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 | D04 | S1883 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | H14 | S1884 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | H15 | S1885 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | J20 | S1888 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | J09 | S1890 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | F05 | S1891 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | H04 | S1895 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | N15 | S1896 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | I13 | S1897 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | F16 | S1898 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | M04 | S1899 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | H08 | S1902 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | O03 | S1904 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | F19 | S1907 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | C16 | S1908 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | B05 | S1909 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | L23 | S1910 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | J11 | S1913 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | I07 | S1914 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | B07 | S1915 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | F04 | S1917 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | L08 | S1920 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | D17 | S1921 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | I19 | S1928 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | K16 | S1929 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | G04 | S1933 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | I09 | S1934 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | E02 | S1941 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | M06 | S1949 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | N16 | S1952 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | E10 | S1956 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | L17 | S1957 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | B11 | S1958 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | K23 | S1959 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | M10 | S1962 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | D13 | S1964 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | B08 | S1965 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | H17 | S1969 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | N21 | S1971 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | C23 | S1972 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | F14 | S1974 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | I11 | S1977 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | J05 | S1978 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | B14 | S1979 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | K11 | S1983 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | N02 | S1986 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | H23 | S1987 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | L19 | S1988 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | M21 | S1994 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | G21 | S2001 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | H09 | S2003 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | G10 | S2005 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | E16 | S2006 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | J19 | S2007 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | N13 | S2011 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | D23 | S2017 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | G05 | S2020 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | N10 | S2021 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | J16 | S2024 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | G09 | S2025 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | F15 | S2028 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | J04 | S2029 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | C18 | S2031 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | K22 | S2032 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | F09 | S2035 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | I12 | S2036 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | N19 | S2037 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | O20 | S2038 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | M02 | S2040 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | M08 | S2043 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | F02 | S2045 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | O10 | S2046 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | F20 | S2047 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | F22 | S2051 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | B02 | S2052 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | G11 | S2054 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | C22 | S2057 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | I04 | S2058 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | D10 | S2060 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | G19 | S2061 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | D16 | S2062 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | C09 | S2064 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | H03 | S2065 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | I05 | S2069 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | F23 | S2074 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | N22 | S2075 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | J06 | S2077 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | M05 | S2078 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | B18 | S2079 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | M03 | S2080 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | G17 | S2084 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | D02 | S2085 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | O02 | S2086 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | C14 | S2091 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | L21 | S2092 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | K02 | S2096 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | I22 | S2097 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | O06 | S2099 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | E04 | S2101 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | K18 | S2102 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA |