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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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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20190221-p4-FDA2 | K14 | S2103 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | C12 | S2104 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | F07 | S2105 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | D20 | S2108 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | L06 | S2110 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | M13 | S2111 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | O15 | S2113 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | J17 | S2114 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | J15 | S2116 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | L20 | S2118 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | N06 | S2119 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | G07 | S2123 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | G18 | S2124 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | J03 | S2125 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | I17 | S2127 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | M16 | S2130 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | H05 | S2131 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | J08 | S2150 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | H19 | S2152 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | O23 | S2154 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | D09 | S2157 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | D19 | S2159 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | E03 | S2167 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | B09 | S2169 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | N11 | S2173 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | K05 | S2181 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | G20 | S2199 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | O21 | S2206 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | E23 | S2208 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | B20 | S2216 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | H12 | S2217 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | I15 | S2221 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | H11 | S2229 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | N05 | S2230 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | M23 | S2233 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | K12 | S2235 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | H02 | S2240 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | J14 | S2248 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | L05 | S2264 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | L18 | S2265 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | K08 | S2286 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | J02 | S2290 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | B06 | S2293 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | E06 | S2296 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | K03 | S2328 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | G06 | S2336 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | I18 | S2350 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | B23 | S2357 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | F18 | S2369 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | C15 | S2373 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | N18 | S2374 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | C11 | S2376 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | I02 | S2381 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | J12 | S2393 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | G22 | S2422 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | O14 | S2442 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | J18 | S2443 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | D06 | S2446 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | F17 | S2451 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | G15 | S2452 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | J13 | S2454 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | G16 | S2455 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | B04 | S2456 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | E11 | S2457 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | F12 | S2458 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | E17 | S2459 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | O11 | S2461 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | C17 | S2467 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | M17 | S2470 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | M18 | S2471 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | C07 | S2473 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | D03 | S2475 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | C13 | S2476 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | F13 | S2479 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | L04 | S2481 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | L16 | S2484 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | D11 | S2485 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | E07 | S2486 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | K17 | S2487 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | F06 | S2489 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | B19 | S2491 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | I06 | S2493 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | E22 | S2494 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | G03 | S2496 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | I21 | S2497 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | K21 | S2499 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | N08 | S2500 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | C04 | S2502 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | J23 | S2504 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | K20 | S2506 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | C05 | S2508 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | E05 | S2509 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | N12 | S2510 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | L07 | S2511 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | O04 | S2512 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | F03 | S2516 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | L13 | S2517 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | M19 | S2519 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | L10 | S2521 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | H07 | S2522 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA |