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titlets.xpt (trial summary, study level parameters)
  • Assumption:  When the experimental unit is derived from the species and strain, such as a cell line, then TESTSYS should be supplied.


Row

STUDYID

ASSAYID

DOMAIN

TSSEQ

TSGRPID

TSPARMCD

TSPARM

TSVAL

TSVALNF

1

8325064AmesTS1
GLPTYPGood Laboratory Practice TypeFDA

2

8325064AmesTS2
GLPTYPGood Laboratory Practice TypeOECD

3

8325064AmesTS1
STSTDTCStudy Start Date2015-07-29

4

8325064AmesTS1
STITLEStudy Title

The Bacterial Reverse Mutation Test, Study 8325064-1


5

8325064AmesTS1
SNDIGVERSEND Implementation Guide VersionTOBACCO IMPLEMENTATION GUIDE VERSION 1.0

6

8325064AmesTS1
SNDCTVERSEND Controlled Terminology VersionSEND Terminology 2021-09-30

7

8325064AmesTS1
SSPONSORSponsor OrganizationExample Sponsor Inc.

8

8325064AmesTS1
SPREFIDSponsor's Study Reference ID
NOT APPLICABLE

9

8325064AmesTS11TSTFNAMTest Facility NameExample Tox Lab Name

10

8325064AmesTS11TSTFLOCTest Facility Location10 Somewhere Street, Montgomery, AL 10000

11

8325064AmesTS11TFCNTRYTest Facility CountryUSA

12

8325064AmesTS11STDIRStudy DirectorDr. R. Smith

13

8325064AmesTS1
GLPFLGLP FlagN

14

8325064AmesTS1
ASTDAssay StandardOECD Test No. 471 

15

8325064AmesTS1
ASTDVAssay Standard Version2020-06-29

16

8325064AmesTS1
SSTYPStudy TypeGENOTOXICITY IN VITRO

17

8325064AmesTS1
SSSTYPStudy Sub TypeBacterial Reverse Mutation Test

18

8325064AmesTS12SPECIESSpeciesSalmonella 

19

8325064AmesTS12STRAINStrainTA98

20

8325064AmesTS12STRAINStrainTA100

21

8325064AmesTS12STRAINStrainTA1535

22

8325064AmesTS12STRAINStrainTA1537

23

8325064AmesTS13SPECIESSpeciesEscherichia coli

24

8325064AmesTS13STRAINStrainWP2 uvrA pKM101
Expand
titleRaw Data Table for Study 8325064

Image Added

Dataset wrap
Nametx.xpt (trial sets)Trial Sets
  • How do we handle "toxic, no revertant colonies"?  (LAK will add 6 records with GTSTAT = NOT DONE, GTREASND = "TOO MUCH CYTOTOXICITY,"
  • Condition of background bacterial lawn?  Slight thinning, Very thin? - refer to SEND team's marked-up table.
    • new Test code of Cytotoxicity with GTORRES = S, V (controlled terms)
    • Each plate we would have one result record for Revertent count and another for the lawn evaluation (NORMAL, SLIGHT THINNING, VERY THIN)
  • When "-" in Mean, Std Dev, Fold Inc - refer to SEND team's marked-up table (GTSTAT = NOT DONE; variety of REASND)
Rowcaps
Rows 1-22:Shows trial set parameters and trial set values that comprise the test conditions for the set SetA. SetA is the first row of the raw data table, see the row labeled "SetA" in the table, Raw Data for Study 8325064.
Rows 2-4:Show two records for Alkaline Phosphatase that were collected 1 day apart and are expected to be reported together. Row 4 shows how to create a derived record (average of the Rows 2 and 3) and flag it as Derived (LBDRVFL = "Y") as well as the record to use as baseline (LBBLFL = "Y").
Rows 6-7:Show a suggested use of the LBSCAT variable. It could be used to further classify types of tests within a laboratory panel (e.g., "DIFFERENTIAL").
Row 9:Shows the proper use of the LBSTAT variable to indicate "NOT DONE," when the fact that the test was done was documented.
Row 12:The subject had Cholesterol measured. The normal range for this test is <200 mg/dL. The value <200 may not be used in the normal range variables LBORNRHI or LBSTNRHI; however, a sponsor may decide, e.g., to enter "0" into LBORNRLO and "199" in LBORNRHI. The sponsor must define the appropriate value for all of the normal range variables.
Row 13:Shows the use of LBUSCHFL to indicate that the test result was obtained from an unscheduled blood collection. In this case, the subject was moribund and a blood sample was taken prior to sacrifice.
Rows 1, 6:Use records in the SUPPLB dataset example to show biological significance assigned by the investigator for test results.
4
Expand
titletx.xpt (trial sets)
RowSTUDYIDASSAYIDDOMAINSETCDSETTXSEQTXPARMCDTXPARMTXVAL
1

