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This example shows trial design and results data for in vitro Neutral Red Cytotoxicity Assay, Relative Absorbance.

Note that Variable Names and Domain abbreviations may change (have not been checked against existing and are not vetted)

  • red font - indicates potential for CT code lists
  • green font - links to other domains
  • purple font - remaining questions to resolve

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

  • 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
  • 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?
RowSTUDYIDASSAYIDDOMAINSETCD
SET (what sponsor calls it)
TXSEQTXPARMCDTXPARMTXVAL
1123NRUTX1-2-B
(plate-col-row in the 96-well plate)
CSC-50
(through SLS-200)
1
PLATENUM. (e.g., 1 or 2)
1
2123NRUTX1-2-BCSC-502
WELLNUM (e.g., 1-A through 10-H)
Number representing the location of the well in a multiple-well plate2-B
3123NRUTX1-2-BCSC-504ITVTYPE
(CT e.g, Product, positive control, negative control, vehicle control, solvent control)
type of intervention articlePRODUCT 

123NRUTX1-2-BCSC-505ITVCONCintervention concentration50

123NRUTX1-2-BCSC-506ITVCONCUintervention unitug/ml

123NRUTX1-2-BCSC-507STRAINStrain/SubstrainSalmonella enterica enterica

123NRUTX1-2-BCSC-508SPDEVIDSponsor defined device identifierPUFFMASTER3k

123NRUTX1-2-BCSC-509DUREFIDSmoking RegimeMedium Intensity Regimen

123NRUTX1-2-BCSC-5010RUN

Assay run number

1


123NRUTX1-2-BCSC-5011SMPLIDSample ID030001

123NRUTX1-2-BCSC-5012SMKEXSYSSmoke Exposure SystemCambridge filter pad, eluted in DMSO

123NRUTX1-2-BCSC-5013REPNUMReplicate Number1

123NRUTX1-2-BCSC-5014TRTDMINTreatment Duration Min47.5

123NRUTX1-2-BCSC-5015TRTDTRGTreatment Duration Target48

123NRUTX1-2-BCSC-5016TRTDMAXTreatment Duration Max48.5

123NRUTX1-2-BCSC-5017TRTDUTreatment Duration UnitHOURS

123NRUTX1-2-BCSC-5018INCBTMPIncubation Temperature37

123NRUTX1-2-BCSC-5019INCBTMPUIncubation Temperature UnitC

123NRUTX1-2-BCSC-5020MEDIAComposition of MediaSartorius HEK293

123NRUTX1-2-BCSC-5021HUMIDAtmospheric Relative Humidity  Percent90

123NRUTX1-2-BCSC-5022ATMCO2Atmospheric CO2 Percent5

123NRUTX1-2-BCSC-5023SPTOBID

Sponsor defined tobacco identifier

CIG01a

123NRUTX1-2-BCSC-5024EXPTYP

Exposure Type

Air Liquid Interface

123NRUTX1-2-BCSC-5025SAMTYPSample TypeWhole Smoke Conditioned Media

123NRUTX1-2-CCSC-501
PLATENUM. (e.g., 1 or 2)
1

123NRUTX1-2-CCSC-502
WELLNUM (e.g., 1-A through 10-H)
Number representing the location of the well in the 96-well plate1-A 

123NRUTX1-2-CCSC-503INTRVNname of the intervention articleCigarette Smoke Condensate

123NRUTX1-2-CCSC-504ITVTYPE
(CT e.g, Product, positive control, negative control)
type of intervention articlePRODUCT

123NRUTX1-2-CCSC-505ITVCONCintervention concentration10

123NRUTX1-2-CCSC-506ITVCONCUintervention unitug/ml

123NRUTX1-2-CCSC-507STRAINStrain/SubstrainSalmonella enterica enterica

123NRUTX1-2-CCSC-508SPDEVIDSponsor defined device identifierPUFFMASTER3k

123NRUTX1-2-CCSC-509DUREFIDSmoking RegimeMedium Intensity Regimen

123NRUTX1-2-CCSC-5010RUN 

Assay run number

1


123NRUTX1-2-CCSC-5011SMPLIDSample ID030001

123NRUTX1-2-CCSC-5012SMKEXSYSSmoke Exposure SystemCambridge filter pad, eluted in DMSO

123NRUTX1-2-CCSC-5013REPNUM Replicate Number1

123NRUTX1-2-CCSC-5014TRTDMINTreatment Duration Min47.5

123NRUTX1-2-CCSC-5015TRTDTRGTreatment Duration Target48

123NRUTX1-2-CCSC-5016TRTDMAXTreatment Duration Max48.5

123NRUTX1-2-CCSC-5017TRTDUTreatment Duration UnitHOURS

123NRUTX1-2-CCSC-5018INCBTMPIncubation Temperature37

123NRUTX1-2-CCSC-5019INCBTMPUIncubation Temperature UnitC

123NRUTX1-2-C
20MEDIAComposition of MediaSartorius HEK293

123NRUTX1-2-CCSC-5021HUMIDAtmospheric Relative Humidity  Percent90

123NRUTX1-2-CCSC-5022ATMCO2Atmospheric CO2 Percent5

123NRUTX1-2-CCSC-5023SPTOBID

Sponsor defined tobacco identifier

CIG01a

123NRUTX1-10-HCSC-5024EXPTYP

Exposure Type

Air Liquid Interface

123NRUTX1-10-HCSC-5025SAMTYPSample TypeWhole Smoke Conditioned Media
...


...





