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titleStudy 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)


EC50 (µg/ml)

0

10

50

75

100

120

140

160

200

110

200

0


1-1

030001

A

1

1

1

0.046

0.046*0.039*0.012*0.030*0.003*0.057*0.032*0.003*0.050*0.044*

0.040


1-1

030001

A

1

1

2

0.048

107

77.7

65.7

30.2

15.6

9.79

5.41

2.49

8.09

0.791

0.014


1-1

030001

A

1

1

3

0.005

98.6

77.4

57.7

35.8

8.09

7.36

3.22

0.791

6.38

0.061

0.050


1-1

030001

A

1

1

4

0.049

94.9

81.5

38.2

31.2

7.60

5.17

3.22

0.791

5.17

0.304

0.017


1-1

030001

A

1

1

5

0.047

111

78.1

64.5

32.9

8.82

5.90

2.74

1.28

10.3

0.547

0.011


1-1

030001

A

1

1

6

0.032

96.6

76.2

48.0

26.8

7.84

4.20

2.74

1.52

8.09

4.93

0.022


1-1

030001

A

1

1

7

0.044

105

77.9

58.2

28.3

8.09

4.68

1.76

0.547

8.57

1.76

0.056


1-1

030001

A

1

1

8

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



EC50 (µg/ml). Effective concentration at 50% cytotoxicity.  (using a specific sigmoidal equation = model). (could also be EC20 or EC30, EC70, etc.)













123

*non-treated control wells














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



EC50  (mg/ml). Effective concentration at 50% cytotoxicity













130123

to.xpt

do.xpt

di.xpt

Expand
titlets.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

1123NRUTS1
GLPTYPGood Laboratory Practice TypeFDA
2123NRUTS2
GLPTYPGood Laboratory Practice TypeOECD
3123NRUTS1
STSTDTCStudy Start Date2022-05-25
4123NRUTS1
STITLEStudy Title

Determination of the in vitro genotoxicity potential using the in vitro Neutral Red Uptake assay


5123NRUTS1
SNDIGVERSEND Implementation Guide VersionTOBACCO IMPLEMENTATION GUIDE VERSION 1.0
6123NRUTS1
SNDCTVERSEND Controlled Terminology VersionSEND Terminology 2021-09-30
7123NRUTS1
SSPONSORSponsor Applicant's OrganizationExample Applicant Inc.
8123NRUTS1
SPREFIDSponsor's Applicant's Study Reference ID
NOT APPLICABLE
9123NRUTS11TSTFNAMTest Facility NameExample Tox Testing Lab Name
10123NRUTS11TSTFLOCTest Facility Location10 Somewhere Street, Montgomery, AL 10000
11123NRUTS11TFCNTRYTest Facility CountryUSA
12123NRUTS11STDIRStudy DirectorDr. R. Smith
13123NRUTS1
GLPFLGLP FlagY
14123NRUTS1
ASTDAssay StandardNIH Publication No. 07-4519
15123NRUTS1
ASTDVAssay Standard Version2006-11
16123NRUTS1
SSTYPStudy TypeGENOTOXICITY IN VITRO
17123NRUTS1
SSSTYPStudy Sub TypeIn Vitro Neutral Red Uptake
18123NRUTS1
SPECIESSpeciesSalmonella enterica 
19123NRUTS1
??Test System??TK6 Normal Human Keratinocyte

