SEND Example.In vitro Neutral Red Cytotoxicity Assay

This example shows a report table, trial design, TOBA-78 - Getting issue details... STATUS and results data for the in vitro neutral red uptake (NRU) cytotoxicity assay TOBA-333 - Getting issue details... STATUS in example study 123.

The following shows example data for study 123 in a report table. This report includes summary statistics (i.e., average, standard deviation, coefficient variation) for each plate and an EC50 TOBA-593 - Getting issue details... STATUS value for the entire assay. In the table below, the light grey shading for plate 1 are values from wells that do not contain the NHK cells. The dark grey shading represents the column and row location within the 96-well plate, and in this example the applicant chose to use these column and row locations to assign their REFID values in the RELREF dataset and GT dataset.

For brevity, the datasets in this example are not comprehensive but are intended to demonstrate a range of proper use.

Neutral Red Cytotoxicity Assay Results (Relative Absorbance Data)
	Sample ID	Smoke Regime	Replicate Number	Plate Number			Relative Assay Plate Absorbance Readings
							Cigarette Smoke Condensate (µg/mL)								SLS (µg/mL)			EC50 (µg/ml)
					Well Column:	1	2	3	4	5	6	7	8	9	10	11	12
					Well Row:	0	10	50	75	100	120	140	160	200	110	200	0
	030001	Medium	1	1	A	0.046*	0.046*	0.039*	0.012*	0.030*	0.003*	0.057*	0.032*	0.003*	0.050*	0.044*	0.040*
	030001	Medium	1	1	B	0.048*	107	77.7	65.7	30.2	15.6	9.79	5.41	2.49	8.09	0.791	0.014*
	030001	Medium	1	1	C	0.005*	98.6	77.4	57.7	35.8	8.09	7.36	3.22	0.791	6.38	0.061	0.050*
	030001	Medium	1	1	D	0.049*	94.9	81.5	38.2	31.2	7.60	5.17	3.22	0.791	5.17	0.304	0.017*
	030001	Medium	1	1	E	0.047*	111	78.1	64.5	32.9	8.82	5.90	2.74	1.28	10.3	0.547	0.011*
	030001	Medium	1	1	F	0.032*	96.6	76.2	48.0	26.8	7.84	4.20	2.74	1.52	8.09	4.93	0.022*
	030001	Medium	1	1	G	0.044*	105	77.9	58.2	28.3	8.09	4.68	1.76	0.547	8.57	1.76	0.056*
	030001	Medium	1	1	H	0.056*	0.013*	0.040*	0.008*	0.013*	0.002*	0.029*	0.018*	0.006*	0.016*	0.024*	0.046*
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
*media without cells
	030001	Medium	1	2	A		93.4	74.0	56.0	35.1	11.8	8.70	5.10	1.98	5.34	1.02
	030001	Medium	1	2	B		102	75.2	53.3	35.1	11.8	7.74	5.58	3.66	5.34	1.02
	030001	Medium	1	2	C		107	79.0	55.0	26.5	10.1	6.06	3.66	1.74	7.02	0.780
	030001	Medium	1	2	D		104	80.2	55.3	29.8	8.94	3.90	3.66	1.50	6.30	0.780
	030001	Medium	1	2	E		101	75.7	54.1	26.7	4.86	4.38	1.26	1.02	6.30	1.02
	030001	Medium	1	2	F		110	85.7	67.7	26.0	5.34	4.62	3.42	1.50	6.30	0.540
	030001	Medium	1	2	G		104	77.8	64.9	27.7	8.22	3.18	2.46	1.02	6.30	0.780
	030001	Medium	1	2	H		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
EC50 (µg/ml). Effective concentration at 50% cytotoxicity. (using a specific sigmoidal equation = model).																		123

Rows 1-2:	Show 2 records for TSPARMCD = "GLPTYP", using TSSEQ to indicate multiple records, since both GLP types apply for this example study.
Row 8:	Shows that the applicant's TOBA-356 - Jira project doesn't exist or you don't have permission to view it. study reference ID is not applicable.
Rows 9-12:	Show that TSGRPID has been used to link records (name, location, country) related to the test facility (TSGRPID = 1). The study director is associated with the test facility.
Rows 14-16:	Show that TSGRPID (TSGRPID=4) has been used to link the information on the testing guideline followed on this study (TSTGDNAM, TSTGDORG, TSTGDVER). TOBA-56 - Jira project doesn't exist or you don't have permission to view it.

ts.xpt

xx.xpt

Row	STUDYID	DOMAIN	TSSEQ	TSGRPID	TSPARMCD	TSPARM	TSVAL	TSVALNF
1	123	TS	1		GLPTYP	Good Laboratory Practice Type	FDA
2	123	TS	2		GLPTYP	Good Laboratory Practice Type	OECD
3	123	TS	1		STSTDTC	Study Start Date	2022-05-25
4	123	TS	1		STITLE	Study Title	Determination of the in vitro genotoxicity potential using the in vitro Neutral Red Uptake assay
5	123	TS	1		SNDIGVER	SEND Implementation Guide Version	TOBACCO IMPLEMENTATION GUIDE VERSION 1.0
6	123	TS	1		SNDCTVER	SEND Controlled Terminology Version	SEND Terminology 2021-09-30
7	123	TS	1		APPLCNT	Applicant Organization	Example Applicant Inc.
8	123	TS	1		APREFID	Applicant Study Reference ID		NOT APPLICABLE
9	123	TS	1	1	TSTFNAM	Test Facility Name	Example Test Lab Name
10	123	TS	1	1	TSTFLOC	Test Facility Location	10 Somewhere Street, Montgomery, AL 10000
11	123	TS	1	1	TFCNTRY	Test Facility Country	USA
12	123	TS	1	1	STDIR	Study Director	Dr. R. Smith
13	123	TS	1		GLPFL	GLP Flag	Y
14	123	TS	1	4	TSTGDNAM	Testing Guideline Name	Publication No. 07-4519
15	123	TS	1	4	TSTGDORG	Testing Guideline Organization	NIH
16	123	TS	1	4	TSTGDVER	Testing Guideline Version	2006-11
17	123	TS	1		SSTYP	Study Type	GENOTOXICITY IN VITRO
18	123	TS	1		GNTXAID	Genetic Toxicology Assay Identifier	NRU
19	123	TS	1		SPECIES	Species	HUMAN
20	123	TS	1		CELLLN	Cell Line	NHK

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TOBA-279 - Getting issue details... STATUS

Rows 1-12:	Show the test conditions for the set with a short name or SETCD value of NRU. The applicant chose this value to represent test conditions for the entire assay.
Rows 13-20:	Show the test conditions for the set with a short name or SETCD value of CSC-50b. The applicant chose this value to represent plate number 1, well row A, well column 3, with a concentration of 50 µg/mL of cigarette smoke condensate as shown in the report table for study 123.
Row 20:	Shows the value for Cell Line (CELLLN) is not applicable because the well is a media-only well, having no NHK cells.
Rows 21-28:	Show the test conditions for the set with a short name or SETCD value of CSC-50. The applicant chose this value to represent plate number 1, well rows B-G, well column 3 and plate number 2, well rows A-H, well column 3. These all have the concentration of 50 µg/mL of cigarette smoke condensate as shown in the report table for study 123.
Rows 29-36:	Show the test conditions for the set with a short name or SETCD value of SLS-110. The applicant chose this value to represent plate number 1, well rows B-G, well column 10, and plate number 2, well rows A-H, well column 10. These all have the concentration of 110 µg/mL of sodium laurel sulfate as shown in the report table for study 123.

tx.xpt

xx.xpt

Row	STUDYID	DOMAIN	SETCD	SET	TXSEQ	TXPARMCD	TXPARM	TXVAL
1	123	TX	NRU	NRU_ASSAY	1	IVTDMIN	In vitro Treatment Duration Minimum	47.5
2	123	TX	NRU	NRU_ASSAY	2	IVTDTRG	In vitro Treatment Duration Target	48
3	123	TX	NRU	NRU_ASSAY	3	IVTDMAX	In vitro Treatment Duration Maximum	48.5
4	123	TX	NRU	NRU_ASSAY	4	IVTDU	In vitro Treatment Duration Unit	HOURS
5	123	TX	NRU	NRU_ASSAY	5	INCBTMP	Incubation Temperature	37
6	123	TX	NRU	NRU_ASSAY	6	INCBTMPU	Incubation Temperature Unit	C
7	123	TX	NRU	NRU_ASSAY	7	SWAVENM	Spectrophotometer Wavelength	540
8	123	TX	NRU	NRU_ASSAY	8	ATMRHP	Atmospheric Relative Humidity Percent	90
9	123	TX	NRU	NRU_ASSAY	9	ATMCO2P	Atmospheric CO2 Percent	5
10	123	TX	NRU	NRU_ASSAY	10	SPDEVID	applicant defined device identifier	PUFFMASTER3k
11	123	TX	NRU	NRU_ASSAY	11	SMKRGM	Smoking Regimen	MEDIUM INTENSITY REGIMEN
12	123	TX	NRU	NRU_ASSAY	12	SPTOBID	Applicant-defined tobacco identifier	CIG01a
13	123	TX	CSC-50b	CSC-50-blank	13	PSETCD	Parent Set Code	NRU
14	123	TX	CSC-50b	CSC-50-blank	14	EXPTYP	Exposure Type	Air Liquid Interface
15	123	TX	CSC-50b	CSC-50-blank	15	SAMTYP	Sample Type	Whole Smoke Conditioned Media
16	123	TX	CSC-50b	CSC-50-blank	16	ITVNAM	Name of the Intervention Article	Tobacco ProdA
17	123	TX	CSC-50b	CSC-50-blank	17	ITVTYPE	Intervention Article Type	PRODUCT
18	123	TX	CSC-50b	CSC-50-blank	18	ITVCONC	Intervention Article Concentration	50
19	123	TX	CSC-50b	CSC-50-blank	19	ITVCONCU	Intervention Article Concentration Unit	ug/ml
20	123	TX	CSC-50b	CSC-50-blank	20	CELLLN	Cell Line	NOT APPLICABLE
21	123	TX	CSC-50	CSC-50	21	PSETCD	Parent Set Code	NRU
22	123	TX	CSC-50	CSC-50	22	EXPTYP	Exposure Type	Air Liquid Interface
23	123	TX	CSC-50	CSC-50	23	SAMTYP	Sample Type	Whole Smoke Conditioned Media
24	123	TX	CSC-50	CSC-50	24	ITVNAM	Intervention Article Name	Tobacco ProdA
25	123	TX	CSC-50	CSC-50	25	ITVTYPE	Intervention Article Type	PRODUCT
26	123	TX	CSC-50	CSC-50	26	ITVCONC	Intervention Article Concentration	50
27	123	TX	CSC-50	CSC-50	27	ITVCONCU	Intervention Article Concentration Unit	ug/ml
28	123	TX	CSC-50	CSC-50	28	CELLLN	Cell Line	NHK
29	123	TX	SLS-110	SLS-110	29	PSETCD	Parent Set Code	NRU
30	123	TX	SLS-110	SLS-110	30	EXPTYP	Exposure Type	Air Liquid Interface
31	123	TX	SLS-110	SLS-110	31	SAMTYP	Sample Type	Liquid
32	123	TX	SLS-110	SLS-110	32	ITVNAM	Intervention Article Name	Sodium Laurel Sulfate
33	123	TX	SLS-110	SLS-110	33	ITVTYPE	Intervention Article Type	POSITIVE CONTROL
34	123	TX	SLS-110	SLS-110	34	ITVCONC	Intervention Article Concentration	110
35	123	TX	SLS-110	SLS-110	35	ITVCONCU	Intervention Article Concentration Unit	ug/ml
36	123	TX	SLS-110	SLS-110	36	CELLLN	Cell Line	NHK

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Please add a row column to your dataset.

TOBA-280 - Getting issue details... STATUS

Row 1:	Shows the REFID of 123NRU that indicates the entire assay.
Rows 2, 5, 8, 9:	Show the REFIDs at the second level, all within the parent assay of 123NRU (REFID values of 1-3b, 1-3, 1-10, 2-10) which have LVLDESC of OBSERVATIONAL UNIT. If this study had recorded summary statistics for an entire trial set (e.g., across both plates for the same dose level), there would be an additional REFID for the trial set (with a LVLDESC of TRIAL SET).
Rows 3-4, 6-7, 10-11:	Show REFID values that the applicant chose, in this case, to represent the plate number (1 or 2), column (1 - 12), and row (A-G) of the 96-well plates.
Rows 3-4:	Show the REFIDs 1-3-A and 1-3-H that indicate two experimental units within the parent trial set of 1-3b.
Rows 6-7:	Show the REFIDs 1-3-B and 1-3-C that indicate two experimental units within the parent trial set of 1-3.
Row 10:	Shows the REFID of 1-10-G that indicates the experimental unit within the parent trial set of 1-10.
Row 11:	Shows the REFID of 2-10-G that indicates the experimental unit within the parent trial set of 2-10.

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relref.xpt

Row	STUDYID	SETCD	REFID	PARENT	LEVEL	LVLDESC
1	123	NRU	123NRU		1	ASSAY
2	123	CSC-50b	1-3b	123NRU	2	OBSERVATIONAL UNIT
3	123	CSC-50b	1-3-A	1-3b	3	EXPERIMENTAL UNIT
4	123	CSC-50b	1-3-H	1-3b	3	EXPERIMENTAL UNIT
5	123	CSC-50	1-3	123NRU	2	OBSERVATIONAL UNIT
6	123	CSC-50	1-3-B	1-3	3	EXPERIMENTAL UNIT
7	123	CSC-50	1-3-C	1-3	3	EXPERIMENTAL UNIT
8	123	SLS-110	1-10	123NRU	2	OBSERVATIONAL UNIT
9	123	SLS-110	2-10	123NRU	2	OBSERVATIONAL UNIT
10	123	SLS-110	1-10-G	1-10	3	EXPERIMENTAL UNIT
11	123	SLS-110	2-10-G	2-10	3	EXPERIMENTAL UNIT

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Please add a row column to your dataset.

TOBA-592 - Getting issue details... STATUS

gt.xpt

Row	STUDYID	DOMAIN	GTSEQ	GTREFID	GTTESTCD	GTTEST	GTORRES	GTORRESU	GTCOLSRT	GTSTRESC	GTSTRESN	GTSTRESU
1	123	GT	1	1-3-B	ABSORB	Absorbance Reading	1.7			1.7	1.7
2	123	GT	2	1-3-B	BKCABS	Background Corrected Absorbance Reading	1.6			1.6	1.6
3	123	GT	3	1-3-B	RELABS	Relative Absorbance Reading	77.7	%		77.7	77.7	%
4	123	GT	4	1-3-C	ABSORB	Absorbance Reading	1.8			1.8	1.8
5	123	GT	5	1-3-C	BKCABS	Background Corrected Absorbance Reading	1.7			1.7	1.7
6	123	GT	6	1-3-C	RELABS	Relative Absorbance Reading	77.4			77.4	77.4
7	123	GT	7	1-3	RELABS	Relative Absorbance Reading	78.2	%	MEAN	78.2	78.2	%
8	123	GT	8	1-3	RELABS	Relative Absorbance Reading	2.9	%	STANDARD DEVIATION	2.9	2.9	%
9	123	GT	9	1-3	RELABS	Relative Absorbance Reading	3.6		COEFFICIENT OF VARIANCE	3.6	3.6
10	123	GT	10	1-10-G	ABSORB	Absorbance Reading	0.7			0.7	0.7
11	123	GT	11	1-10-G	BKCABS	Background Corrected Absorbance Reading	0.6			0.6	0.6
12	123	GT	12	1-10-G	RELABS	Relative Absorbance Reading	8.57			8.57	8.57
13	123	GT	13	1-10	RELABS	Relative Absorbance Reading	8.94	%	MEAN	8.94	8.94
14	123	GT	14	1-10	RELABS	Relative Absorbance Reading	2.72	%	STANDARD DEVIATION	2.72	2.72
15	123	GT	15	1-10	RELABS	Relative Absorbance Reading	30.5		COEFFICIENT OF VARIANCE	30.5	30.5
16	123	GT	16	2-10-G	ABSORB	Absorbance Reading	0.9
17	123	GT	17	2-10-G	BKCABS	Background Corrected Absorbance Reading	0.8
18	123	GT	18	2-10-G	RELABS	Relative Absorbance Reading	6.30			6.30	6.30
19	123	GT	19	2-10	RELABS	Relative Absorbance Reading	5.91	%	MEAN	5.91	5.91
20	123	GT	20	2-10	RELABS	Relative Absorbance Reading	0.83	%	STANDARD DEVIATION	0.83	0.83
21	123	GT	21	2-10	RELABS	Relative Absorbance Reading	14.1		COEFFICIENT OF VARIANCE	14.1	14.1
22	123	GT	22	123NRU	EC50CYTX TOBA-132 - Jira project doesn't exist or you don't have permission to view it.	Effective Concentration of 50 Percent Cytotoxicity	123	ug/ml		123	123	ug/ml

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SEND Example.In vitro Neutral Red Cytotoxicity Assay