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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

red font - indicates potential for CT code lists
green font - links to other domains

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title	Study 123, Report Table

The following shows the tabulated data as shown in the report for this study:

Neutral Red Cytotoxicity Assay Results (Relative Absorbance Data)
Run-Port Number	Sample ID	Smoke Fraction	Replicate Number	Plate Number	Well Number	Relative Assay Plate Absorbance Readings
						Cigarette Smoke Condensate (µg/mL)								SLS (µg/mL)
						10	50	75	100	120	140	160	200	110	200
1-1	030001	A	1	1	1	100	83.0	56.7	29.5	13.0	8.57	4.44	1.76	13.7	0.547
1-1	030001	A	1	1	2	107	77.7	65.7	30.2	15.6	9.79	5.41	2.49	8.09	0.791
1-1	030001	A	1	1	3	98.6	77.4	57.7	35.8	8.09	7.36	3.22	0.791	6.38	0.061
1-1	030001	A	1	1	4	94.9	81.5	38.2	31.2	7.60	5.17	3.22	0.791	5.17	0.304
1-1	030001	A	1	1	5	111	78.1	64.5	32.9	8.82	5.90	2.74	1.28	10.3	0.547
1-1	030001	A	1	1	6	96.6	76.2	48.0	26.8	7.84	4.20	2.74	1.52	8.09	4.93
1-1	030001	A	1	1	7	105	77.9	58.2	28.3	8.09	4.68	1.76	0.547	8.57	1.76
1-1	030001	A	1	1	8	95.2	74.0	47.2	24.4	8.57	3.71	3.47	0.304	11.2	0.791
Average						101	78.2	54.5	29.9	9.70	6.17	3.37	1.19	8.94	1.22
Std. Dev.						6	2.9	9.4	3.6	2.95	2.19	1.12	0.72	2.72	1.58
Coeff. Var.						5.8	3.6	17.2	11.9	30.4	35.5	33.1	61.0	30.5	129.9
1-1	030001	A	1	2	1	93.4	74.0	56.0	35.1	11.8	8.70	5.10	1.98	5.34	1.02
1-1	030001	A	1	2	2	102	75.2	53.3	35.1	11.8	7.74	5.58	3.66	5.34	1.02
1-1	030001	A	1	2	3	107	79.0	55.0	26.5	10.1	6.06	3.66	1.74	7.02	0.780
1-1	030001	A	1	2	4	104	80.2	55.3	29.8	8.94	3.90	3.66	1.50	6.30	0.780
1-1	030001	A	1	2	5	101	75.7	54.1	26.7	4.86	4.38	1.26	1.02	6.30	1.02
1-1	030001	A	1	2	6	110	85.7	67.7	26.0	5.34	4.62	3.42	1.50	6.30	0.540
1-1	030001	A	1	2	7	104	77.8	64.9	27.7	8.22	3.18	2.46	1.02	6.30	0.780
1-1	030001	A	1	2	8	103	71.6	58.9	25.5	9.42	4.14	3.90	1.26	4.38	0.780
Average						103	77.4	58.1	29.0	8.82	5.34	3.63	1.71	5.91	0.840
Std. Dev.						5	4.4	5.3	4.0	2.63	1.97	1.37	0.86	0.83	0.170
Coeff. Var.						4.6	5.6	9.2	13.6	29.8	36.9	37.6	50.0	14.1	20.2

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title	ts.xpt (trial summary, study level parameters)

Assumption: The intent of this dataset is to provide a summary of trial (study) information. This is not subject-level data.
Assumption: Study A Trial (study) can have more than one assay type
Assumption: ASSAYID value of ALL means indicates that 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)

NRUNRUNRUNRUNRUNRUNRUNRUNRUNRUNRUNRUNRUNRUNIH Publication 07-4519NRU200611NRUNRUNeutral Red UptakeNRUSalmonella enterica NRUSalmonella enterica entericaNormal Human KeratinocyteTraditional combustible 1-1030001SMKFRCA1

Row	STUDYID	ASSAYID	DOMAIN	TSSEQ	TSGRPID	TSPARMCD	TSPARM	TSVAL	TSVALNF
1	123	ALL	TS	1		GLPTYP	Good Laboratory Practice Type	FDA
2	123	ALL	TS	2		GLPTYP	Good Laboratory Practice Type	OECD
3	123	ALL	TS	1		STSTDTC	Study Start Date	2022-05-25
4	123	ALL	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	ALL	TS	1		SNDIGVER	SEND Implementation Guide Version	TOBACCO IMPLEMENTATION GUIDE VERSION 1.0
6	123	ALL	TS	1		SNDCTVER	SEND Controlled Terminology Version	SEND Terminology 2021-09-30
7	123	ALL	TS	1		SSPONSOR	Sponsor Organization	Example Sponsor Inc.
8	123	ALL	TS	1		SPREFID	Sponsor's Study Reference ID		NOT APPLICABLE
9	123	ALL	TS	1	1	TSTFNAM	Test Facility Name	Example Tox Lab Name
10	123	ALL	TS	1	1	TSTFLOC	Test Facility Location	10 Somewhere Street, Montgomery, AL 10000
11	123	ALL	TS	1	1	TFCNTRY	Test Facility Country	USA
...	123	ALL	TS	1	1	STDIR	Study Director	Dr. R. Smith
	123	ALL	TS	1		GLPFL	GLP Flag	Y
	123	MNvit	TS	1		ASTD	Assay Standard	OECD Test No.	487
	123	MNvit	TS	1		ASTDV	Assay Standard Version	2016-07-	29
	123	MNvit	TS	1		SSTYP	Study Type	GENOTOXICITY IN VITRO
	123	MNvit	TS	1		SSSTYP	Study Sub Type	In Vitro	Micronucleus
	123	MNvit	TS	1		SPECIES	Species	Homo Sapiens
	123	MNvit	TS	1	STRAIN	Strain/Substrain		??	Test System?	TK6 Lymphoblastoid Suspension Cells
	123	NRU	TS	1	??	Test System??		ASTD	Assay Standard	NIH Publication No. 07-4519
	123	NRU	TS	1	REGIME	Smoking Regime		ASTDV	Assay Standard Version	2006-11
	123	NRU	TS	1	RUNPRT	run-port number?? (always same for whole assay?)		SSTYP	Study Type	GENOTOXICITY IN VITRO
	123	NRU	TS	1	SMPLID	Sample ID		SSSTYP	Study Sub Type	In Vitro Neutral Red Uptake
	123	NRU	TS	1		SPECIES	Smoke Fraction	Species	Salmonella enterica
	123	NRU	TS	1	REPNUM	Replicate Number		??	Test System??	Normal Human Keratinocyte

