SEND Example.In vitro Bacterial Reverse Mutation Assay

This is an example showing the report table, trial design, and results from the in vitro bacterial reverse mutation test of an example study, Study #8325064. This bacterial reverse mutation test uses four different amino acid-requiring strains of Salmonella typhimurium (S. typhimurium) and one strain of Escherichia coli (E. coli) to detect point mutations, which involve substitution, addition or deletion of one or a few DNA base pairs.

In this example, the Trial Summary dataset, ts.xpt, includes many informational fields that may provide context at the study level, for Study 8325064. Also, TSGRPID has been used to link records (name, location, country) related to the test facility (TSGRPID = 1) and records related to the Test Site (TSGRPID = 2). The Study Director is associated with the Test Facility and the Principal Investigator is associated with the Test Site. Finally, the Primary Treatment CAS Registry Number is not known and this is recorded as an empty TSVAL and UNKNOWN in the corresponding TSVALNF.

This table shows the assay results for Study 8325064, Test Article TA1, and three strains of Salmonella (TA98, TA100, and TA1535) at varying concentrations. For ease of reference, each row has been labeled in the right hand margin with the sponsor defined trial set label (e.g., SetA). For brevity, the remaining tables (e.g., additional strains, samples prepared without metabolic activation, etc.) are not included.

Rows 1-2:	Show two records for TSPARMCD = "GLPTYP", using TSSEQ to indicate multiple records, since both GLP Types apply for this example study.
Row 8:	Shows that the sponsor's 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 18-24:	Show that this example study includes two different species of bacteria and a total of five strains.
Rows 18-22:	Show that TSGRPID (TSGRPID = 2) has been used to link the information for one species (Salmonella) with four different strains that are tested in this example study.
Rows 23-24:	Show that TSGRPID (TSGRPID = 3) has been used to link the information for one species (Escherichia coli) with the strain that is tested in this example study.

ts.xpt

xx.xpt

Row	STUDYID	ASSAYID	DOMAIN	TSSEQ	TSGRPID	TSPARMCD	TSPARM	TSVAL	TSVALNF
1	8325064	Ames	TS	1		GLPTYP	Good Laboratory Practice Type	FDA
2	8325064	Ames	TS	2		GLPTYP	Good Laboratory Practice Type	OECD
3	8325064	Ames	TS	1		STSTDTC	Study Start Date	2015-07-29
4	8325064	Ames	TS	1		STITLE	Study Title	The Bacterial Reverse Mutation Test, Study 8325064-1
5	8325064	Ames	TS	1		SNDIGVER	SEND Implementation Guide Version	TOBACCO IMPLEMENTATION GUIDE VERSION 1.0
6	8325064	Ames	TS	1		SNDCTVER	SEND Controlled Terminology Version	SEND Terminology 2021-09-30
7	8325064	Ames	TS	1		SSPONSOR	Sponsor Organization	Example Sponsor Inc.
8	8325064	Ames	TS	1		SPREFID	Sponsor's Study Reference ID		NOT APPLICABLE
9	8325064	Ames	TS	1	1	TSTFNAM	Test Facility Name	Example Tox Lab Name
10	8325064	Ames	TS	1	1	TSTFLOC	Test Facility Location	10 Somewhere Street, Montgomery, AL 10000
11	8325064	Ames	TS	1	1	TFCNTRY	Test Facility Country	USA
12	8325064	Ames	TS	1	1	STDIR	Study Director	Dr. R. Smith
13	8325064	Ames	TS	1		GLPFL	GLP Flag	N
14	8325064	Ames	TS	1		ASTD	Assay Standard	OECD Test No. 471
15	8325064	Ames	TS	1		ASTDV	Assay Standard Version	2020-06-29
16	8325064	Ames	TS	1		SSTYP	Study Type	GENOTOXICITY IN VITRO
17	8325064	Ames	TS	1		SSSTYP	Study Sub Type	Bacterial Reverse Mutation Test
18	8325064	Ames	TS	1	2	SPECIES	Species	Salmonella
19	8325064	Ames	TS	1	2	STRAIN	Strain	TA98
20	8325064	Ames	TS	1	2	STRAIN	Strain	TA100
21	8325064	Ames	TS	1	2	STRAIN	Strain	TA1535
22	8325064	Ames	TS	1	2	STRAIN	Strain	TA1537
23	8325064	Ames	TS	1	3	SPECIES	Species	Escherichia coli
24	8325064	Ames	TS	1	3	STRAIN	Strain	WP2 uvrA pKM101

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Dataset Wrapper Debug Message

Please add a row column to your dataset.

This example trial set dataset, tx.xpt, shows information about the test conditions for SetA and SetR in this example study. For brevity, this does not show information for SetF, SetG, or any other sets. A fully formed tx.xpt for this example study would include information about the test conditions for all sets.

Rows 1-22:	Show trial set parameters and trial set values that comprise the test conditions for the set SetA. SetA is the data for the vehicle control (i.e., Strain of TA98, vehicle control with concentration value of 0). SetA is associated with the first row, labeled "SetA", in the report table for example study 8325064.
Rows 23-44:	Show trial set parameters and trial set values that comprise the test conditions for the set SetR. SetR is the data for the vehicle control (i.e., Strain of TA100, positive control with a concentration value of 2). SetR is associated with the eighteenth row, labeled "SetR", in the report table for example study 8325064.

tx.xpt

tx.xpt trial sets.xpt

Row	STUDYID	ASSAYID	DOMAIN	SETCD	SET	TXSEQ	TXPARMCD	TXPARM	TXVAL
1	8325064	Ames	TX	SetA	A-TA98-C0	1	SPECIES	Species	Salmonella typhimurium
2	8325064	Ames	TX	SetA	A-TA98-C0	2	STRAIN	Strain/Substrain	TA98
3	8325064	Ames	TX	SetA	A-TA98-C0	3	METACT	Metabolic Activation
4	8325064	Ames	TX	SetA	A-TA98-C0	4	METACTFL	Y/N presence of metabolic activation	N
5	8325064	Ames	TX	SetA	A-TA98-C0	5	TRTDMIN	Treatment Duration Minimum	71.5
6	8325064	Ames	TX	SetA	A-TA98-C0	6	TRTDTRG	Treatment Duration Target	72
7	8325064	Ames	TX	SetA	A-TA98-C0	7	TRTDMAX	Treatment Duration Maximum	72.5
8	8325064	Ames	TX	SetA	A-TA98-C0	8	TRTDU	Treatment Duration Unit	HOURS
9	8325064	Ames	TX	SetA	A-TA98-C0	9	INCBTMP	Incubation Temperature	37
10	8325064	Ames	TX	SetA	A-TA98-C0	10	INCBTMPU	Incubation Temperature Unit	C
11	8325064	Ames	TX	SetA	A-TA98-C0	11	HUMID	Atmospheric Relative Humidity Percent	50
12	8325064	Ames	TX	SetA	A-TA98-C0	12	ATMCO2	Atmospheric CO2 Percent	5
13	8325064	Ames	TX	SetA	A-TA98-C0	13	SPTOBID	Sponsor defined tobacco identifier	CIG01a
14	8325064	Ames	TX	SetA	A-TA98-C0	14	EXPTYP	Exposure Type (See TIG NC workstream minutes 30-Jan here: Nonclinical)	Submerged
15	8325064	Ames	TX	SetA	A-TA98-C0	15	SAMTYP	Sample Type	Total Particulate Matter in PBS
16	8325064	Ames	TX	SetA	A-TA98-C0	16	INTRVN	name of the intervention article	TA1
17	8325064	Ames	TX	SetA	A-TA98-C0	17	ITVTYPE	type of intervention article	Vehicle Control
18	8325064	Ames	TX	SetA	A-TA98-C0	18	ITVCONC	Concentration of intervention article	0