ou.xpt. Observational and Experimental Units domain

Expand
titletx.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?
2-BPRODUCT 50ug/mlSTRAINPUFFMASTER3kMedium Intensity Regimen10103000112SMKEXSYSCambridge filter pad, eluted in DMSO147.5481648.5HOURS18CSC50CSC5024Air Liquid InterfaceCSC50CSC5025Whole Smoke Conditioned MediaCSC50CSC50CSC501-A CSC50CSC503Cigarette Smoke CondensateCSC50CSC50PRODUCTCSC50CSC505CSC50CSC50ug/mlCSC50CSC507Salmonella enterica entericaCSC50CSC508SPDEVID device PUFFMASTER3kCSC50CSC509Medium Intensity RegimenCSC50CSC50101CSC50CSC5011CSC50CSC50Cambridge filter pad, eluted in DMSOCSC50CSC5013REPNUM 1CSC50CSC501447.5CSC50CSC501548CSC50CSC501648.5CSC50CSC5017HOURSCSC50CSC5018
RowSTUDYIDASSAYIDDOMAINSETCD
SET (what sponsor calls it)
TXSEQTXPARMCDTXPARMTXVAL
1123NRUTXCSC-50CSC-501
PLATENUM. (e.g., 1 or 2)
1TRTDMINTreatment Duration Minimum47.5
2123NRUTXCSC-50CSC-502
WELLNUM (e.g., 1-A through 10-H)
Number representing the location of the well in a multiple-well plateTRTDTRGTreatment Duration Target48
3123NRUTXCSC-50CSC-5034ITVTYPE
(CT e.g, Product, positive control, negative control, vehicle control, solvent control)
type of intervention articleTRTDMAXTreatment Duration Maximum48.5
4123NRUTXCSC-50CSC-505ITVCONCintervention concentration4TRTDUTreatment Duration UnitHOURS
5123NRUTXCSC-50CSC-506ITVCONCUintervention unit5INCBTMPIncubation Temperature37
6123NRUTXCSC-50CSC-506INCBTMPUIncubation Temperature UnitC
7123Strain/SubstrainSalmonella enterica entericaNRU123NRUTXCSC-50CSC-5078SPDEVIDSponsor defined device identifierWAVELGTHSpectrophotometer  WAVELENGTH IN NANOMETERS540
8123NRUTXCSC-50CSC-5089DUREFIDSmoking RegimeHUMIDAtmospheric Relative Humidity  Percent90
9123NRUTXCSC-50CSC-509ATMCO2RUN

Assay run number

Atmospheric CO2 Percent5
10123NRUTXCSC-50CSC-5011SMPLIDSample ID10SPTOBID

Sponsor defined tobacco identifier

CIG01a
11123NRUTXCSC-50CSC-5011EXPTYPSmoke Exposure System

Exposure Type

Air Liquid Interface???
12123NRUTXCSC-50CSC-5013REPNUMReplicate Number12SAMTYPSample TypeWhole Smoke Conditioned Media???
13123NRUTXCSC-50CSC-5014TRTDMINTreatment Duration Min13INTRVNName of the Intervention ArticleTobacco ProdA
14123NRUTXCSC-50CSC-5015TRTDTRGTreatment Duration Target14ITVTYPE
(CT e.g, Product, positive control, negative control, vehicle control, solvent control)
type of intervention articlePRODUCT 
15123NRUTXCSC-50CSC-5015ITVCONCTRTDMAXTreatment Duration Maxintervention concentration50
16123NRUTXCSC-50CSC-5017TRTDUTreatment Duration Unit16ITVCONCUintervention unitug/ml
17123NRUTXCSC-50CSC-5017STRAINStrain/SubstrainSalmonella enterica enterica
18INCBTMPIncubation Temperature37123NRUTXCSC-50CSC-501918INCBTMPUIncubation Temperature UnitC
SPDEVIDSponsor defined device identifierPUFFMASTER3k
19WAVELGTHSpectrophotometer  WAVELENGTH IN NANOMETERS540123NRUTXCSC-50CSC-502119HUMIDAtmospheric Relative Humidity  Percent90123NRUTXCSC-50DUREFIDSmoking RegimeMedium Intensity Regimen
20CSC-5022ATMCO2Atmospheric CO2 Percent5123NRUTXCSC-50CSC-502320SPTOBID

Sponsor defined tobacco identifier

CIG01a
21123NRUTXSLS-110SLS-1101TRTDMINEXPTYP

Exposure Type

Treatment Duration Minimum47.5
22123NRUTXSLS-110SLS-1102TRTDTRGSAMTYPSample TypeTreatment Duration Target48
23123NRUTXSLS-110CSC-501
PLATENUM. (e.g., 1 or 2)
1SLS-1103TRTDMAXTreatment Duration Maximum48.5
24123NRUTXSLS-110SLS-11042
WELLNUM (e.g., 1-A through 10-H)
Number representing the location of the well in the 96-well plateTRTDUTreatment Duration UnitHOURS
25123NRUTXSLS-110SLS-1105INTRVNname of the intervention articleINCBTMPIncubation Temperature37
26123NRUTXSLS-110SLS-11064ITVTYPE
(CT e.g, Product, positive control, negative control)
type of intervention articleINCBTMPUIncubation Temperature UnitC
27123NRUTXSLS-110SLS-1107ITVCONCintervention concentration10WAVELGTHSpectrophotometer  WAVELENGTH IN NANOMETERS540
28123NRUTXSLS-110SLS-11086ITVCONCUintervention unitHUMIDAtmospheric Relative Humidity  Percent90
29123NRUTXSLS-110SLS-1109ATMCO2STRAINStrain/SubstrainAtmospheric CO2 Percent5
30123NRUTXSLS-110SLS-11010SPTOBID

Sponsor defined

tobacco identifier

CIG01a
31123NRUTXSLS-110SLS-11011EXPTYPDUREFIDSmoking Regime

Exposure Type

Air Liquid Interface
32123NRUTXSLS-110SLS-11012SAMTYPRUN 

Assay run number

Sample TypeWhole Smoke Conditioned Media
33123NRUTXSLS-110SLS-11013SMPLIDSample ID030001INTRVNName of the Intervention ArticleSodium Laurel Sulfate
34123NRUTXSLS-110SLS-12SMKEXSYSSmoke Exposure System11014ITVTYPE
(CT e.g, Product, positive control, negative control, vehicle control, solvent control)
type of intervention articlePOSITIVE CONTROL
35123NRUTXSLS-110SLS-11015ITVCONCReplicate Numberintervention concentration200
36123NRUTXSLS-110SLS-11016ITVCONCUTRTDMINTreatment Duration Minintervention unitug/ml
37123NRUTXSLS-110SLS-11017STRAINTRTDTRGTreatment Duration TargetStrain/SubstrainSalmonella enterica enterica
38123NRUTXSLS-110SLS-11018TRTDMAXTreatment Duration MaxSPDEVIDSponsor defined device identifierPUFFMASTER3k
39123NRUTXSLS-110SLS-11019DUREFIDTRTDUTreatment Duration UnitSmoking RegimeMedium Intensity Regimen
40123NRUTXSLS-110SLS-11020INCBTMPIncubation Temperature37123NRUTXCSC-50CSC-5019INCBTMPUIncubation Temperature UnitC
123NRUTX20MEDIAComposition of MediaSartorius HEK293123NRUTXCSC-50CSC-5021HUMIDAtmospheric Relative Humidity  Percent90123NRUTXCSC-50CSC-5022ATMCO2Atmospheric CO2 Percent5123NRUTXCSC-50CSC-5023SPTOBID

Sponsor defined tobacco identifier

CIG01a123NRUTXCSC-50CSC-5024EXPTYP

Exposure Type

Air Liquid Interface123NRUTXCSC-50CSC-5025SAMTYPSample TypeWhole Smoke Conditioned Media......123NRUTXSLS-110SLS-1101PLATENUMPlate number1  123NRUTXSLS-110SLS-1102WELLNUMNumber representing the location of the well in the 96-well plate10-H123NRUTXSLS-110SLS-1103INTRVNname of the intervention articlesodium laurel sulfate123NRUTXSLS-110SLS-1104ITVTYPEtype of intervention articlePOSITIVE CONTROL123NRUTXSLS-110SLS-1105ITVCONCintervention concentration200123NRUTXSLS-110SLS-1106ITVCONCUintervention unitug/ml123NRUTXSLS-110SLS-1107STRAINStrain/SubstrainSalmonella enterica enterica123NRUTXSLS-110SLS-1108SPDEVIDSponsor defined device identifierPUFFMASTER3k123NRUTXSLS-110SLS-1109DUREFIDSmoking RegimeMedium Intensity Regimen123NRUTXSLS-110SLS-11010RUN 

Assay run number

1

123NRUTXSLS-110SLS-11011SMPLIDSample ID030001123NRUTXSLS-110SLS-11012SMKEXSYSSmoke Exposure SystemCambridge filter pad, eluted in DMSO123NRUTXSLS-110SLS-11013REPNUM Replicate Number1123NRUTXSLS-110SLS-11014TRTDMINTreatment Duration Min47.5123NRUTXSLS-110SLS-11015TRTDTRGTreatment Duration Target48123NRUTXSLS-110SLS-11016TRTDMAXTreatment Duration Max48.5123NRUTXSLS-110SLS-11017TRTDUTreatment Duration UnitHOURS123NRUTXSLS-110SLS-11018INCBTMPIncubation Temperature37123NRUTXSLS-110SLS-11019INCBTMPUIncubation Temperature UnitC
123NRUTXSLS-110SLS-11020MEDIAComposition of MediaSartorius HEK293123NRUTXSLS-110SLS-11021HUMIDAtmospheric Relative Humidity  Percent90123NRUTXSLS-110SLS-11022ATMCO2Atmospheric CO2 Percent5123NRUTXSLS-110SLS-11023SPTOBID

Sponsor defined tobacco identifier

CIG01a123NRUTXSLS-110SLS-11024EXPTYP

Exposure Type

Air Liquid Interface123NRUTXSLS-110SLS-11025SAMTYPSample TypeWhole Smoke Conditioned Media...123NRUTXSLS-110SLS-1101PLATENUMPlate number2123NRUTXSLS-110SLS-1102WELLNUMNumber representing the location of the well in the 96-well plate10-H123NRUTXSLS-110SLS-1103INTRVNname of the intervention articlesodium laurel sulfate123NRUTXSLS-110SLS-1104ITVTYPEtype of intervention articlePOSITIVE CONTROL123NRUTXSLS-110SLS-1105ITVCONCintervention concentration200123NRUTXSLS-110SLS-1106ITVCONCUintervention unitug/ml123NRUTXSLS-110SLS-1107STRAINStrain/SubstrainSalmonella enterica enterica123NRUTXSLS-110SLS-1108SPDEVIDSponsor defined device identifierPUFFMASTER3k123NRUTXSLS-110SLS-1109DUREFIDSmoking RegimeMedium Intensity Regimen123NRUTXSLS-110SLS-11010RUN 

Assay run number

1

123NRUTXSLS-110SLS-11011SMPLIDSample ID030001123NRUTXSLS-110SLS-11012SMKEXSYSSmoke Exposure SystemCambridge filter pad, eluted in DMSO123NRUTXSLS-110SLS-11013REPNUM Replicate Number1123NRUTXSLS-110SLS-11014TRTDMINTreatment Duration Min47.5123NRUTXSLS-110SLS-11015TRTDTRGTreatment Duration Target48123NRUTXSLS-110SLS-11016TRTDMAXTreatment Duration Max48.5123NRUTXSLS-110SLS-11017TRTDUTreatment Duration UnitHOURS123NRUTXSLS-110SLS-11018INCBTMPIncubation Temperature37123NRUTXSLS-110SLS-11019INCBTMPUIncubation Temperature UnitC
123NRUTXSLS-110SLS-11020MEDIAComposition of MediaSartorius HEK293123NRUTXSLS-110SLS-11021HUMIDAtmospheric Relative Humidity  Percent90123NRUTXSLS-110SLS-11022ATMCO2Atmospheric CO2 Percent5123NRUTXSLS-110SLS-11023SPTOBID

Sponsor defined tobacco identifier

CIG01a123NRUTXSLS-110SLS-11024EXPTYP

Exposure Type

Air Liquid Interface123NRUTXSLS-110SLS-11025SAMTYPSample TypeWhole Smoke Conditioned Media...
Expand
titleei.xpt Entity Identifiers (dm-like)
RowSTUDYIDASSAYIDDOMAINSETCD (from TX)

EUID

OBUID

RUNID 

1123NRUOUCSC-50

1-B-3

1-B-3

1

2123NRUOUCSC-50

1-C-3

1-C-3

1

3123NRUOUSLS-110

1-G-10

1-G-10

1

4123NRUOUSLS-110

2-G-10

2-G-10

1

SPTOBID

Sponsor defined tobacco identifier

CIG01a
Expand
titleou.xpt Observational and Experimental Units Domain

ou.xpt. Observational and Experimental Units domain

Experimental unit - The unit to which the treatment is applied, eg. Test tube

Observational unit - The unit on which the response is measured. (This may not be the same as the experimental unit.)


