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-p3-FDA1 | G16 | S1713 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p3-FDA1 | N14 | Tunicamycin_c1a | 0.15 | uM | HepG2-CHOP-GFP | 24 | Rep1 | Control | |
20190221-p3-FDA1 | O23 | Tunicamycin_c2a | 0.34 | uM | HepG2-CHOP-GFP | 24 | Rep1 | Control | |
20190221-p3-FDA1 | J06 | Tunicamycin_c3a | 0.77 | uM | HepG2-CHOP-GFP | 24 | Rep1 | Control | |
20190221-p3-FDA1 | K04 | Tunicamycin_c4a | 1.73 | uM | HepG2-CHOP-GFP | 24 | Rep1 | Control | |
20190221-p3-FDA1 | M11 | Tunicamycin_c5a | 3.9 | uM | HepG2-CHOP-GFP | 24 | Rep1 | Control | |
20190221-p3-FDA1 | N20 | Tunicamycin_c6a | 8.77 | uM | HepG2-CHOP-GFP | 24 | Rep1 | Control | |
20190221-p3-FDA1 | M21 | Tunicamycin_c7a | 19.73 | uM | HepG2-CHOP-GFP | 24 | Rep1 | Control | |
20190221-p3-FDA1 | M09 | Tunicamycin_c8a | 44.4 | uM | HepG2-CHOP-GFP | 24 | Rep1 | Control | |
20190221-p3-FDA1 | O02 | Tunicamycin_c1b | 0.15 | uM | HepG2-CHOP-GFP | 24 | Rep1 | Control | |
20190221-p3-FDA1 | I20 | Tunicamycin_c2b | 0.34 | uM | HepG2-CHOP-GFP | 24 | Rep1 | Control | |
20190221-p3-FDA1 | F09 | Tunicamycin_c3b | 0.77 | uM | HepG2-CHOP-GFP | 24 | Rep1 | Control | |
20190221-p3-FDA1 | N03 | Tunicamycin_c4b | 1.73 | uM | HepG2-CHOP-GFP | 24 | Rep1 | Control | |
20190221-p3-FDA1 | O22 | Tunicamycin_c5b | 3.9 | uM | HepG2-CHOP-GFP | 24 | Rep1 | Control | |
20190221-p3-FDA1 | G10 | Tunicamycin_c6b | 8.77 | uM | HepG2-CHOP-GFP | 24 | Rep1 | Control | |
20190221-p3-FDA1 | N15 | Tunicamycin_c7b | 19.73 | uM | HepG2-CHOP-GFP | 24 | Rep1 | Control | |
20190221-p3-FDA1 | N07 | Tunicamycin_c8b | 44.4 | uM | HepG2-CHOP-GFP | 24 | Rep1 | Control | |
20190221-p3-FDA1 | I15 | Mitomycin_1 | 150 | uM | HepG2-CHOP-GFP | 24 | Rep1 | Control | |
20190221-p3-FDA1 | N02 | Mitomycin_2 | 150 | uM | HepG2-CHOP-GFP | 24 | Rep1 | Control | |
20190221-p3-FDA1 | N05 | Mitomycin_3 | 150 | uM | HepG2-CHOP-GFP | 24 | Rep1 | Control | |
20190221-p3-FDA1 | I17 | Mitomycin_4 | 150 | uM | HepG2-CHOP-GFP | 24 | Rep1 | Control | |
20190221-p3-FDA1 | D19 | DMSO_1 | 0.5 | uM | HepG2-CHOP-GFP | 24 | Rep1 | Control | |
20190221-p3-FDA1 | J13 | DMSO_2 | 0.5 | uM | HepG2-CHOP-GFP | 24 | Rep1 | Control | |
20190221-p3-FDA1 | N10 | DMSO_3 | 0.5 | uM | HepG2-CHOP-GFP | 24 | Rep1 | Control | |
20190221-p3-FDA1 | D21 | DMSO_4 | 0.5 | uM | HepG2-CHOP-GFP | 24 | Rep1 | Control | |
20190221-p3-FDA1 | N16 | DMSO_5 | 0.5 | uM | HepG2-CHOP-GFP | 24 | Rep1 | Control | |
20190221-p3-FDA1 | F06 | DMSO_6 | 0.5 | uM | HepG2-CHOP-GFP | 24 | Rep1 | Control | |
20190221-p3-FDA1 | E13 | DMSO_7 | 0.5 | uM | HepG2-CHOP-GFP | 24 | Rep1 | Control | |
20190221-p3-FDA1 | B16 | DMSO_8 | 0.5 | uM | HepG2-CHOP-GFP | 24 | Rep1 | Control | |
20190221-p4-FDA2 | N03 | S1717 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | E08 | S1718 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | O18 | S1719 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | J10 | S1721 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | H06 | S1723 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | C08 | S1724 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | M12 | S1727 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | M07 | S1730 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | B13 | S1732 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | C02 | S1733 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | K19 | S1734 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | D08 | S1735 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | M11 | S1736 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | K09 | S1738 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | G02 | S1740 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | D22 | S1741 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | M22 | S1742 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | D12 | S1743 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | K10 | S1744 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | D21 | S1747 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | F21 | S1748 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | B03 | S1756 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | K06 | S1759 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | K13 | S1760 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | B10 | S1761 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | N14 | S1762 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | J21 | S1763 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | C20 | S1764 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | F11 | S1770 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | O05 | S1771 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | F08 | S1773 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | H22 | S1774 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | O19 | S1775 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | B17 | S1776 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | B12 | S1777 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | D05 | S1782 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | G23 | S1784 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | K15 | S1786 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | K07 | S1787 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | I14 | S1789 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | J22 | S1790 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | B22 | S1792 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | O22 | S1794 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | B21 | S1801 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | O07 | S1802 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | M09 | S1806 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | E13 | S1807 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | N07 | S1808 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | O08 | S1816 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | H20 | S1828 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | E14 | S1829 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | L03 | S1830 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | E21 | S1831 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | D14 | S1832 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | C06 | S1833 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | K04 | S1836 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | L22 | S1839 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | L09 | S1840 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | C19 | S1843 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | O13 | S1845 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | E15 | S1847 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | D07 | S1848 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | B16 | S1854 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | H21 | S1859 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | L15 | S1865 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | N17 | S1866 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | M14 | S1869 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | I08 | S1876 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | O17 | S1878 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | E20 | S1880 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA | |
20190221-p4-FDA2 | B15 | S1881 | 50 | uM | HepG2-CHOP-GFP | 24 | Rep1 | FDA |