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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HepG2-CHOP-GFP | B10 | S3188 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | H09 | S3189 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | J10 | S3195 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | N17 | S3196 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | N05 | S3200 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | H10 | S3201 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | C07 | S3204 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | D18 | S3208 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | O15 | S3209 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | I17 | S3212 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | L04 | S3621 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | N10 | S3636 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | O19 | S3637 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | M09 | S3638 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | D03 | S3640 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | I19 | S3646 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | H03 | S3648 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | M11 | S3655 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | B14 | S3663 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | H23 | S3664 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | G13 | S3669 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | N04 | S3671 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | B06 | S3672 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | F13 | S3673 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | O23 | S3681 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | E23 | S3687 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | I18 | S3690 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | K23 | S3694 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | L06 | S3697 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | D10 | S3698 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | N12 | S3701 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | J02 | S3706 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | I11 | S3714 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | C09 | S3716 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | N11 | S3717 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | G10 | S3718 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | D05 | S3719 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | N06 | S3722 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | I08 | S3723 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | E22 | S3726 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | L12 | S3727 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | I23 | S3728 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | B08 | S3729 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | O08 | S3730 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | L03 | S3731 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | I20 | S3732 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | D22 | S3735 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | E06 | S3738 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | B18 | S3739 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | O09 | S3741 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | C12 | S3742 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | H20 | S3743 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | M03 | S3746 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | O07 | S3747 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | C11 | S3751 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | I14 | S4000 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | H17 | S4001 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | B11 | S4002 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | N03 | S4003 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | M02 | S4005 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | K02 | S4007 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | J04 | S4009 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | C16 | S4010 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | H05 | S4011 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | H22 | S4012 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | N08 | S4014 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | C04 | S4016 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | N18 | S4017 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | C23 | S4019 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | M20 | S4020 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | D23 | S4021 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | J09 | S4022 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | J12 | S4023 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | J18 | S4025 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | O21 | S4026 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | E02 | S4031 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | I02 | S4034 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | G18 | S4035 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | N16 | S4037 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | C21 | S4038 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | G05 | S4040 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | B03 | S4041 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | M23 | S4042 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | I13 | S4043 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | F03 | S4044 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | J03 | S4045 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | K10 | S4046 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | G08 | S4048 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | F20 | S4049 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | J14 | S4050 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | N21 | S4051 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | H06 | S4053 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | D21 | S4054 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | B17 | S4056 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | E11 | S4058 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | M06 | S4059 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | L19 | S4060 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | J21 | S4061 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | B02 | S4062 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA | |
HepG2-CHOP-GFP | C14 | S4063 | 50 | uM | 20190222-p3-FDA3 | 24 | Rep3 | FDA |