Selected Cell
Cell:
Value:
InvestigationInformation
StudyInformation
AssayInformation
AssayConditions
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| #Template info | |||||||||
| #TemplateVersion | LEI-MIHCSME_userTemplate_v3 | version 3 is updated version including recommendations by users, plus ISA and REMBI compliant. | |||||||
| #DateTemplateGenerated | Jan-20-2023 | ||||||||
| #CreatedBy | RH | ||||||||
| Annotation_groups | Key | Value | Comments_User | Description_Examples_Values | |||||
| DataOwner | First Name | Matthijs | First Name | ||||||
| DataOwner | Middle Name(s) | Middle Name(s) if any | |||||||
| DataOwner | Last Name | Vlasveld | Last Name | ||||||
| DataOwner | User name | vlasveldmp | Institutional user name | ||||||
| DataOwner | Institute | LACDR | Institute level, eg. Universiteit Leiden, Faculty of Science, Institute of Biology | ||||||
| DataOwner | E-Mail Address | m.p.vlasveld@lacdr.leidenuniv.nl | Institution email address | ||||||
| DataOwner | ORCID investigator | orcid id as url, eg. https://orcid.org/0000-0002-3704-3675 | |||||||
| DataCollaborator | ORCID Data Collaborator | ORCID is of collaborator with experimental, collection or analysis part of this investigation | |||||||
| DataCollaborator | ORCID Data Collaborator | ORCID is of collaborator with experimental, collection or analysis part of this investigation | |||||||
| InvestigationInformation | Project ID | IMI2 eTRANSAFE | EU/NWO/consortium ID – Examples: EuTOX | ||||||
| InvestigationInformation | Investigation Title | Is integrated stress response related expression of CHOP predictive for DILI | High level concept to link related studies. Could be the main hypothesis/question you want to investigate as part of your research. Could be a chapter/thesis of your work. | ||||||
| InvestigationInformation | Investigation internal ID | iMV01 | Corresponding internal ID for your investigation. | ||||||
| InvestigationInformation | Investigation description | Development of High-throughput screening pipeline for Drug Safety Assessment | Short description for your investigation. | ||||||
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| # comments: | |||||||||
| # | |||||||||
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| Annotation_groups | Key | Value | Comments_User | Description_Examples_Values | |||||
| Study | Study Title | The integrated stress response-related expression of CHOP due to mitochondrial toxicity is predictive for drug-induced liver injury liability. | Manuscript/chapter/publication/paragraph title describing purpose or intention for one or multiple assays (screens/experiments) | ||||||
| Study | Study internal ID | sMV03 | Study ID, linked to ELN or lab journal | ||||||
| Study | Study Description | High throughput screen of FDA approved drugs on HepG2 CHOP-GFP reproter, followed by downstream hit analysis | Description of study with additional unstructured information about this study possibly not covered elsewhere in this template. | ||||||
| Study | Study Key Words | drug-induced liver injury, high-throughput screening, CHOP, mitochondrial toxicity, integrated stress response | List of key words associated with your study (EFO-terms). Examples: FDA approved drugs, Kinase inhibitors, DNA damage response, Unfolded protein response, Oxidative stress response, Inflammatory signaling, chemical similarity | ||||||
| Biosample | Biosample Taxon | NCBITAXON:9606 | NCBI-taxon id, human = NCBITAXON:9606; | ||||||
| Biosample | Biosample description | Genetically modified human hepatoma HepG2 cell line using bacterial artificial cloning | Description of biosample genotype; Additional unstructured information about organisms used in this experiment. | ||||||
| Biosample | Biosample Organism | Human | Which organism is your cell lines or tissue from. Examples: Human or mouse | ||||||
| Biosample | Number of cell lines used | 1 | In case multiple cell lines are used indicate here | ||||||
| Library | Library File Name | FDA_lib_v2.xlsx | Library file info | ||||||
| Library | Library File Format | xlsx | Library file info | ||||||
| Library | Library Type | Compound library | Library file info | ||||||
| Library | Library Manufacturer | Selleck Chem | Library file info | ||||||
| Library | Library Version | 2018-08-01T0:0:0+0000 | Library file info | ||||||
| Library | Library Experimental Conditions | NA | Any experimental conditions some cells were grown under as part of the study enter the information here e.g. different environmental stress conditions, or mutant background compared to wild type. | ||||||
| Library | Quality Control Description | NA | A brief description of the kind of quality control measures that were taken. | ||||||
| Protocols | HCS library protocol | SOP_FDA-KI_library_primaryScreen_v1.3.docx | Url/doi protocols.io or ELN associated url. At least SOP/protocol filename | ||||||
| Protocols | growth protocol | SOP_FDA-KI_library_primaryScreen_v1.3.docx | Url/doi protocols.io or ELN associated url. At least SOP/protocol filename | ||||||
| Protocols | treatment protocol | SOP_FDA-KI_library_primaryScreen_v1.3.docx | Url/doi protocols.io or ELN associated url. At least SOP/protocol filename | ||||||
| Protocols | HCS data analysis protocol | SOP_FDA-KI_library_primaryScreen_DataAnalysis_v1.1.docx | Url/doi protocols.io or ELN associated url. At least SOP/protocol filename | ||||||
| Plate | Plate type | uclear | Example: uclear | ||||||
| Plate | Plate type Manufacturer | Greiner Bio-One | Example: Greiner Bio-One | ||||||
| Plate | Plate type Catalog number | 781081 | Example:781081 | ||||||
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| Annotation_groups | Key | Value | Comments_User | Description_Examples_Values | |||||
| Assay | Assay Title | High-throughput screen of HepG2 CHOP-GFP reporter | Screen name | ||||||
| Assay | Assay internal ID | aMV01 | Experimental ID, e.g. aMV-010, linked to ELN or labjournal | ||||||
| Assay | Assay Description | High-throughput screen of HepG2 CHOP-GFP reporter using FDA approved drugs and kinase inhibitors | Description of screen plus additional unstructured information about screen not covered elsewhere. Stages of HCS: either primary screen, secondary screen or validation screen. EFO terms | ||||||
| Assay | Assay number of biological replicates | 3 | Total number of biol. Repl. | ||||||
| Assay | Number of plates | 24 | Total number of plates, n-plates | ||||||
| Assay | Assay Technology Type | confocal microscopy | Imaging method, Fbbi terms. | ||||||
| Assay | Assay Type | high content screen of cells in treated with a compound library | List of options: sub types of HCS e.g. Gene Knock down, RNAi, compount, EFO terms | ||||||
| Assay | Assay External URL | NA | ELN or any other external url link to this screen. | ||||||
| Assay | Assay data URL | https://omeroweb.services.universiteitleiden.nl/webclient/?show=screen-1460 | OMERO url link to this screen. | ||||||
| AssayComponent | Imaging protocol | SOP_FDAKIScreen.docx | Url to protocols.io or protocols in ELN, at least protocol file name or free text description of imaging protocol | ||||||
| AssayComponent | Sample preparation protocol | SOP_FDAKIScreen.docx | Sample preparation method (Formaldahude (PFA) fixed tissue, Live cells, unfixed tissue). FBbi terms | ||||||
| Biosample | Cell lines storage location | N2 tank 4th flour | Storage location according to Database used or at least location e.g. Example -150 liquid N2 tank 4th floor GE4.xx | ||||||
| Biosample | Cell lines clone number | 16 | Storage location DB info | ||||||
| Biosample | Cell lines Passage number | 18 | Passage number of your cells. In case different passage number is used for the replicates, please indicate it in Comment_users. | ||||||
| ImageData | Image number of pixelsX | 512 | Indicate number of pixels in x in images | ||||||
| ImageData | Image number of pixelsY | 512 | Indicate number of pixels in y in images | ||||||
| ImageData | Image number of z-stacks | 1 | Indicate number z stacks in image, single image is z=1 | ||||||
| ImageData | Image number of channels | 2 | Indicate number of channels in your image, single channel image c=1, including your TD channel | ||||||
| ImageData | Image number of timepoints | 1 | Indicate number of time point(s) in your image | ||||||
| ImageData | Image sites per well | 2 | Number of fields, numeric value | ||||||
| ImageAcquisition | Microscope id | Nikon 3 | Url to micrometa app file link or other url describing your microscope. At least Microscope name. | ||||||
| Specimen | Channel Transmission id | NA | Channel id is dependent on different machines, first or last. If No transmission is acquired state NA | ||||||
| Specimen | Channel 1 visualization method | Hoechst 33342 | Visualization method (example: Hoechst staining ) | ||||||
| Specimen | Channel 1 entity | DNA | Entity visualized (example: DNA ) | ||||||
| Specimen | Channel 1 label | Nuclei | Label used for entity (example:Nuclei) Best practice to use similar label as your CP-pipeline | ||||||
| Specimen | Channel 1 id | 1 | sequential id of channel order in your image | ||||||
| Specimen | Channel 2 visualization method | fluorescent protein tag | Visualization method (example: GFP ) | ||||||
| Specimen | Channel 2 entity | DDIT3 | Entity visualized (example: MAP1LC3B ) | ||||||
| Specimen | Channel 2 label | CHOP-GFP | Label used for entity (example:GFP-LC3) Best practice to use similar label as your CP-pipeline | ||||||
| Specimen | Channel 2 id | 2 | sequential id of channel order in your image | ||||||
| Specimen | Channel 3 visualization method | propidium iodide | Visualization method (example: PI staining ) | ||||||
| Specimen | Channel 3 entity | DNA | Entity visualized (example: Death cell DNA ) | ||||||
| Specimen | Channel 3 label | PI | Label used for entity (example:PI) Best practice to use similar label as your CP-pipeline | ||||||
| Specimen | Channel 3 id | 3 | sequential id of channel order in your image | ||||||
| Specimen | Channel 4 visualization method | Visualization method (example: Apoptotic marker Annexin V staining ) | |||||||
| Specimen | Channel 4 entity | Entity visualized (example: Apoptotic cells ) | |||||||
| Specimen | Channel 4 label | Label used for entity (example:Annexin-V) Best practice to use similar label as your CP-pipeline | |||||||
| Specimen | Channel 4 id | sequential id of channel order in your image |
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| HepG2-CHOP-GFP | C11 | S1363 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | N05 | S1462 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | F03 | S1490 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | K12 | S1531 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | H20 | S1561 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | H19 | S1590 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | I06 | S2163 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | G16 | S2202 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | O04 | S2221 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | K14 | S1005 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | C15 | S1018 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | I10 | S1032 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | J15 | S1042 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | C09 | S1064 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | M14 | S1077 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | M13 | S1093 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | D23 | S1106 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | I15 | S1117 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | L08 | S1143 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | J05 | S1169 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | M22 | S1194 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | D21 | S1249 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | K06 | S1360 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | M05 | S1458 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | D04 | S1486 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | G20 | S1526 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | C06 | S1556 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | F12 | S1574 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | B05 | S2158 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | O03 | S2194 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | C20 | S2218 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | L07 | S1011 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | K07 | S1023 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | F09 | S1036 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | L18 | S1048 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | I13 | S1070 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | N20 | S1088 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | H21 | S1102 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | L09 | S1112 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | F06 | S1124 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | G17 | S1153 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | C03 | S1177 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | B21 | S1220 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | G14 | S1274 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | F15 | S1378 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | B06 | S1470 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | H17 | S1494 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | K02 | S1532 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | L12 | S1568 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | J20 | S1802 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | E15 | S2179 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | H09 | S2205 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | B11 | S2226 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | N10 | S1006 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | O13 | S1020 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | N11 | S1033 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | B13 | S1043 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | K23 | S1065 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | O11 | S1078 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | F05 | S1094 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | O19 | S1107 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | G02 | S1118 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | B17 | S1145 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | L22 | S1170 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | D13 | S1205 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | M04 | S1264 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | J08 | S1361 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | C21 | S1459 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | M19 | S1487 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | I21 | S1529 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | O17 | S1557 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | B14 | S1577 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | C19 | S2161 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | B22 | S2198 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | G13 | S2219 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | H18 | S1012 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | G03 | S1025 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | D07 | S1038 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | G06 | S1049 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | D09 | S1072 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | O15 | S1089 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | H07 | S1103 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | C02 | S1113 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | I07 | S1133 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | E09 | S1154 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | J06 | S1178 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | N16 | S1226 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | D17 | S1275 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | D16 | S1392 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | N23 | S1474 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | J07 | S1519 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | O21 | S1533 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | G21 | S1570 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | F18 | S2013 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | K21 | S2185 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | E06 | S2207 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | O22 | S2227 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | J13 | S1008 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | K08 | S1021 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI | |
| HepG2-CHOP-GFP | D12 | S1034 | 50 | uM | 20190222-p7-KIN1 | 24 | Rep3 | KI |
