InVitro Neutral Red Cytotoxicity Assay Results Example 1 revisited!

This example shows trial design and results data for in vitro Neutral Red Cytotoxicity Assay, Relative Absorbance.

Neutral Red Uptake Assay for Mainstream Tobacco Smoke: The neutral red uptake assay provides a quantitative estimation of the number of viable cells in a culture. It is one of the most used cytotoxicity tests with many biomedical and environmental applications. It is based on the ability of viable cells to incorporate and bind the supravital dye neutral red in the lysosomes.

Note that Variable Names and Domain abbreviations may change (have not been checked against existing and are not vetted)

Red Font = has/should have CT

Grey-shaded cells = ignore for now (until we model other tests)

Because a study contains one or more Assays, we have both: STUDYID and ASSAYID

Assumption: Study can have more than one assay type
Assumption: ASSAYID value of ALL means it applies to all assays in the study
Replaced the ASSAYID values of MNT with MNvit (term used in OECD #487) - is this better? This is not a controlled term so we can use anything but what we use in our IG examples are often used in industry implementations so we should use realistic and best practice values as much as possible.
BLEO & CPA - are positive controls, should this be included/where is this captured? — in results for the record / row?
Where is TK6 cell type? is this test system (see below)

Row	STUDYID	ASSAYID	DOMAIN	TSSEQ	TSGRPID	TSPARMCD	TSPARM	TSVAL	TSVALNF
1	123	NRU	TS	1		GLPTYP	Good Laboratory Practice Type	FDA
2	123	NRU	TS	2		GLPTYP	Good Laboratory Practice Type	OECD
3	123	NRU	TS	1		STSTDTC	Study Start Date	2022-05-25
4	123	NRU	TS	1		STITLE	Study Title	Determination of the in vitro genotoxicity potential of 10 tobacco products in both the in vitro Micronucleus Assay and the in vitro Neutral Red Uptake
5	123	NRU	TS	1		SNDIGVER	SEND Implementation Guide Version	TOBACCO IMPLEMENTATION GUIDE VERSION 1.0
6	123	NRU	TS	1		SNDCTVER	SEND Controlled Terminology Version	SEND Terminology 2021-09-30
7	123	NRU	TS	1		SSPONSOR	Sponsor Organization	Example Sponsor Inc.
8	123	NRU	TS	1		SPREFID	Sponsor's Study Reference ID		NOT APPLICABLE
9	123	NRU	TS	1	1	TSTFNAM	Test Facility Name	Example Tox Lab Name
10	123	NRU	TS	1	1	TSTFLOC	Test Facility Location	10 Somewhere Street, Montgomery, AL 10000
11	123	NRU	TS	1	1	TFCNTRY	Test Facility Country	USA
...	123	NRU	TS	1	1	STDIR	Study Director	Dr. R. Smith
	123	NRU	TS	1		GLPFL	GLP Flag	Y
	123	NRU	TS	1		ASTD	Assay Standard	NIH Publication No. 07-4519
	123	NRU	TS	1		ASTDV	Assay Standard Version	2006-11
	123	NRU	TS	1		SSTYP	Study Type	GENOTOXICITY IN VITRO
	123	NRU	TS	1		SSSTYP	Study Sub Type	In Vitro Neutral Red Uptake
	123	NRU	TS	1		SPECIES	Species	Salmonella enterica
	123	NRU	TS	1		STRAIN	Strain/Substrain	Salmonella enterica enterica
	123	NRU	TS	1		??	Test System??	Normal Human Keratinocyte
	123	NRU	TS	1		REGIME	Smoking Regime	Traditional combustible
	123	NRU	TS	1		RUNPRT	run-port number?? (always same for whole assay?)	1-1
	123	NRU	TS	1		SMPLID	Sample ID	030001
	123	NRU	TS	1		SMKFRC	Smoke Fraction	A
	123		TS	1		REPNUM	Replicate Number	1

During CT definition/reviews will decide appropriate TXPARM and TXVAL; For now, we just include good example values based on our experience
TXPARMCD/TXPARM = TSPARMCD/TSPARM

