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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20190221-p7-FDA5	K07	S8034	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	O11	S8041	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	M03	S8048	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	M15	S8051	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	E18	S8057	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	E17	S8064	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	N03	S8067	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	F21	S8078	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	E13	S8103	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	H20	S8116	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	B17	S8134	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	G19	S8135	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	L21	S8138	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	G03	S8146	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	C10	S8183	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	N13	S8195	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	F13	S8205	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	N08	S8219	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	G22	S8241	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	L05	S8266	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	H03	S8294	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	G07	S8432	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	F17	S8558	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	J20	S8565	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	N23	S8594	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	J02	S1011	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	F18	S1018	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	J06	S1023	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	H09	S1026	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	I07	S1042	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	H18	S1119	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	C23	S1148	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	J14	S1230	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	E07	S1238	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	M09	S1258	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	O23	S1357	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	G21	S1390	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	H13	S1431	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	B20	S1457	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	I06	S1491	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	N06	S1500	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	O22	S1540	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	M02	S1630	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	H08	s1635	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	F06	S1688	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	N22	S1714	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	L11	S1725	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	B06	S1737	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	D07	S1754	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	B18	S1799	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	L15	S1805	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	I04	S1811	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	E22	S1813	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	G17	S1823	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	F09	S1827	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	J03	s1835	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	M13	S1855	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	J08	S1903	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	B21	S1940	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	I15	S2044	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	L12	S2059	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	L14	S2067	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	F04	S2087	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	K17	S2090	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	L03	S2126	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	G18	S2128	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	K15	S2180	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	O15	S2460	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	H17	S2482	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	I23	S2505	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	M17	S2525	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	F20	S2528	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	E10	S2536	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	C04	S2551	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	D19	S2556	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	I13	S2567	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	F11	S2741	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	M04	S2830	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	L17	S2875	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	O19	S3012	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	L22	S3015	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	K13	S3061	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	I12	S3066	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	H07	S3170	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	H06	S3639	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	N20	S3647	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	K11	S4081	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	C13	S4106	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	J17	S4113	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	L20	S4118	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	J09	S4171	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	O14	S4210	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	F03	S4502	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	E16	S4538	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	O05	S4633	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	K18	S4650	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	D15	S4661	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	C05	S4668	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	I21	S4675	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA
20190221-p7-FDA5	E03	S4734	50	uM	HepG2-CHOP-GFP	24	Rep1	FDA