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title	tx.xpt (trial sets)

During CT definition/reviews will decide appropriate TXPARM and TXVAL; Treatment duration may be controlled; For now, we just include good example values based on our experienceTXPARMCD/TXPARM = TSPARMCD/TSPARM
Assumption: The Trial Sets (TX) domain provides the list of distinct sets of subjects having different experimental factors, treatment factors, inherent characteristics, or distinct sponsor designations as specified in the trial design.
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)
- needs to be allowed to vary down to the well level / result level

8PRODUCT2A

Row	STUDYID	ASSAYID	DOMAIN	SETCD	SET (what sponsor calls it)	TXSEQ	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			1			STRAIN	Strain/Substrain	Salmonella enterica enterica
	123	NRU		1			REGIME	Smoking Regime	Traditional combustible
	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	1	RUN	Assay run number (how is this different from REPNUM)	1
	123	NRU		1			PORT	Port ID	1
	123	NRU		1			SMPLID	Sample ID	030001
	123	NRU		1			SMKFRC	Smoke Fraction	A
	123	NRU		1			REPNUM	Replicate Number	1
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	10-	H
	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
	123	MNvit	TX	A1			METACT	Metabolic Activation (should there be two parms? Presence, type)?	+S9
	123	MNvit	TX	A1			TRTDRTRG	Treatment Duration target. (how do we show 3-6 hour range? start/end, target and tolerance?, one text field not-analyzable)	3
	123	MNvit	TX
	123	MNvit	TX				TRTDRTOL	Treatment Duration Tolerance
	123	MNvit	TX				TRTDURU	Treatment Duration Unit (this is for both TRTDURT, TRTDURTOL)	H
	123	MNvit	TX				INTRVN	name of the intervention article	Bleomycin or Cyclophosphamid A
	123	MNvit	TX				ITVTYPE	type of intervention article	choices of values: product; negative control; positive control
	123	MNvit	TX	A1			ITVCONC	Concentration of i a	0
	123	MNvit	TX	A1			ITVCONCU	Concentration Unit	ug/ml

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title	gt.xpt (similar to LB)

Image Added

Row	STUDYID	ASSAYID	DOMAIN	TXCD	GTSEQ	GTTESTCD	GTTEST	GTCELLEV (cells evaluated)	GTORRES	GTORRESU	GTSTRESC	GTSTRESN	GTSTRESU	GTDTC
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
1	123	MNvit	GT	A2	1	RICC	Relative Increase in Cell Count	134	15.7	%	15.7	15.7	%	2022-05-25
2	123	MNvit	GT	A2	2	RCC	Relative Cell Count	134	13.0	%	13.0	13.0	%	2022-05-25
3	123	MNvit	GT	A2	3	RPD	Relative Population Doubling	134	7.9	%	7.9	7.9	%	2022-05-25
4	123	MNvit	GT	A2	4	MNCELLS	Micronucleated Cells	3266	20	Cells	20	20	Cells	2022-05-25
5	123	MNvit	GT	A2	5	MNCELLS	Micronucleated Cells	2190	17	Cells	17	17	Cells	2022-05-25
6	123	MNvit	GT	A2	6	MNCELLS	Micronucleated Cells	2758	13	Cells	13	13	Cells	2022-05-25
7	123	MNvit	GT	A2	7	MNCELLS	Micronucleated Cells	2714	21	Cells	21	21	Cells	2022-05-25
8	123	MNvit	GT	A2	8	AVGREL	Average Relative MN Frequency		0.66	%	0.66	0.66	%	2022-05-25
9	123	MNvit	GT	A1	1	RICC	Relative Increase in Cell Count	154	0	%	0	0	%	2022-05-25
10	123	MNvit	GT	A1	2	RCC	Relative Cell Count	154	0	%	0	0	%	2022-05-25
11	123	MNvit	GT	A1	3	RPD	Relative Population Doubling	154	0	%	0	0	%	2022-05-25
12	123	MNvit	GT	A1	4	MNCELLS	Micronucleated Cells	3266	15	Cells	15	15	Cells	2022-05-25
13	123	MNvit	GT	A1	5	MNCELLS	Micronucleated Cells	2190	13	Cells	13	13	Cells	2022-05-25
14	123	MNvit	GT	A1	6	MNCELLS	Micronucleated Cells	2758	17	Cells	17	17	Cells	2022-05-25
15	123	MNvit	GT	A1	7	MNCELLS	Micronucleated Cells	2714	12	Cells	12	12	Cells	2022-05-25
16	123	MNvit	GT	A1	8	AVGREL	Average Relative MN Frequency		0.57	%	0.57	0.57	%	2022-05-25

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Old Version 7

New Version 8

Key

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)

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)