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	K08	S4012	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	K21	S4014	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	D22	S4016	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	H22	S4017	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	L06	S4019	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	J23	S4020	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	O10	S4021	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	N11	S4022	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	M22	S4023	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	O16	S4025	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	G16	S4026	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	C10	S4031	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	O07	S4034	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	F16	S4035	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	F05	S4037	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	M06	S4038	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	G03	S4040	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	J03	S4041	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	E18	S4042	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	D23	S4043	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	C20	S4044	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	H13	S4045	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	B04	S4046	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	K16	S4048	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	J20	S4049	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	N14	S4050	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	M09	S4051	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	K19	S4053	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	I20	S4054	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	E04	S4056	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	J04	S4058	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	B19	S4059	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	O23	S4060	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	H03	S4061	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	O22	S4062	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	B20	S4063	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	L03	S4064	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	N17	S4068	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	M19	S4070	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	F14	S4071	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	M21	S4072	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	H02	S4073	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	J14	S4074	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	N19	S4075	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	N06	S4077	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	C18	S4078	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	N02	S4079	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	K15	S4080	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	F21	S4082	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	E15	S4083	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	K12	S4084	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	F09	S4086	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	G09	S4088	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	N10	S4089	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	D13	S4090	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	E10	S4091	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	C17	S4092	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	M02	S4095	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	E05	S4097	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	J21	S4098	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	N15	S4099	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	L17	S4100	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	O17	S4101	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	E20	S4102	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	M05	S4105	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	H14	S4110	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	E03	S4111	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	C16	S4112	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	G20	S4114	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	N04	S4119	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	J05	S4120	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	I15	S4122	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_114723_397	D04	Tunicamycin_c1a	0.15	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_114723_397	H09	Tunicamycin_c2a	0.34	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_114723_397	N23	Tunicamycin_c3a	0.77	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_114723_397	F12	Tunicamycin_c4a	1.73	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_114723_397	D19	Tunicamycin_c5a	3.9	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_114723_397	M14	Tunicamycin_c6a	8.77	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_114723_397	F20	Tunicamycin_c7a	19.73	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_114723_397	H20	Tunicamycin_c8a	44.4	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_114723_397	M04	Tunicamycin_c1b	0.15	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_114723_397	M03	Tunicamycin_c2b	0.34	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_114723_397	F10	Tunicamycin_c3b	0.77	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_114723_397	N22	Tunicamycin_c4b	1.73	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_114723_397	L04	Tunicamycin_c5b	3.9	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_114723_397	L23	Tunicamycin_c6b	8.77	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_114723_397	I07	Tunicamycin_c7b	19.73	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_114723_397	D12	Tunicamycin_c8b	44.4	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_114723_397	M20	Mitomycin_1	150	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_114723_397	G08	Mitomycin_2	150	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_114723_397	E09	Mitomycin_3	150	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_114723_397	F23	Mitomycin_4	150	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_114723_397	H07	DMSO_1	0.5	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_114723_397	B05	DMSO_2	0.5	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_114723_397	D16	DMSO_3	0.5	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_114723_397	B17	DMSO_4	0.5	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_114723_397	L21	DMSO_5	0.5	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_114723_397	L14	DMSO_6	0.5	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_114723_397	C12	DMSO_7	0.5	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_114723_397	D21	DMSO_8	0.5	uM	HepG2-CHOP-GFP	24	Rep2	Control