LEI-MIHCSME - empty template

Selected Cell

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InvestigationInformation StudyInformation AssayInformation AssayConditions

#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			First Name
DataOwner	Middle Name(s)			Middle Name(s) if any
DataOwner	Last Name			Last Name
DataOwner	User name			Institutional user name
DataOwner	Institute			Institute level, eg. Universiteit Leiden, Faculty of Science, Institute of Biology
DataOwner	E-Mail Address			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			EU/NWO/consortium ID – Examples: EuTOX
InvestigationInformation	Investigation Title			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			Corresponding internal ID for your investigation.
InvestigationInformation	Investigation description			Short description for your investigation.

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Annotation_groups	Key	Value	Comments_User	Description_Examples_Values
Study	Study Title			Manuscript/chapter/publication/paragraph title describing purpose or intention for one or multiple assays (screens/experiments)
Study	Study internal ID			Study ID, linked to ELN or lab journal
Study	Study Description			Description of study with additional unstructured information about this study possibly not covered elsewhere in this template.
Study	Study Key Words			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			NCBI-taxon id, human = NCBITAXON:9606;
Biosample	Biosample description			Description of biosample genotype; Additional unstructured information about organisms used in this experiment.
Biosample	Biosample Organism			Which organism is your cell lines or tissue from. Examples: Human or mouse
Biosample	Number of cell lines used			In case multiple cell lines are used indicate here
Library	Library File Name			Library file info
Library	Library File Format			Library file info
Library	Library Type			Library file info
Library	Library Manufacturer			Library file info
Library	Library Version			Library file info
Library	Library Experimental Conditions			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			A brief description of the kind of quality control measures that were taken.
Protocols	HCS library protocol			Url/doi protocols.io or ELN associated url. At least SOP/protocol filename
Protocols	growth protocol			Url/doi protocols.io or ELN associated url. At least SOP/protocol filename
Protocols	treatment protocol			Url/doi protocols.io or ELN associated url. At least SOP/protocol filename
Protocols	HCS data analysis protocol			Url/doi protocols.io or ELN associated url. At least SOP/protocol filename
Plate	Plate type			Example: uclear
Plate	Plate type Manufacturer			Example: Greiner Bio-One
Plate	Plate type Catalog number			Example:781081

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Annotation_groups	Key	Value	Comments_User	Description_Examples_Values
Assay	Assay Title			Screen name
Assay	Assay internal ID			Experimental ID, e.g. aMV-010, linked to ELN or labjournal
Assay	Assay Description			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			Total number of biol. Repl.
Assay	Number of plates			Total number of plates, n-plates
Assay	Assay Technology Type			Imaging method, Fbbi terms.
Assay	Assay Type			List of options: sub types of HCS e.g. Gene Knock down, RNAi, compount, EFO terms
Assay	Assay External URL			ELN or any other external url link to this screen.
Assay	Assay data URL			OMERO url link to this screen.
AssayComponent	Imaging protocol			Url to protocols.io or protocols in ELN, at least protocol file name or free text description of imaging protocol
AssayComponent	Sample preparation protocol			Sample preparation method (Formaldahude (PFA) fixed tissue, Live cells, unfixed tissue). FBbi terms
Biosample	Cell lines storage location			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			Storage location DB info
Biosample	Cell lines Passage number			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			Indicate number of pixels in x in images
ImageData	Image number of pixelsY			Indicate number of pixels in y in images
ImageData	Image number of z-stacks			Indicate number z stacks in image, single image is z=1
ImageData	Image number of channels			Indicate number of channels in your image, single channel image c=1, including your TD channel
ImageData	Image number of timepoints			Indicate number of time point(s) in your image
ImageData	Image sites per well			Number of fields, numeric value
ImageAcquisition	Microscope id			Url to micrometa app file link or other url describing your microscope. At least Microscope name.
Specimen	Channel Transmission id			Channel id is dependent on different machines, first or last. If No transmission is acquired state NA
Specimen	Channel 1 visualization method			Visualization method (example: Hoechst staining )
Specimen	Channel 1 entity			Entity visualized (example: DNA )
Specimen	Channel 1 label			Label used for entity (example:Nuclei) Best practice to use similar label as your CP-pipeline
Specimen	Channel 1 id			sequential id of channel order in your image
Specimen	Channel 2 visualization method			Visualization method (example: GFP )
Specimen	Channel 2 entity			Entity visualized (example: MAP1LC3B )
Specimen	Channel 2 label			Label used for entity (example:GFP-LC3) Best practice to use similar label as your CP-pipeline
Specimen	Channel 2 id			sequential id of channel order in your image
Specimen	Channel 3 visualization method			Visualization method (example: PI staining )
Specimen	Channel 3 entity			Entity visualized (example: Death cell DNA )
Specimen	Channel 3 label			Label used for entity (example:PI) Best practice to use similar label as your CP-pipeline
Specimen	Channel 3 id			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

#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 '#'.
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Plate	Well	Treatment	Dose	DoseUnit	CellLine	TimeTreatment	ReplID	remarks