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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| # comments: | |||||||||
| # | |||||||||
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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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| #List of each well and plate containing entity, dose and other characteristics required for your study. | |||||||||
| #Examples of other characteristics might be but not limited to, library.cas, geneIDs, control.binary(0,1), cloneID, PassageNumber | |||||||||
| #Please, do not insert any empty row without '#' above the table below. For additional info or comments please use a Comment line indicated by a '#'. | |||||||||
| # | |||||||||
| Plate | Well | Treatment | Dose | DoseUnit | CellLine | TimeTreatment | ReplID | remarks | |
| 20190207-p1-KIN1 | K09 | S2549 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | N16 | S2564 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | L18 | S2577 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | E22 | S2589 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | F05 | S2603 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | G06 | S2615 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | M23 | S2693 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | C18 | S2760 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | L07 | S2797 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | K19 | S2874 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | H13 | S3022 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | K15 | S3035 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | H14 | S3051 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | D16 | S3063 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | M08 | S3078 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | F16 | S3113 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | F08 | S3132 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | O06 | S3149 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | K12 | S3163 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | K23 | S3180 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | K14 | S3181 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | F18 | S3199 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | L20 | S3635 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | H06 | S3659 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | B22 | S3684 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | B19 | S3711 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | J22 | S3724 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | B20 | S3733 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | H20 | S3745 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | K17 | S4004 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | I18 | S4024 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | H11 | S4039 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | C10 | S4047 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | N18 | S4057 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | O11 | S4065 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | I15 | S4076 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | G11 | S4085 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | J20 | S4096 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | D08 | S4107 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
| 20190207-p1-KIN1 | C03 | S4123 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | B03 | S1003 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | H04 | S1017 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | O21 | S1028 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | G18 | S1040 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | J16 | S1056 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | D03 | S1076 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | D22 | S1092 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | G08 | S1105 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | C21 | S1116 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | O16 | S1138 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | C17 | S1167 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | J11 | S1181 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | B12 | S1244 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | G04 | S1352 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | N11 | S1454 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | J04 | S1485 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | E10 | S1524 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | N05 | S1555 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | I20 | S1573 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | C05 | S2134 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | K10 | S2193 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | O03 | S2216 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | K22 | S1010 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | C07 | S1022 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | F07 | S1035 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | G12 | S1046 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | N06 | S1068 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | M02 | S1084 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | L04 | S1101 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | J05 | S1111 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | N02 | S1120 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | H18 | S1152 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | J13 | S1173 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | B10 | S1219 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | B23 | S1267 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | H15 | S1363 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | D06 | S1462 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | J12 | S1490 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | L16 | S1531 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | I10 | S1561 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | K08 | S1590 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | K03 | S2163 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | M07 | S2202 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | I21 | S2221 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | E09 | S1005 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | O15 | S1018 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | N15 | S1032 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | E12 | S1042 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | J18 | S1064 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | F13 | S1077 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | E21 | S1093 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | F23 | S1106 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | J07 | S1117 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | H16 | S1143 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI | |
| 20190207-p1-KIN1 | J06 | S1169 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | KI |
