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 3:	Shows that this study was conducted as a GLP study.
Rows 4-5:	Show the study start date and study title.
Rows 6-7:	Show the version of SEND Implementation Guide and version of Controlled Terminology used in this study.
Row 8:	Shows the applicant's organization.
Row 9:	TOBA-356 - Jira project doesn't exist or you don't have permission to view it. Shows that the applicant's study reference ID is not applicable.
Rows 10-13:	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.
Row 17:	Shows the study type for this study.
Row 18:	Shows that this study includes a Neutral Red Uptake Assay.
Rows 19-20:	Show that the species is human and the cell line is NHK in this study.

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		GLPFL	GLP Flag	Y
4	123	TS	1		STSTDTC	Study Start Date	2022-05-25
5	123	TS	1		STITLE	Study Title	Determination of the in vitro genotoxicity potential using the in vitro Neutral Red Uptake assay
6	123	TS	1		SNDIGVER	SEND Implementation Guide Version	TOBACCO IMPLEMENTATION GUIDE VERSION 1.0
7	123	TS	1		SNDCTVER	SEND Controlled Terminology Version	SEND Terminology 2021-09-30
8	123	TS	1		APPLCNT	Applicant Organization	Example Applicant Inc.
9	123	TS	1		APREFID	Applicant Study Reference ID		NOT APPLICABLE
10	123	TS	1	1	TSTFNAM	Test Facility Name	Example Test Lab Name
11	123	TS	1	1	TSTFLOC	Test Facility Location	10 Somewhere Street, Montgomery, AL 10000
12	123	TS	1	1	TFCNTRY	Test Facility Country	USA
13	123	TS	1	1	STDIR	Study Director	Dr. R. Smith
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. 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	IVTDMIN	In vitro Treatment Duration Minimum	47.5
14	123	TX	CSC-50b	CSC-50-blank	14	IVTDTRG	In vitro Treatment Duration Target	48
15	123	TX	CSC-50b	CSC-50-blank	15	IVTDMAX	In vitro Treatment Duration Maximum	48.5
16	123	TX	CSC-50b	CSC-50-blank	16	IVTDU	In vitro Treatment Duration Unit	HOURS
17	123	TX	CSC-50b	CSC-50-blank	17	INCBTMP	Incubation Temperature	37
18	123	TX	CSC-50b	CSC-50-blank	18	INCBTMPU	Incubation Temperature Unit	C
19	123	TX	CSC-50b	CSC-50-blank	19	SWAVENM	Spectrophotometer Wavelength	540
20	123	TX	CSC-50b	CSC-50-blank	20	ATMRHP	Atmospheric Relative Humidity Percent	90
21	123	TX	CSC-50b	CSC-50-blank	21	ATMCO2P	Atmospheric CO2 Percent	5
22	123	TX	CSC-50b	CSC-50-blank	22	SPDEVID	applicant defined device identifier	PUFFMASTER3k
23	123	TX	CSC-50b	CSC-50-blank	23	SMKRGM	Smoking Regimen	MEDIUM INTENSITY REGIMEN
24	123	TX	CSC-50b	CSC-50-blank	24	SPTOBID	Applicant-defined tobacco identifier	CIG01a
25	123	TX	CSC-50b	CSC-50-blank	25	EXPTYP	Exposure Type	Air Liquid Interface
26	123	TX	CSC-50b	CSC-50-blank	26	SAMTYP	Sample Type	Whole Smoke Conditioned Media
27	123	TX	CSC-50b	CSC-50-blank	27	ITVNAM	Name of the Intervention Article	Tobacco ProdA
28	123	TX	CSC-50b	CSC-50-blank	28	ITVTYPE	Intervention Article Type	PRODUCT
29	123	TX	CSC-50b	CSC-50-blank	29	ITVCONC	Intervention Article Concentration	50
30	123	TX	CSC-50b	CSC-50-blank	30	ITVCONCU	Intervention Article Concentration Unit	ug/ml
31	123	TX	CSC-50b	CSC-50-blank	31	CELLLN	Cell Line	NOT APPLICABLE
32	123	TX	CSC-50	CSC-50	32	IVTDMIN	In vitro Treatment Duration Minimum	47.5
33	123	TX	CSC-50	CSC-50	33	IVTDTRG	In vitro Treatment Duration Target	48
34	123	TX	CSC-50	CSC-50	34	IVTDMAX	In vitro Treatment Duration Maximum	48.5
35	123	TX	CSC-50	CSC-50	35	IVTDU	In vitro Treatment Duration Unit	HOURS
36	123	TX	CSC-50	CSC-50	36	INCBTMP	Incubation Temperature	37
37	123	TX	CSC-50	CSC-50	37	INCBTMPU	Incubation Temperature Unit	C
38	123	TX	CSC-50	CSC-50	38	SWAVENM	Spectrophotometer Wavelength	540
39	123	TX	CSC-50	CSC-50	39	ATMRHP	Atmospheric Relative Humidity Percent	90
40	123	TX	CSC-50	CSC-50	40	ATMCO2P	Atmospheric CO2 Percent	5
41	123	TX	CSC-50	CSC-50	41	SPDEVID	applicant defined device identifier	PUFFMASTER3k
42	123	TX	CSC-50	CSC-50	42	SMKRGM	Smoking Regimen	MEDIUM INTENSITY REGIMEN
43	123	TX	CSC-50	CSC-50	43	SPTOBID	Applicant-defined tobacco identifier	CIG01a
44	123	TX	CSC-50	CSC-50	44	EXPTYP	Exposure Type	Air Liquid Interface
45	123	TX	CSC-50	CSC-50	45	SAMTYP	Sample Type	Whole Smoke Conditioned Media
46	123	TX	CSC-50	CSC-50	46	ITVNAM	Intervention Article Name	Tobacco ProdA
47	123	TX	CSC-50	CSC-50	47	ITVTYPE	Intervention Article Type	PRODUCT
48	123	TX	CSC-50	CSC-50	48	ITVCONC	Intervention Article Concentration	50
49	123	TX	CSC-50	CSC-50	49	ITVCONCU	Intervention Article Concentration Unit	ug/ml
50	123	TX	CSC-50	CSC-50	50	CELLLN	Cell Line	NHK
51	123	TX	SLS-110	SLS-110	51	IVTDMIN	In vitro Treatment Duration Minimum	47.5
52	123	TX	SLS-110	SLS-110	52	IVTDTRG	In vitro Treatment Duration Target	48
53	123	TX	SLS-110	SLS-110	53	IVTDMAX	In vitro Treatment Duration Maximum	48.5
54	123	TX	SLS-110	SLS-110	54	IVTDU	In vitro Treatment Duration Unit	HOURS
55	123	TX	SLS-110	SLS-110	55	INCBTMP	Incubation Temperature	37
56	123	TX	SLS-110	SLS-110	56	INCBTMPU	Incubation Temperature Unit	C
57	123	TX	SLS-110	SLS-110	57	SWAVENM	Spectrophotometer Wavelength	540
58	123	TX	SLS-110	SLS-110	58	ATMRHP	Atmospheric Relative Humidity Percent	90
59	123	TX	SLS-110	SLS-110	59	ATMCO2P	Atmospheric CO2 Percent	5
60	123	TX	SLS-110	SLS-110	60	SPDEVID	applicant defined device identifier	PUFFMASTER3k
61	123	TX	SLS-110	SLS-110	61	SMKRGM	Smoking Regimen	MEDIUM INTENSITY REGIMEN
62	123	TX	SLS-110	SLS-110	62	SPTOBID	Applicant-defined tobacco identifier	CIG01a
63	123	TX	SLS-110	SLS-110	63	EXPTYP	Exposure Type	Air Liquid Interface
64	123	TX	SLS-110	SLS-110	64	SAMTYP	Sample Type	Liquid
65	123	TX	SLS-110	SLS-110	65	ITVNAM	Intervention Article Name	Sodium Laurel Sulfate
66	123	TX	SLS-110	SLS-110	66	ITVTYPE	Intervention Article Type	POSITIVE CONTROL
67	123	TX	SLS-110	SLS-110	67	ITVCONC	Intervention Article Concentration	110 TOBA-600 - Jira project doesn't exist or you don't have permission to view it.
68	123	TX	SLS-110	SLS-110	68	ITVCONCU	Intervention Article Concentration Unit	ug/ml
69	123	TX	SLS-110	SLS-110	69	CELLLN	Cell Line	NHK

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Please remove extraneous empty columns.

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TOBA-461 - Getting issue details... STATUS

The applicant chose to define the REFID values to indicate the Plate, the Column, and the Row of the wells of the 96-well plate in use, such that the well on plate 2, column 10, row G would assigned a REFID of 2-10-G.

Row 1:	Shows the REFID of 123NRU that indicates the entire assay.
Rows 2-4:	Show the REFIDs at the second level, all within the parent assay of 123NRU (REFID values of 1-3, 1-10, 2-10) which have LVLDESC of OBSERVATIONAL SUMMARY. 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 5-6:	Show the REFIDs 1-3-A and 1-3-H that indicate two experimental units that are also observational units within the SETCD of CSC-50b that have the parent REFID of 123NRU.
Rows 7-8:	Show the REFIDs 1-3-B and 1-3-C that indicate two experimental units that are also observational units within the SETCD of CSC-50 that have the parent REFID of 1-3.
Row 9:	Shows the REFID of 1-10-G that indicates the experimental unit that is also an observational unit within the SETCD of SLS-110 that has the parent REFID of 1-10.
Row 10:	Shows the REFID of 2-10-G that indicates the experimental unit that is also an observational unit within the SETCD of SLS-110 that has the parent REFID of 2-10.

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relref.xpt

	OLD Row	STUDYID	SETCD	REFID	PARENT	LEVEL	LVLDESC
1	1	123	NRU TOBA-475 - Jira project doesn't exist or you don't have permission to view it.	123NRU		1	ASSAY
2	5	123	CSC-50	1-3	123NRU	2	OBSERVATIONAL SUMMARY
3	8	123	SLS-110	1-10	123NRU	2	OBSERVATIONAL SUMMARY
4	9	123	SLS-110	2-10	123NRU	2	OBSERVATIONAL SUMMARY
5	3	123	CSC-50b	1-3-A	123NRU	2	EXPERIMENTAL UNIT/OBSERVATIONAL UNIT
6	4	123	CSC-50b	1-3-H	123NRU	2	EXPERIMENTAL UNIT/OBSERVATIONAL UNIT
7	6	123	CSC-50	1-3-B	1-3	3	EXPERIMENTAL UNIT/OBSERVATIONAL UNIT
8	7	123	CSC-50	1-3-C	1-3	3	EXPERIMENTAL UNIT/OBSERVATIONAL UNIT
9	10	123	SLS-110	1-10-G	1-10	3	EXPERIMENTAL UNIT/OBSERVATIONAL UNIT
10	11	123	SLS-110	2-10-G	2-10	3	EXPERIMENTAL UNIT/OBSERVATIONAL UNIT

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TOBA-592 - Getting issue details... STATUS

Certain data (Absorbance Reading and Background Corrected Absorbance Reading) are not shown in the sample report table above but are included here for completeness of the NRU assay.

Rows 1-3:	Show the experimental unit data for GTREFID 1-3-B.
Rows 4-6:	Show the experimental unit data for GTREFID 1-3-C.
Rows 7-9:	Show the data for the entire trial set, GTREFID=1-3.
Rows 10-12:	Show the experimental unit data for GTREFID 1-10-G
Rows 13-15:	Show the data for the entire trial set, GTREFID=1-10
Rows 16-18:	Show the experimental unit data for GTREFID 2-10-G.
Rows 19-21:	Show the data for the entire trial set, GTREFID=2-10
Row 22:	Shows the data for the entire assay, GTREFID=123NRU.

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 TOBA-598 - Jira project doesn't exist or you don't have permission to view it.	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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TOBA-280 - Getting issue details... STATUS

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SEND Example.In vitro Neutral Red Cytotoxicity Assay