RowSTUDYIDASSAYIDDOMAINSETCD (from TX)

EUID

OBUID

1123NRUOUCSC-50

1-3-B

1-3-B

2123NRUOUCSC-50

1-3-C

1-3-C

3123NRUOUSLS-110

1-11-G

1-11-G

4123NRUOUSLS-110

2-11-G

2-11-G

Experimental unit - The unit to which the treatment is applied, eg. Test tube

Observational unit - The unit on which the response is measured. (This may not be the same as the experimental unit.)

Expand
titlegt.xpt (similar to LB)

cells growing in plate, treat cells in the plate, then add NRU dye, then extract NRU (the OBUID) dye and transfer to another plate (put in spectrophotometer & read).

.  

      Image Added  Image AddedImage Added


RowSTUDYIDASSAYIDDOMAINSETCDEUID OBUIDGTSEQGTTESTCDGTTESTGTORRESGTORRESUGTCOLSRT (coll. summ. result type)GTSTRESCGTSTRESNGTSTRESU

123NRUGTCSC-501-3-B1-3-B1ABSORBAbsorbance Reading1.7 (0.0 - 2.0)

1.71.7

123NRUGTCSC-501-3-B1-3-B2BKCABSBackground Corrected Absorbance Reading1.6

1.61.6

123NRUGTCSC-501-3-B1-3-B3RELABSRelative Absorbance Reading77.7%
77.777.7%

123NRUGTCSC-50

4RELABSRelative Absorbance Reading 78.2%MEAN78.278.2%

123NRUGTCSC-50

5RELABSRelative Absorbance Reading 2.9%STANDARD DEVIATION2.92.9%

123NRUGTCSC-50

6RELABSRelative Absorbance Reading 3.6
COEFFICIENT OF VARIANCE3.63.6

123NRUGTCSC-50

7
RowSTUDYIDASSAYIDDOMAINSETCD (in TX)EUID OBUID  
1123MLAOUA1 4_-S9_C31.3_BVC1
2123MLAOUA14_-S9_C31.3_BVC2
3123MLAOUA14_-S9_C31.3_BVC3
4123MLAOUA1 4_-S9_C31.3_BTFT1
5123MLAOUA14_-S9_C31.3_BTFT2
6123MLAOUA14_-S9_C31.3_BTFT3
7123MLAOUA24_-S9_C500_BVC1
8123MLAOUA24_-S9_C500_BVC2
9123MLAOUA24_-S9_C500_BVC3
10123MLAOUA24_-S9_C500_BTFT1
11123MLAOUA24_-S9_C500_BTFT2
12123MLAOUA24_-S9_C500_BTFT3
Expand
titlegt.xpt (similar to LB)

Image Removed

cells growing in plate, treat cells in the plate, then add NRU dye, then extract NRU (the OBUID) dye and transfer to another plate (put in spectrophotometer & read).

.  

      Image Removed  Image RemovedImage Removed

*** Lou Ann:

new pictures with blank media on perimeter

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

RowSTUDYIDASSAYIDDOMAINSETCDEUID OBUIDGTSEQGTTESTCDGTTESTGTORRESGTORRESUGTCOLSRT (coll. summ. result type)GTSTRESCGTSTRESNGTSTRESU123NRUGT1-2-B1-2-B1-2-B1ABSORBAbsorbance Reading1.7 (0.0 - 2.0)1.71.7123NRUGT1-2-B1BKCABSBackground Corrected Absorbance Reading1.61.61.6123NRUGT1-2-B1RELABSRelative Absorbance Reading77.7%77.777.7%123NRUGT1
EC50Effective Concentration of 50 Percent Cytotoxicity123ug/ml
123123ug/ml

123NRUGT
1-2-C
1RELABSRelative Absorbance Reading77.4

77.477.4
...














80123NRUGT
1-11-G
1RELABSRelative Absorbance Reading8.57ug/ml
8.578.57ug/ml
...



...









160123NRUGT
2-11-G
1RELABSRelative Absorbance Reading6.30ug/ml
6.306.30ug/ml