Row	STUDYID	ASSAYID	DOMAIN	SETCD	SET (what sponsor calls it)	TXPARMCD	TXPARM	TXVAL
1	123	NRU	TX	1-1-A (plate-col-row in the 96-well plate)	CSC-10 (through SLS-200)	PLATENUM. (e.g., 1 or 2)	1	1
2	123	NRU	TX	1-1-A	CSC-10	WELLNUM (e.g., 1-A through 10-H)	Number representing the location of the well in the 96-well plate	1-A
3	123	NRU	TX	1-1-A	CSC-10	INTRVN	name of the intervention article	Cigarette Smoke Condensate
4	123	NRU	TX	1-1-A	CSC-10	ITVTYPE (CT e.g, Product, positive control, negative control)	type of intervention article	PRODUCT
5	123	NRU	TX	1-1-A	CSC-10	ITVCONC	intervention concentration	10
6	123	NRU	TX	1-1-A	CSC-10	ITVCONCU	intervention unit	ug/ml
7	123	NRU	TX	1-1-B	CSC-10	PLATENUM	Plate number	1
8	123	NRU	TX	1-1-B	CSC-10	WELLNUM	Number representing the location of the well in the 96-well plate	2-A
9	123	NRU	TX	1-1-B	CSC-10	INTRVN	name of the intervention article	Cigarette Smoke Condensate
10	123	NRU	TX	1-1-B	CSC-10	ITVTYPE	type of intervention article	PRODUCT
11	123	NRU	TX	1-1-B	CSC-10	ITVCONC	intervention concentration	10
12	123	NRU	TX	1-1-B	CSC-10	ITVCONCU	intervention unit	ug/ml
...				...
	123	NRU	TX	1-10-H	SLS-10	PLATENUM	Plate number	1
	123	NRU	TX	1-10-H	SLS-10	WELLNUM	Number representing the location of the well in the 96-well plate	10-H
	123	NRU	TX	1-10-H	SLS-10	INTRVN	name of the intervention article	sodium laurel sulfate
	123	NRU	TX	1-10-H	SLS-10	ITVTYPE	type of intervention article	POSITIVE CONTROL
	123	NRU	TX	1-10-H	SLS-10	ITVCONC	intervention concentration	200
	123	NRU	TX	1-10-H	SLS-10	ITVCONCU	intervention unit	ug/ml
...				...
	123	NRU	TX	2-10-H	SLS-10	PLATENUM	Plate number	2
	123	NRU	TX	2-10-H	SLS-10	WELLNUM	Number representing the location of the well in the 96-well plate	2-A
	123	NRU	TX	2-10-H	SLS-10	INTRVN	name of the intervention article	sodium laurel sulfate
	123	NRU	TX	2-10-H	SLS-10	ITVTYPE	type of intervention article	POSITIVE CONTROL
	123	NRU	TX	2-10-H	SLS-10	ITVCONC	intervention concentration	200
	123	NRU	TX	2-10-H	SLS-10	ITVCONCU	intervention unit	ug/ml

Row	STUDYID	ASSAYID	DOMAIN	TXCD	GTSEQ	GTTESTCD	GTTEST	GTORRES	GTORRESU	GTSTRESC	GTSTRESN	GTSTRESU
1	123	NRU	GT	1-1-A	1	RELABS	Relative Absorbance Reading	100	ug/ml	100	100	ug/ml
2	123	NRU	GT	1-1-B	1	RELABS	Relative Absorbance Reading	107	ug/ml	100	100	ug/ml
3	123	NRU	GT	1-1-C	1	RELABS	Relative Absorbance Reading	98.6	ug/ml	100	100	ug/ml
54	123	NRU	GT	1-1-D	1	RELABS	Relative Absorbance Reading	94.9	ug/ml	100	100	ug/ml
6	123	NRU	GT	1-1-E	1	RELABS	Relative Absorbance Reading	111
7	123	NRU	GT	1-1-F	1	RELABS	Relative Absorbance Reading	96.9
8	123	NRU	GT	1-1-G	1	RELABS	Relative Absorbance Reading	105
9	123	NRU	GT	1-1-H	1	RELABS	Relative Absorbance Reading	95.2
10	123	NRU	GT	1-2-A	1	RELABS	Relative Absorbance Reading	83.0
11	123	NRU	GT	1-2-B	1	RELABS	Relative Absorbance Reading	77.7
...				...
80	123	NRU	GT	1-10-H	1	RELABS	Relative Absorbance Reading	0.791
...				...
160	123	NRU	GT	2-10-H	1	RELABS	Relative Absorbance Reading	0.780

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Note that Variable Names and Domain abbreviations may change (have not been checked against existing and are not vetted)

Red Font = has/should have CT

Grey-shaded cells = ignore for now (until we model other tests)

Because a study contains one or more Assays, we have both: STUDYID and ASSAYID

SET (what sponsor calls it)

(plate-col-row in the 96-well plate)

(through SLS-200)

PLATENUM. (e.g., 1 or 2)

WELLNUM (e.g., 1-A through 10-H)

(CT e.g, Product, positive control, negative control)