Example template HepG2 CHOP-GFP

Selected Cell

Cell:

Value:

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	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.

# 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

# 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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20190215_114723_397	J12	S2565	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	N16	S2566	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	K23	S2569	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	B23	S2570	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	E13	S2573	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	B18	S2574	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	D09	S2576	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	H19	S2579	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	B15	S2581	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	K04	S2582	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	E02	S2583	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	K20	S2584	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	E14	S2585	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	D18	S2586	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	G18	S2593	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	N03	S2594	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	N18	S2596	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	I17	S2597	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	B08	S2599	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	I21	S2601	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	E19	S2602	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	I14	S2605	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	I02	S2606	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	L05	S2607	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	B14	S2608	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	F04	S2610	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	L08	S2613	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	K22	S2614	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	B10	S2625	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	N13	S2658	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	J15	S2664	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	D07	S2665	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	H23	S2667	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	H05	S2673	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	G23	S2680	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	G14	S2721	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	O21	S2727	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	K18	S2730	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	O18	S2736	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	I05	S2753	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	G21	S2755	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	F08	S2757	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	C19	S2768	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	N05	S2787	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	B16	S2789	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	O05	S2790	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	J07	S2791	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	B06	S2792	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	C15	S2794	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	B02	S2803	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	C14	S2807	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	K17	S2814	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	L19	S2823	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	F11	S2851	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	D03	S2853	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	C23	S2868	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	J06	S2900	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	D20	S2902	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	O19	S2907	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	M15	S2922	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	E16	S2925	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	E21	S3000	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	L02	S3001	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	G22	S3002	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	J17	S3005	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	C08	S3008	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	H21	S3017	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	H17	S3018	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	O20	S3019	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	H16	S3021	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	I12	S3023	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	I22	S3024	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	B09	S3027	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	N07	S3031	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	L11	S3032	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	K06	S3033	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	F07	S3034	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	J02	S3036	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	H10	S3037	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	I11	S3038	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	O08	S3043	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	L15	S3045	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	G06	S3046	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	I03	S3047	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	I06	S3052	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	J08	S3053	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	K13	S3054	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	F06	S3057	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	F13	S3059	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	O14	S3060	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	F22	S3062	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	G15	S3064	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	I18	S3067	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	L22	S3070	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	O06	S3073	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	M08	S3075	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	J13	S3076	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	K03	S3077	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	H08	S3079	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	M11	S3080	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA