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_104342_220	B19	S2328	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	D02	S2336	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	N20	S2350	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	K02	S2357	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	I18	S2369	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	L22	S2373	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	M18	S2374	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	L11	S2376	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	K13	S2381	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	H14	S2393	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	I12	S2422	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	N07	S2442	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	K09	S2443	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	L03	S2446	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	H03	S2451	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	C12	S2452	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	H11	S2454	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	H05	S2455	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	N23	S2456	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	C18	S2457	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	G23	S2458	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	J20	S2459	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	C03	S2461	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	D17	S2467	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	B22	S2470	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	I04	S2471	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	M09	S2473	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	F02	S2475	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	G19	S2476	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	M15	S2479	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	F12	S2481	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	C15	S2484	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	L08	S2485	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	O03	S2486	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	I21	S2487	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	L12	S2489	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	M04	S2491	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	J08	S2493	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	C02	S2494	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	O02	S2496	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	E17	S2497	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	I05	S2499	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	J23	S2500	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	D21	S2502	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	L05	S2504	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	G14	S2506	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	E08	S2508	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	H04	S2509	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	I02	S2510	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	C09	S2511	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	C05	S2512	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	J14	S2516	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	D03	S2517	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	D08	S2519	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	D11	S2521	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	J05	S2522	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	D05	S2524	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	J19	S2529	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	L06	S2534	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	J22	S2535	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	O09	S2537	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	F20	S2538	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	D10	S2541	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	D15	S2542	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	L15	S2543	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_104342_220	G08	Tunicamycin_c1a	0.15	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_104342_220	I17	Tunicamycin_c2a	0.34	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_104342_220	O17	Tunicamycin_c3a	0.77	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_104342_220	G16	Tunicamycin_c4a	1.73	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_104342_220	J15	Tunicamycin_c5a	3.9	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_104342_220	G02	Tunicamycin_c6a	8.77	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_104342_220	E11	Tunicamycin_c7a	19.73	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_104342_220	N18	Tunicamycin_c8a	44.4	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_104342_220	D22	Tunicamycin_c1b	0.15	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_104342_220	N03	Tunicamycin_c2b	0.34	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_104342_220	C13	Tunicamycin_c3b	0.77	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_104342_220	F13	Tunicamycin_c4b	1.73	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_104342_220	K03	Tunicamycin_c5b	3.9	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_104342_220	O22	Tunicamycin_c6b	8.77	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_104342_220	E13	Tunicamycin_c7b	19.73	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_104342_220	O23	Tunicamycin_c8b	44.4	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_104342_220	J04	Mitomycin_1	150	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_104342_220	O12	Mitomycin_2	150	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_104342_220	G21	Mitomycin_3	150	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_104342_220	E02	Mitomycin_4	150	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_104342_220	M05	DMSO_1	0.5	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_104342_220	N14	DMSO_2	0.5	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_104342_220	N15	DMSO_3	0.5	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_104342_220	G06	DMSO_4	0.5	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_104342_220	I20	DMSO_5	0.5	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_104342_220	E20	DMSO_6	0.5	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_104342_220	O18	DMSO_7	0.5	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_104342_220	O20	DMSO_8	0.5	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_114723_397	K11	S2550	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	D15	S2552	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	K07	S2553	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	D02	S2555	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	F18	S2557	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	I10	S2559	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	N21	S2561	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA