-5 Q1880 + Xanthohumol 6754-58-1 Q4753 + +Experimental design[] Time point Time point_unit Replicates Detection instrument Instrument manufacturer Measured entity Measured entity_unit Substrate Endpoint Endpoint_unit + 10 minutes 2 Gamma Counter counts per minute counts per minute T3 T3 uptake % +