19	8325064	Ames	TX	SetA	A-TA98-C0	19	ITVCONCU	Concentration Unit	ug/plate
20	8325064	Ames	TX	SetA	A-TA98-C0	20	TRTV	Treatment Vehicle	DMSO
21	8325064	Ames	TX	SetA	A-TA98-C0	21	SPDEVID	Sponsor defined device identifier	PUFFMASTER3K
22	8325064	Ames	TX	SetA	A-TA98-C0	22	DUREFID	Smoke Regimen	Medium Intensity Regimen
23	8325064	Ames	TX	SetR	R-TA100-C2	1	SPECIES	Species	Salmonella typhimurium
24	8325064	Ames	TX	SetR	R-TA100-C2	2	STRAIN	Strain/Substrain	TA100
25	8325064	Ames	TX	SetR	R-TA100-C2	3	METACT	Metabolic Activation
26	8325064	Ames	TX	SetR	R-TA100-C2	4	METACTFL	Y/N presence of metabolic activation	N
27	8325064	Ames	TX	SetR	R-TA100-C2	5	TRTDMIN	Treatment Duration Minimum	71.5
28	8325064	Ames	TX	SetR	R-TA100-C2	6	TRTDTRG	Treatment Duration Target	72
29	8325064	Ames	TX	SetR	R-TA100-C2	7	TRTDMAX	Treatment Duration Maximum	72.5
30	8325064	Ames	TX	SetR	R-TA100-C2	8	TRTDU	Treatment Duration Unit	HOURS
31	8325064	Ames	TX	SetR	R-TA100-C2	9	INCBTMP	Incubation Temperature	37
32	8325064	Ames	TX	SetR	R-TA100-C2	10	INCBTMPU	Incubation Temperature Unit	C
33	8325064	Ames	TX	SetR	R-TA100-C2	11	HUMID	Atmospheric Relative Humidity Percent	50
34	8325064	Ames	TX	SetR	R-TA100-C2	12	ATMCO2	Atmospheric CO2 Percent	5
35	8325064	Ames	TX	SetR	R-TA100-C2	13	SPTOBID	Sponsor defined tobacco identifier	CIG01a
36	8325064	Ames	TX	SetR	R-TA100-C2	14	EXPTYP	Exposure Type	Submerged
37	8325064	Ames	TX	SetR	R-TA100-C2	15	SAMTYP	Sample Type	Total Particulate Matter in PBS
38	8325064	Ames	TX	SetR	R-TA100-C2	16	INTRVN	name of the intervention article	TA1
39	8325064	Ames	TX	SetR	R-TA100-C2	17	ITVTYPE	type of intervention article	Positive Control
40	8325064	Ames	TX	SetR	R-TA100-C2	18	ITVCONC	Concentration of intervention article	2
41	8325064	Ames	TX	SetR	R-TA100-C2	19	ITVCONCU	Concentration Unit	ug/plate
42	8325064	Ames	TX	SetR	R-TA100-C2	20	TRTV	Treatment Vehicle	DMSO
43	8325064	Ames	TX	SetR	R-TA100-C2	21	SPDEVID	Sponsor defined device identifier	PUFFMASTER3K
44	8325064	Ames	TX	SetR	R-TA100-C2	22	DUREFID	Smoke Regimen	Medium Intensity Regimen

Dataset Debug Messages

There are ten leading, trailing, or non-breaking spaces in the dataset.
Please remove all hyperlinks from the dataset.

Dataset Wrapper Debug Message

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Observational Unit Identifiers (OBUIDs) are defined by the sponsor to uniquely identify the observational unit within an experimental unit. In this example the sponsor chose to define the EUIDs based on trial sets (e.g., F) and OBUIDs based on the position of the tube in one of multiple exposure/incubation plates (e.g, 6_1 for plate 6, position 1).

Rows 1-5:	Show the values for OBUID within the experimental unit identifier, A, for Set A, as defined in the trial set dataset.
Rows 6-8:	Show the values for OBUID within the experimental unit identifier, F, for Set F, as defined in the trial set dataset.
Rows 9-11:	Show the values for OBUID within the experimental unit identifier, G, for Set G, as defined in the trial set dataset.
Rows 12-14:	Show the values for OBUID within the experimental unit identifier, R, for Set R, as defined in the trial set dataset.

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ou.xpt observational and experimentat unit identifiers.xpt

Row	STUDYID	ASSAYID	DOMAIN	SETCD	EUID	OBUID
1	8325064	Ames	OU	SetA	A	0_1
2	8325064	Ames	OU	SetA	A	0_2
3	8325064	Ames	OU	SetA	A	0_3
4	8325064	Ames	OU	SetA	A	0_4
5	8325064	Ames	OU	SetA	A	0_5
6	8325064	Ames	OU	SetF	F	6_1
7	8325064	Ames	OU	SetF	F	6_2
8	8325064	Ames	OU	SetF	F	6_3
9	8325064	Ames	OU	SetG	G	7_1
10	8325064	Ames	OU	SetG	G	7_2
11	8325064	Ames	OU	SetG	G	7_3
12	8325064	Ames	OU	SetR	R	18_1
13	8325064	Ames	OU	SetR	R	18_2
14	8325064	Ames	OU	SetR	R	18_3

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Rows 1-7:	Show values collected for the set, SetA.
Rows 8-16:	Show values collected for the set, SetF. Revertent colonies were counted and each value is associated with a record to show a postfix of code of "V".
Rows 17-19:	Show values collected for the set, SetG. Each record for this EUID shows the postfix code of "T". No revertent colonies were counted and there are no summary values collected.
Rows 20-25:	Show values collected for the set, SetR.
Rows 6-7, 14-16, 23-25:	Show summary values collected (e.g., MEAN, STANDARD DEVIATION, and/or FOLD INCREASE) that apply to all of the observational units and the entire experimental unit, as shown by OBUID = "ALL" and EUID = "ALL".

gt.xpt

gt.xpt.xpt

Row	STUDYID	ASSAYID	DOMAIN	TXSETCD	EUID	OUID	GTSEQ	GTTESTCD	GTTEST	GTORRES	GTORRESU	GTCOLSRT (coll. summ. result type)	GTSTRESC	GTSTRESN	GTSTRESU	GTSTAT	GTREASND	GTMETHOD	GTDTC
1	8325064	Ames	GT	SETA	A	0_1	1	RPP	Revertant Numbers Per Plate	26	COLONIES		26	26	COLONIES			INSTRUMENT COUNTED	2015-08-03
2	8325064	Ames	GT	SETA	A	0_2	2	RPP	Revertant Numbers Per Plate	35	COLONIES		35	35	COLONIES			INSTRUMENT COUNTED	2015-08-03
3	8325064	Ames	GT	SETA	A	0_3	3	RPP	Revertant Numbers Per Plate	39	COLONIES		39	39	COLONIES			INSTRUMENT COUNTED	2015-08-03
4	8325064	Ames	GT	SETA	A	0_4	4	RPP	Revertant Numbers Per Plate	35	COLONIES		35	35	COLONIES			INSTRUMENT COUNTED	2015-08-03
5	8325064	Ames	GT	SETA	A	0_5	5	RPP	Revertant Numbers Per Plate	30	COLONIES		30	30	COLONIES			INSTRUMENT COUNTED	2015-08-03
6	8325064	Ames	GT	SETA	A	ALL	6	RPP	Revertant Numbers Per Plate	33.0	COLONIES	MEAN	33.0	33.0	COLONIES				2015-08-03
7	8325064	Ames	GT	SETA	A	ALL	7	RPP	Revertant Numbers Per Plate	5.0	COLONIES	STANDARD DEVIATION	5.0	5.0	COLONIES				2015-08-03
8	8325064	Ames	GT	SETF	F	6_1	1	RPP	Revertant Numbers Per Plate	8	COLONIES		8	8	COLONIES			MANUALLY COUNTED	2015-08-03
9	8325064	Ames	GT	SETF	F	6_1	2	CYTOTOX	Cytotoxicity	Very thin background bacterial lawn			V						2015-08-03
10	8325064	Ames	GT	SETF	F	6_2	3	RPP	Revertant Numbers Per Plate	10	COLONIES		10	10	COLONIES			MANUALLY COUNTED	2015-08-03
11	8325064	Ames	GT	SETF	F	6_2	2	CYTOTOX	Cytotoxicity	Very thin background bacterial lawn			V						2015-08-03
12	8325064	Ames	GT	SETF	F	6_3	4	RPP	Revertant Numbers Per Plate	12	COLONIES		12	12	COLONIES			MANUALLY COUNTED	2015-08-03
13	8325064	Ames	GT	SETF	F	6_3	2	CYTOTOX	Cytotoxicity	Very thin background bacterial lawn			V						2015-08-03
14	8325064	Ames	GT	SETF	ALL	ALL	5	RPPMEAN	Mean of Revertant Numbers Per Plate	10.0	COLONIES	MEAN	10.0	10.0	COLONIES				2015-08-03
15	8325064	Ames	GT	SETF	ALL	ALL	6	RPPSTDDV	Standard Deviation of Revertant Numbers Per Plate	2.0	COLONIES	STANDARD DEVIATION	2.0	2.0	COLONIES				2015-08-03
16	8325064	Ames	GT	SETF	ALL	ALL	7	RPPFDINC	Fold Increase of Revertant Numbers Per Plate	0.3	COLONIES	FOLD INCREASE	0.3	0.3	COLONIES				2015-08-03
17	8325064	Ames	GT	SETG	G	5_1	1	CYTOTOX	Cytotoxicity	Toxic No Revertant Colonies			T			NOT DONE	TOO MUCH CYTOTOXICITY		2015-08-03
18	8325064	Ames	GT	SETG	G	5_2	2	CYTOTOX	Cytotoxicity	Toxic No Revertant Colonies			T			NOT DONE	TOO MUCH CYTOTOXICITY		2015-08-03
19	8325064	Ames	GT	SETG	G	5_3	3	CYTOTOX	Cytotoxicity	Toxic No Revertant Colonies			T			NOT DONE	TOO MUCH CYTOTOXICITY		2015-08-03
20	8325064	Ames	GT	SETR	R	18_1	1	RPP	Revertant Numbers Per Plate	812	COLONIES		812	812	COLONIES			INSTRUMENT COUNTED	2015-08-03
21	8325064	Ames	GT	SETR	R	18_2	2	RPP	Revertant Numbers Per Plate	912	COLONIES		912	912	COLONIES			INSTRUMENT COUNTED	2015-08-03
22	8325064	Ames	GT	SETR	R	18_3	3	RPP	Revertant Numbers Per Plate	839	COLONIES		839	839	COLONIES			INSTRUMENT COUNTED	2015-08-03
23	8325064	Ames	GT	SETR	R	ALL	4	RPPMEAN	Mean of Revertant Numbers Per Plate	854.3	COLONIES	MEAN	854.3	854.3	COLONIES				2015-08-03
24	8325064	Ames	GT	SETR	R	ALL	5	RPPSTDDV	Standard Deviation of Revertant Numbers Per Plate	51.7	COLONIES	STANDARD DEVIATION	51.7	51.7	COLONIES				2015-08-03
25	8325064	Ames	GT	SETR	R	ALL	6	RPPFLDINC	Fold Increase of Revertant Numbers Per Plate	6.4	COLONIES	FOLD INCREASE	6.4	6.4	COLONIES				2015-08-03

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SEND Example.In vitro Bacterial Reverse Mutation Assay