This is an example showing trial design and results data of Study #123 for the determination of the in vitro genotoxicity potential of 10 tobacco products in the in vitro Micronucleus Assay

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

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

Assumption: The intent of this dataset is to provide a summary of trial (study) information. This is not subject-level data.
Assumption: A Trial (study) can have more than one assay type
Assumption: ASSAYID value of ALL indicates that it applies to all assays in the study
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
For the items highlighted in orange - what is the lowest level where this could vary? e.g. at the level of a well in a 96-well plate, or a slide vs. assay level vs. product level
- Smoke Regime needs to be allowed to vary down to the well level / result level
- run - also at result level
- port - (smoking product on the machine, you assign a run number or port-number for multiple replicates depending on linear vs. rotary machines; machine bias), needs to be allowed to vary down to the well level / result level)
- replicate - (e.g., multiple samples from one vial), could be a replicate per exposure (e.g., 3 plates, multiple analyses for exposure)
- sample ID - typically a unique number assigned (at CRO) or supplied by sponsor - result level
- Smoke fraction - result level (e.g.tpm particulate vs. gas gvp)

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		??	Test System?	TK6 Lymphoblastoid Suspension Cells
	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		??	Test System??	Normal Human Keratinocyte

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 experience
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.

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
	123	NRU		1		STRAIN	Strain/Substrain	Salmonella enterica enterica
	123	NRU		1		REGIME	Smoking Regime	Traditional combustible
	123	NRU		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

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

Below this line are domains we currently do not see a use for

(Do we need this? a single element (treatment)?)

Row	STUDYID	ASSAYID	DOMAIN	ETCD	ELEMENT

(Do we need this? one arm for each trial set?)

Row	STUDYID	ASSAYID	DOMAIN	ARMCD	ARM	TAETORD	ETCD	ELEMENT

Not needed.

Row

STUDYID

DOMAIN

ENID (Entity ID)

RICC

RCC

RPD

Sum of cell ev.

Cells with MN

SMKFID (Smoke Fraction)

REPLCTID

(Replicate Number)

PLATEID (Plate ID)

COLID

(Column number)

ROWID (Row number)

SETCD (Set Code, TX)

RFSTDTC

RFENDTC

RFXSTDTC

RFXENDTC

RFCSTDTC

RFCENDTC

ARMCD

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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)

Below this line are domains we currently do not see a use for

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In vitro Micronucleus Assay Example 1

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)

Below this line are domains we currently do not see a use for