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title	Study 123, Report Table

The following shows the tabulated data as it is represented in a report for this study. This report includes summary statistics (e.g. Average, Standard Deviation, Coeff. Var.); however, statistics are not included in the SEND standard and will not be represented in the SEND domains example.

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

to.xpt

do.xpt

di.xpt

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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: 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
Sponsor should be "applicant", how do we represent this? In text explanation in the IG? In definition in CT/Parmcd/Parm? ** Need to have CT discussion, include Erin M.**
TK6, human keratinocyte, is this the "test system"?
Can we draft a starting list of Study Types and Sub Types to submit to CT now?
Is there a dictionary of species and/or strain that we would use? (see example)

Row	STUDYID	ASSAYID	DOMAIN	TSSEQ	TSGRPID	TSPARMCD	TSPARM	TSVAL	TSVALNF
1	123	NRU	TS	1		GLPTYP	Good Laboratory Practice Type	FDA
2	123	NRU	TS	2		GLPTYP	Good Laboratory Practice Type	OECD
3	123	NRU	TS	1		STSTDTC	Study Start Date	2022-05-25
4	123	NRU	TS	1		STITLE	Study Title	Determination of the in vitro genotoxicity potential using the in vitro Neutral Red Uptake assay
5	123	NRU	TS	1		SNDIGVER	SEND Implementation Guide Version	TOBACCO IMPLEMENTATION GUIDE VERSION 1.0
6	123	NRU	TS	1		SNDCTVER	SEND Controlled Terminology Version	SEND Terminology 2021-09-30
7	123	NRU	TS	1		SSPONSOR	~~Sponsor~~ Applicant's Organization	Example Applicant Inc.
8	123	NRU	TS	1		SPREFID	~~Sponsor's~~ Applicant's Study Reference ID		NOT APPLICABLE
9	123	NRU	TS	1	1	TSTFNAM	Test Facility Name	Example ~~Tox~~ Testing Lab Name
10	123	NRU	TS	1	1	TSTFLOC	Test Facility Location	10 Somewhere Street, Montgomery, AL 10000
11	123	NRU	TS	1	1	TFCNTRY	Test Facility Country	USA
12	123	NRU	TS	1	1	STDIR	Study Director	Dr. R. Smith
13	123	NRU	TS	1		GLPFL	GLP Flag	Y
14	123	NRU	TS	1		ASTD	Assay Standard	NIH Publication No. 07-4519
15	123	NRU	TS	1		ASTDV	Assay Standard Version	2006-11
16	123	NRU	TS	1		SSTYP	Study Type	GENOTOXICITY IN VITRO
17	123	NRU	TS	1		SSSTYP	Study Sub Type	In Vitro Neutral Red Uptake
18	123	NRU	TS	1		SPECIES	Species	Salmonella enterica
19	123	NRU	TS	1		??	Test System??	TK6 Normal Human Keratinocyte

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title	tx.xpt (trial sets)

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~~ applicant designations as specified in the trial design.
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
Where are the details of the smoke regime defined/submitted today? (e.g., puff profile = Bell shaped puffing volumes; Puff Block = 50%, etc.)
Smoke fraction? is this indicator of processing of material from smoke machine..we used Smoke Exposure System - ok?
Incubate cells (37 ºC ±1 ºC, 90% ±10% humidity, and 5% ±1% CO2/air) - these are ranges, do we model for ranges?
- https://ntp.niehs.nih.gov/iccvam/docs/protocols/ivcyto-nhk.pdf