123NRUTX1-10-HSLS-1101PLATENUMPlate number1  

123NRUTX1-10-HSLS-1102WELLNUMNumber representing the location of the well in the 96-well plate10-H

123NRUTX1-10-HSLS-1103INTRVNname of the intervention articlesodium laurel sulfate

123NRUTX1-10-HSLS-1104ITVTYPEtype of intervention articlePOSITIVE CONTROL

123NRUTX1-10-HSLS-1105ITVCONCintervention concentration200

123NRUTX1-10-HSLS-1106ITVCONCUintervention unitug/ml

123NRUTX1-10-HSLS-1107STRAINStrain/SubstrainSalmonella enterica enterica

123NRUTX1-10-HSLS-1108SPDEVIDSponsor defined device identifierPUFFMASTER3k

123NRUTX1-10-HSLS-1109DUREFIDSmoking RegimeMedium Intensity Regimen

123NRUTX1-10-HSLS-11010RUN 

Assay run number

1


123NRUTX1-10-HSLS-11011SMPLIDSample ID030001

123NRUTX1-10-HSLS-11012SMKEXSYSSmoke Exposure SystemCambridge filter pad, eluted in DMSO

123NRUTX1-10-HSLS-11013REPNUM Replicate Number1

123NRUTX1-10-HSLS-11014TRTDMINTreatment Duration Min47.5

123NRUTX1-10-HSLS-11015TRTDTRGTreatment Duration Target48

123NRUTX1-10-HSLS-11016TRTDMAXTreatment Duration Max48.5

123NRUTX1-10-HSLS-11017TRTDUTreatment Duration UnitHOURS

123NRUTX1-10-HSLS-11018INCBTMPIncubation Temperature37

123NRUTX1-10-HSLS-11019INCBTMPUIncubation Temperature UnitC

123NRUTX1-10-HSLS-11020MEDIAComposition of MediaSartorius HEK293

123NRUTX1-10-HSLS-11021HUMIDAtmospheric Relative Humidity  Percent90

123NRUTX1-10-HSLS-11022ATMCO2Atmospheric CO2 Percent5

123NRUTX1-10-HSLS-11023SPTOBID

Sponsor defined tobacco identifier

CIG01a

123NRUTX1-10-HSLS-11024EXPTYP

Exposure Type

Air Liquid Interface

123NRUTX1-10-HSLS-11025SAMTYPSample TypeWhole Smoke Conditioned Media
...


...





123NRUTX2-10-HSLS-1101PLATENUMPlate number2

123NRUTX2-10-HSLS-1102WELLNUMNumber representing the location of the well in the 96-well plate10-H

123NRUTX2-10-HSLS-1103INTRVNname of the intervention articlesodium laurel sulfate

123NRUTX2-10-HSLS-1104ITVTYPEtype of intervention articlePOSITIVE CONTROL

123NRUTX2-10-HSLS-1105ITVCONCintervention concentration200

123NRUTX2-10-HSLS-1106ITVCONCUintervention unitug/ml

123NRUTX2-10-HSLS-1107STRAINStrain/SubstrainSalmonella enterica enterica

123NRUTX2-10-HSLS-1108SPDEVIDSponsor defined device identifierPUFFMASTER3k

123NRUTX2-10-HSLS-1109DUREFIDSmoking RegimeMedium Intensity Regimen

123NRUTX2-10-HSLS-11010RUN 

Assay run number

1


123NRUTX2-10-HSLS-11011SMPLIDSample ID030001

123NRUTX2-10-HSLS-11012SMKEXSYSSmoke Exposure SystemCambridge filter pad, eluted in DMSO

123NRUTX2-10-HSLS-11013REPNUM Replicate Number1

123NRUTX2-10-HSLS-11014TRTDMINTreatment Duration Min47.5

123NRUTX2-10-HSLS-11015TRTDTRGTreatment Duration Target48

123NRUTX2-10-HSLS-11016TRTDMAXTreatment Duration Max48.5

123NRUTX2-10-HSLS-11017TRTDUTreatment Duration UnitHOURS

123NRUTX2-10-HSLS-11018INCBTMPIncubation Temperature37

123NRUTX2-10-HSLS-11019INCBTMPUIncubation Temperature UnitC

123NRUTX2-10-HSLS-11020MEDIAComposition of MediaSartorius HEK293

123NRUTX2-10-HSLS-11021HUMIDAtmospheric Relative Humidity  Percent90

123NRUTX2-10-HSLS-11022ATMCO2Atmospheric CO2 Percent5

123NRUTX2-10-HSLS-11023SPTOBID

Sponsor defined tobacco identifier

CIG01a

123NRUTX2-10-HSLS-11024EXPTYP

Exposure Type

Air Liquid Interface

123NRUTX2-10-HSLS-11025SAMTYPSample TypeWhole Smoke Conditioned Media
...








  • 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

In this example, SETCD and ENID are the same value.  

RowSTUDYIDASSAYIDDOMAINENID (Entity ID)SETCD (from TX)

RUNID 


123NRUEI1-2-B1-2-B

1


123NRUEI1-2-E?1-2-E

2





2-11-G2-11-G

1





2-11-F?2-11-F

2

.  

       

*** 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

RowSTUDYIDASSAYIDDOMAINENID GTSEQGTTESTCDGTTESTGTORRESGTORRESUGTSTRESCGTSTRESNGTSTRESU
1123NRUGT1-2-B1RELABSRelative Absorbance Reading77.7ug/ml77.777.7ug/ml
2123NRUGT1-2-C1RELABSRelative Absorbance Reading77.4ug/ml77.477.4ug/ml
...











80123NRUGT1-11-G1RELABSRelative Absorbance Reading8.57ug/ml8.578.57ug/ml
...


...







160123NRUGT2-11-G1RELABSRelative Absorbance Reading6.30ug/ml6.306.30ug/ml
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