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_150544_094	B15	Empty_16	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	B21	Empty_17	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	I15	Empty_18	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	C13	Empty_19	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	G09	Empty_20	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	O18	Empty_21	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	B13	Empty_22	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	C22	Empty_23	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	J17	Empty_24	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	L16	Empty_25	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	E02	Empty_26	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	N22	Empty_27	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	J15	Empty_28	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	K03	Empty_29	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	K22	Empty_30	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	G06	Empty_31	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	I07	Empty_32	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	C03	Empty_33	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	D15	Empty_34	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	M09	Empty_35	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	B18	Empty_36	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	N08	Empty_37	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	B23	Empty_38	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	O19	Empty_39	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	C06	Empty_40	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	H05	Empty_41	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	B04	Empty_42	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	J18	Empty_43	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	F14	Empty_44	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	M08	Empty_45	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	F02	Empty_46	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	J19	Empty_47	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	F13	Empty_48	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	F06	Empty_49	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	J02	Empty_50	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	K08	Empty_51	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	D10	Empty_52	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	D21	Empty_53	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	N19	Empty_54	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	D19	Empty_55	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	M05	Empty_56	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	H16	Empty_57	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	M17	Empty_58	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	N11	Empty_59	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	D23	Empty_60	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	E10	Empty_61	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	O22	Empty_62	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	H04	Empty_63	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	C16	Empty_64	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	F22	Empty_65	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	M12	Empty_66	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	N17	Empty_67	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	O02	Empty_68	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	C11	Empty_69	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	D07	Empty_70	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	G05	Empty_71	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	L11	Empty_72	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	F12	Empty_73	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	J13	Empty_74	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	J11	Empty_75	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	F03	Empty_76	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	O11	Empty_77	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	M15	Empty_78	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	D04	Empty_79	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	I02	Empty_80	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	H08	Empty_81	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	O05	Empty_82	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	G14	Empty_83	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	L17	Empty_84	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	D14	Empty_85	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	C18	Empty_86	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	H21	Empty_87	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	C02	Empty_88	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	M11	Empty_89	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	G02	Empty_90	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	I03	Empty_91	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	H09	Empty_92	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	D06	Empty_93	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	H10	Empty_94	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	H12	Empty_95	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	F18	Empty_96	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	L12	Empty_97	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	N02	Empty_98	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	L10	Empty_99	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	J04	Empty_100	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	G10	Empty_101	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	B09	Empty_102	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	O15	Empty_103	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	I09	Empty_104	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	K16	Empty_105	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	G08	Empty_106	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	N03	Empty_107	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	M03	Empty_108	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	L13	Empty_109	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	N23	Empty_110	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	B06	Empty_111	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	I06	Empty_112	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	O08	Empty_113	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	E08	Empty_114	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA
20190215_150544_094	H17	Empty_115	0.001	uM	HepG2-CHOP-GFP	24	Rep2	FDA