1A1A71A891A1A1A121A1A1516171A191A201A1A221A231A71011121314151619212223

Row	STUDYID	ASSAYID	DOMAIN	SETCD	SET (what sponsor calls it)	TXSEQ	TXPARMCD	TXPARM	TXVAL
1	123	NRU	TX	1-12-AB (plate-col-row in the 96-well plate)	CSC-10 (through SLS-200)	1	PLATENUM. (e.g., 1 or 2)	1	1
2	123	NRU	TX	1-12-AB	CSC-10	2	WELLNUM (e.g., 1-A through 10-H)	Number representing the location of the well in the 96a multiple-well plate	12-A B
3	123	NRU	TX	1-12-AB	CSC-10	3	~~INTRVN~~	~~name of the intervention article~~	~~Cigarette Smoke Condensate~~	4	123	NRU	TX	1-1-A	CSC-10	4	ITVTYPE (CT e.g, Product, positive control, negative control, vehicle control, solvent control)	type of intervention article	PRODUCT 5
	123	NRU	TX	1-	2-	B	CSC-10	5	ITVCONC	intervention concentration	10	650
	123	NRU	TX	1-	2-	B	CSC-10	6	ITVCONCU	intervention unit	ug/ml
	123	123	NRU	TX	1-	2-	B	CSC-10	7	STRAIN	Strain/Substrain	Salmonella enterica enterica
	123	NRU	TX	1-12-AB	CSC-10	8	SPDEVID	Sponsor defined device identifier	PUFFMASTER3k
	123	NRU	TX	1-	2-	B	CSC-10	9	DUREFID	Smoking Regime	Medium Intensity Regimen
	10	123	NRU	TX	1-	2-	B	CSC-10	10	RUN	Assay run number	1
	11	123	NRU	TX	1-	2-	B	CSC-10	11	SMPLID	Sample ID	030001
	123	NRU	TX	1-	2-	B	CSC-10	12	SMKEXSYS	Smoke Exposure System	Cambridge filter pad, eluted in DMSO
	13	123	NRU	TX	1-	2-	B	CSC-10	13	REPNUM	Replicate Number	1
	14	123	NRU	TX	1-12-AB	CSC-10	14	TRTDMIN	Treatment Duration Min	47.5
	123	NRU	TX	1-12-AB	CSC-10	15	TRTDTRG	Treatment Duration Target	48
	123	NRU	TX	1-12-AB	CSC-10	16	TRTDMAX	Treatment Duration Max	48.5
	123	NRU	TX	1-12-AB	CSC-10	17	TRTDU	Treatment Duration Unit	HOURS
	18	123	NRU	TX	1-	2-	B	CSC-10	18	INCBTMP	Incubation Temperature	37
	123	NRU	TX	1-	2-	B	CSC-10	19	INCBTMPU	Incubation Temperature Unit	C
	123	NRU	TX	1-	2-	B	CSC-10	20	MEDIA	Composition of Media	Sartorius HEK293
	21	123	NRU	TX	1-	2-	B	CSC-10	21	HUMID	Atmospheric Relative Humidity Percent	90
	123	NRU	TX	1-	2-	B	CSC-10	22	ATMCO2	Atmospheric CO2 Percent	5
	123	NRU	TX	1-	2-	B	CSC-10	23	SPTOBID	Sponsor defined tobacco identifier	CIG01a
	1	123	NRU	TX	1-1-B	CSC-10	1	PLATENUM. (e.g., 1 or 2)	1	1
	2	123	NRU	TX	1-1-B	CSC-10	2	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-B	CSC-10	3	INTRVN	name of the intervention article	Cigarette Smoke Condensate
	4	123	NRU	TX	1-1-B	CSC-10	4	ITVTYPE (CT e.g, Product, positive control, negative control)	type of intervention article	PRODUCT5
	123	NRU	TX	1-1-B	CSC-10	5	ITVCONC	intervention concentration	106
	123	NRU	TX	1-1-B	CSC-10	6	ITVCONCU	intervention unit	ug/ml
	123	NRU	TX	1-1-B	CSC-10	7	STRAIN	Strain/Substrain	Salmonella enterica enterica
	8	123	NRU	TX	1-1-B	CSC-10	8	SPDEVID	Sponsor defined device identifier	PUFFMASTER3k9
	123	NRU	TX	1-1-B	CSC-10	9	DUREFID	Smoking Regime	Medium Intensity Regimen
	123	NRU	TX	1-1-B	CSC-10	10	RUN	Assay run number	1
	123	NRU	TX	1-1-B	CSC-10	11	SMPLID	Sample ID	030001
	123	NRU	TX	1-1-B	CSC-10	12	SMKEXSYS	Smoke Exposure System	Cambridge filter pad, eluted in DMSO
	123	NRU	TX	1-1-B	CSC-10	13	REPNUM	Replicate Number	1
	123	NRU	TX	1-1-B	CSC-10	14	TRTDMIN	Treatment Duration Min	47.5
	123	NRU	TX	1-1-B	CSC-10	15	TRTDTRG	Treatment Duration Target	48
	123	123	NRU	TX	1-1-B	CSC-10	16	TRTDMAX	Treatment Duration Max	48.5
	17	123	NRU	TX	1-1-B	CSC-10	17	TRTDU	Treatment Duration Unit	HOURS
	18	123	NRU	TX	1-1-B	CSC-10	18	INCBTMP	Incubation Temperature	37
	123	NRU	TX	1-1-B	CSC-10	19	INCBTMPU	Incubation Temperature Unit	C
	20	123	NRU	TX	1-1-B	CSC-10	20	MEDIA	Composition of Media	Sartorius HEK293
	123	NRU	TX	1-1-B	CSC-10	21	HUMID	Atmospheric Relative Humidity Percent	90
	123	NRU	TX	1-1-B	CSC-10	22	ATMCO2	Atmospheric CO2 Percent	5
	123	NRU	TX	1-1-B	CSC-10	23	SPTOBID	Sponsor defined tobacco identifier	CIG01a
...				...
	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
...				...

Expand

title	ei.xpt Entity Identifiers (dm-like)

Entity IDs are unique within the assay (and a study can have many assays)
Replicates vs. Run
- need planned (ei.xpt) separate from the actual (gt.xpt)
- If tests run at the same time, they are replicates and are assigned the same RUNID
- If tests are run at separate times, they are runs and the RUNIDs are distinct
Different runs would be expected to have different ENID and GTDTC values. In ei.xpt, these are distinguished by different RUNID values.
Entities that are replicates of each other would be expected to
- have different ENID values
- be in the same trial set (SETCD values)
- have the same RUNID values

Row

STUDYID

ASSAYID

DOMAIN

ENID (Entity ID)

SETCD (from TX)

RUNID

REPLCTID

(Replicate Number)

PLATEID (Plate ID)

COLID

(Column number)

ROWID (Row number)

123

NRU

EI

1-2-B

1

1-8-3 (plate - col- row)

123

NRU

EI

1-3-B

1

Expand

title	gt.xpt (similar to LB)

Image Added

Image Added Image Added

ADD ei.xpt

*** Lou Ann:

new pictures with blank media on perimeter. Column 1 and Col 12, Row A and H

gt 2B through 11G will be labeled in the picture

Data values in gt.xpt will be from 2b (1a), 2c (2b), 10g (not 10H) on both plates

83.0B777

Row	STUDYID	ASSAYID	DOMAIN	ENID	GTSEQ	GTTESTCD	GTTEST	GTORRES	GTORRESU	GTSTRESC	GTSTRESN	GTSTRESU
1	123	NRU	GT	1-12-AB	1	RELABS	Relative Absorbance Reading	10077.7	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
4	123	NRU	GT	1-1-D	1	RELABS	Relative Absorbance Reading	94.9	ug/ml	100	100	ug/ml
5	123	NRU	GT	1-1-E	1	RELABS	Relative Absorbance Reading	111	ug/ml	111	111	ug/ml
77.7	77.7	123	NRU	GT	1-1-F	1	RELABS	Relative Absorbance Reading	96.9	ug/ml	96.9	96.9	ug/ml	123	NRU	GT	1-1-G	1	RELABS	Relative Absorbance Reading	105	ug/ml	105	105	ug/ml	123	NRU	GT	1-1-H	1	RELABS	Relative Absorbance Reading	95.2	ug/ml	95.2	95.2	ug/ml	10	123	NRU	GT	1-2-A	1	RELABS	Relative Absorbance Reading	ug/ml
2	83.0	83.0	ug/ml	11	123	NRU	GT	1-2-	C	1	RELABS	Relative Absorbance Reading	77.	4	ug/ml	77.	4	77.	4	ug/ml
...	...
80	123	NRU	GT	1-10-H	1	RELABS	Relative Absorbance Reading	08.79157	ug/ml	08.791570	8.79157	ug/ml
...				...
160	123	NRU	GT	2-10-H	1	RELABS	Relative Absorbance Reading	06.78030	ug/ml	06.780300	6.78030	ug/ml

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Versions Compared

Old Version 34

New Version 35

Key

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, vehicle control, solvent control)

PLATENUM. (e.g., 1 or 2)

WELLNUM (e.g., 1-A through 10-H)

(CT e.g, Product, positive control, negative control)