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_125532_791	F18	DMSO_2	0.5	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_125532_791	F11	DMSO_3	0.5	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_125532_791	J08	DMSO_4	0.5	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_125532_791	D16	DMSO_5	0.5	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_125532_791	N10	DMSO_6	0.5	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_125532_791	M08	DMSO_7	0.5	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_125532_791	H10	DMSO_8	0.5	uM	HepG2-CHOP-GFP	24	Rep2	Control
20190215_125532_791	L19	Empty_1	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_125532_791	C14	Empty_2	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	E19	S1001	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	I12	S1014	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	N14	S1039	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	I03	S1060	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	C19	S1091	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	J15	S1130	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	I16	S1156	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	M11	S1188	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	F05	S1196	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	H20	S1207	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	J03	S1229	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	D19	S1250	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	O19	S1261	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	J16	S1282	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	E17	S1294	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	M08	S1324	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	N22	S1333	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	M14	S1356	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	J05	S1374	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	I19	S1385	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	O04	S1386	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	L18	S1398	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	K04	S1409	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	F04	S1437	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	G19	S1452	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	D23	S1469	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	H21	S1488	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	K14	S1509	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	E02	S1538	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	K22	S1569	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	C08	S1610	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	L09	S1620	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	D22	S1628	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	I14	S1641	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	G15	S1651	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	C18	S1665	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	L19	S1677	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	K17	S1691	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	G23	S1704	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	K16	S1715	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	I15	S1716	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	I10	S1729	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	J20	S1739	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	F10	S1750	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	L12	S1768	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	D02	S1778	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	N10	S1793	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	O08	S1825	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	B08	S1837	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	K12	S1856	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	M07	S1894	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	L21	S1905	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	D09	S1916	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	C13	S1937	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	K15	S1960	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	F20	S1975	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	L08	S1992	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	K11	S2016	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	N02	S2030	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	C11	S2041	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	D13	S2042	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	D20	S2055	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	E09	S2066	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	O22	S2082	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	O11	S2098	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	L03	S2109	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	O07	S2121	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	E18	S2151	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	H23	S2179	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	K06	S2226	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	M19	S2344	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	O16	S2388	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	K10	S2453	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	F11	S2466	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	J23	S2480	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	F17	S2492	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	L07	S2503	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	G12	S2515	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	N13	S2533	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	D05	S2547	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	M15	S7077	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	D03	S7083	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	C23	S7128	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	I18	S7155	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	D08	S7156	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	G09	S7157	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	I05	S7158	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	F19	S7161	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	E14	S7179	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	M06	S7205	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_140000_820	O12	S7215	50	uM	HepG2-CHOP-GFP	24	Rep2	FDA