Below the SETS shown in the TX table are rows A, F, I, and R (probably don't need R)         Image Removed

RowSTUDYIDASSAYIDDOMAINSETCD
SET (what sponsor calls it)
TXSEQTXPARMCDTXPARMTXVAL
18325064AmesTX

SetA

A-TA98-C01SPECIESSpeciesSalmonella typhimurium
28325064AmesTXSetAA-TA98-C02STRAINStrain/SubstrainTA98
38325064AmesTX

SetA 

A-TA98-C03METACTMetabolic Activation  
8325064AmesTX
SetA 

SetA

A-TA98-C0
4
1SPECIES
METACTFLY/N presence of metabolic activationN
SpeciesSalmonella typhimurium
2
5
8325064AmesTXSetAA-TA98-C0
5
2
TRTDMINTreatment Duration Minimum71.5
STRAINStrain/SubstrainTA98
3
6
8325064AmesTX
SetA

SetA 

A-TA98-C0
6
3
TRTDTRGTreatment Duration Target72
METACTMetabolic Activation  
4
7
8325064AmesTX
SetA

SetA 

A-TA98-C0
7
4
TRTDMAXTreatment Duration Maximum72.5
METACTFLY/N presence of metabolic activationN
5
8
8325064AmesTXSetAA-TA98-C0
8
5
TRTDU
TRTDMINTreatment Duration
Unit
Minimum
HOURS
71.5
9
68325064AmesTXSetAA-TA98-C0
9
6
INCBTMPIncubation Temperature37
TRTDTRGTreatment Duration Target72
7
10
8325064AmesTXSetAA-TA98-C0
10
7
INCBTMPUIncubation Temperature UnitC
TRTDMAXTreatment Duration Maximum72.5
8
11
8325064AmesTXSetAA-TA98-C0
11
8
HUMIDAtmospheric Relative Humidity  Percent50
TRTDUTreatment Duration UnitHOURS
9
12
8325064AmesTXSetAA-TA98-C0
12
9
ATMCO2Atmospheric CO2 Percent5
INCBTMPIncubation Temperature37
10
13
8325064AmesTXSetAA-TA98-C0
13
10
SPTOBID

Sponsor defined tobacco identifier

CIG01a
INCBTMPUIncubation Temperature UnitC
11
14
8325064AmesTXSetAA-TA98-C0
14
11
EXPTYP

Exposure Type (See TIG NC workstream minutes 30-Jan here: Nonclinical)

Submerged
HUMIDAtmospheric Relative Humidity  Percent50
12
15
8325064AmesTXSetAA-TA98-C0
15
12
SAMTYP 

Sample Type

Total Particulate Matter in PBS
ATMCO2Atmospheric CO2 Percent5
13
16
8325064AmesTXSetAA-TA98-C0
16
13
INTRVN

name of the intervention article

TA1
SPTOBID

Sponsor defined tobacco identifier

CIG01a
14
17
8325064AmesTXSetAA-TA98-C0
17
14
ITVTYPE

type of intervention article

Vehicle Control
EXPTYP

Exposure Type (See TIG NC workstream minutes 30-Jan here: Nonclinical)

Submerged
15
18
8325064AmesTXSetAA-TA98-C0
18
15
ITVCONCConcentration of intervention article0
SAMTYP 

Sample Type

Total Particulate Matter in PBS
16
19
8325064AmesTXSetAA-TA98-C0
19
16
ITVCONCUConcentration Unitug/plate
INTRVN

name of the intervention article

TA1
17
20
8325064AmesTXSetAA-TA98-C0
20TRTVTreatment VehicleDMSO21
17ITVTYPE

type of intervention article

Vehicle Control
188325064AmesTXSetAA-TA98-C0
21
18
SPDEVIDSponsor defined device identifierPUFFMASTER3K
ITVCONCConcentration of intervention article0
19
22
8325064AmesTXSetAA-TA98-C0
22DUREFIDSmoke Regimen
19ITVCONCUConcentration Unitug/plate
20
Medium Intensity Regimen
8325064AmesTX

SetF

(row 6)

SetAA
F
-TA98-
C5001SPECIES
C020TRTVTreatment VehicleDMSO
21
Species
8325064AmesTX

SetF

2STRAINStrain/Substrain
SetAA-TA98-C021SPDEVIDSponsor defined device identifierPUFFMASTER3K
22
23
8325064AmesTX

SetF

3METACT
SetAA-TA98-C022DUREFIDSmoke RegimenMedium Intensity Regimen
23
Metabolic Activation  
8325064AmesTX

SetF

4METACTFLY/N presence of metabolic activation

(row 6)

F-TA98-C5001SPECIESSpecies
24
N
8325064AmesTX

SetF

TRTDRTOLTreatment Duration Tolerance8325064AmesTXSetFTRTDURUTreatment Duration Unit (this is for both TRTDURT, TRTDURTOL)
F-TA98-C5002STRAINStrain/Substrain
258325064AmesTX

SetF

INTRVN

name of the intervention article

(Tobacco ProdA, Bleomycin or Cyclophosphamid A)

F-TA98-C5003METACTMetabolic Activation  
26
TA1
8325064AmesTX

SetF

ITVTYPE

type of intervention article

choices of values:  product; negative control; positive control

F-TA98-C5004METACTFLY/N presence of metabolic activationN
27
Product
8325064AmesTXSetF
ITVCONCConcentration of intervention article
F-TA98-C500
TRTDRTOLTreatment Duration Tolerance
28
500
8325064AmesTXSetF
ITVCONCUConcentration Unitug/plate
F-TA98-C500
TRTDURUTreatment Duration Unit (this is for both TRTDURT, TRTDURTOL)

8325064AmesTXSetF
STRAINStrain/Substrain
F-TA98-C500
INTRVN

name of the intervention article

(Tobacco ProdA, Bleomycin or Cyclophosphamid A)

TA1
TA98

8325064AmesTXSetF
REGIMESmoking RegimeISO Regime
F-TA98-C500
ITVTYPE

type of intervention article

choices of values:  product; negative control; positive control

Product
...

8325064AmesTX

SetG (row 7) do G not I!!!

METACTMetabolic Activation  (should there be two parms? Presence, type)?
SetFF-TA98-C500
ITVCONCConcentration of intervention article500
None

8325064AmesTX
SetGTRTDRTRGTreatment Duration target. (how do we show 3-6 hour range?  start/end, target and tolerance?, one text field not-analyzable)
SetFF-TA98-C500
ITVCONCUConcentration Unitug/plate

8325064AmesTX
SetGTRTDRTOL
SetFF-TA98-C500
STRAINStrain/SubstrainTA98
Treatment Duration Tolerance

8325064AmesTX
SetGTRTDURUTreatment Duration Unit (this is for both TRTDURT, TRTDURTOL)
SetFF-TA98-C500
REGIMESmoking RegimeISO Regime
...











































































































































8325064AmesTX

SetG

INTRVN

name of the intervention article

(Tobacco ProdA, Bleomycin or Cyclophosphamid A)

(row 7) do G not I!!!



METACTMetabolic Activation  (should there be two parms? Presence, type)?None
2-Nitrofluorine

8325064AmesTXSetG
ITVTYPE

type of intervention article

choices of values:  product; negative control; positive control

Positive Control


TRTDRTRGTreatment Duration target. (how do we show 3-6 hour range?  start/end, target and tolerance?, one text field not-analyzable)

8325064AmesTXSetG
ITVCONCConcentration of intervention article5


TRTDRTOLTreatment Duration Tolerance

8325064AmesTXSetG
ITVCONCUug/plate


TRTDURU
Concentration Unit
Treatment Duration Unit (this is for both TRTDURT, TRTDURTOL)

8325064AmesTXSetG
REGIMESmoking RegimeISO...SetG


INTRVN

name of the intervention article

(Tobacco ProdA, Bleomycin or Cyclophosphamid A)

2-Nitrofluorine

8325064AmesTX

SetR

(Row 18)

METACTMetabolic Activation  (should there be two parms? Presence, type)?
SetG

ITVTYPE

type of intervention article

choices of values:  product; negative control; positive control

Positive Control
None

8325064AmesTXSetG

SetR

TRTDRTRGTreatment Duration target. (how do we show 3-6 hour range?  start/end, target and tolerance?, one text field not-analyzable)


ITVCONCConcentration of intervention article5

8325064AmesTX
SetRTRTDRTOL
SetG

ITVCONCUConcentration Unitug/plate
Treatment Duration Tolerance

8325064AmesTX
SetRTRTDURUTreatment Duration Unit (this is for both TRTDURT, TRTDURTOL)
SetG

REGIMESmoking RegimeISO
...


SetG





8325064AmesTX

SetR

INTRVN

name of the intervention article

(Tobacco ProdA, Bleomycin or Cyclophosphamid A)

(Row 18)



METACTMetabolic Activation  (should there be two parms? Presence, type)?None

8325064AmesTX

SetR



TRTDRTRGTreatment Duration target. (how do we show 3-6 hour range?  start/end, target and tolerance?, one text field not-analyzable)
4-Nitroquinoline-1-oxide


8325064AmesTXSetR
ITVTYPE

type of intervention article

choices of values:  product; negative control; positive control



TRTDRTOLTreatment Duration Tolerance

8325064AmesTXSetR

TRTDURUTreatment Duration Unit (this is for both TRTDURT, TRTDURTOL)
Positive Control


8325064AmesTX
SetRITVCONCConcentration of intervention article28325064AmesTXSetRITVCONCUConcentration Unitug/plate8325064AmesTXSetRSTRAINStrain/SubstrainTA988325064AmesTXSetRREGIMESmoking RegimeISO
Expand

Ou.xpt!!!

SetR

INTRVN

name of the intervention article

(Tobacco ProdA, Bleomycin or Cyclophosphamid A)

4-Nitroquinoline-1-oxide

8325064AmesTXSetR

ITVTYPE

type of intervention article

choices of values:  product; negative control; positive control

Positive Control

8325064AmesTXSetR

ITVCONCConcentration of intervention article2

8325064AmesTXSetR

ITVCONCUConcentration Unitug/plate

8325064AmesTXSetR

STRAINStrain/SubstrainTA98

8325064AmesTXSetR

REGIMESmoking RegimeISO
Dataset wrap
Nameou.xpt Observational and Experimental Unit Identifiers
Rowcaps
Row 1:Shows values collected for the set, SetA, as shown in the 
Rows 2-4:Show two records for Alkaline Phosphatase that were collected 1 day apart and are expected to be reported together. Row 4 shows how to create a derived record (average of the Rows 2 and 3) and flag it as Derived (LBDRVFL = "Y") as well as the record to use as baseline (LBBLFL = "Y").
Rows 6-7:Show a suggested use of the LBSCAT variable. It could be used to further classify types of tests within a laboratory panel (e.g., "DIFFERENTIAL").
Row 9:Shows the proper use of the LBSTAT variable to indicate "NOT DONE," when the fact that the test was done was documented.
Row 12:The subject had Cholesterol measured. The normal range for this test is <200 mg/dL. The value <200 may not be used in the normal range variables LBORNRHI or LBSTNRHI; however, a sponsor may decide, e.g., to enter "0" into LBORNRLO and "199" in LBORNRHI. The sponsor must define the appropriate value for all of the normal range variables.
Row 13:Shows the use of LBUSCHFL to indicate that the test result was obtained from an unscheduled blood collection. In this case, the subject was moribund and a blood sample was taken prior to sacrifice.
Rows 1, 6:Use records in the SUPPLB dataset example to show biological significance assigned by the investigator for test results.
Dataset2

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 (in TX)EUID OBUID  
18325064AmesOUSetA
VC1
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)
Expand
titlegt.xpt (similar to LB)
Dataset wrap
Namegt.xpt
Rowcaps
Rows 1-7:Show values collected for the set, SetA. 
Rows 8-15:Shows values collected for the set, SetF.  
Rows 6-7:Show a suggested use of the LBSCAT variable. It could be used to further classify types of tests within a laboratory panel (e.g., "DIFFERENTIAL").
Rows 6,7,12,13, x,x,x,x:Show values collected (e.g., MEAN, STANDARD DEVIATION, and/or FOLD INCREASE) that apply to all of the observational units within the experimental unit, as show by OBUID = "ALL". 
Row 9:Shows the proper use of the LBSTAT variable to indicate "NOT DONE," when the fact that the test was done was documented.
Row 12:The subject had Cholesterol measured. The normal range for this test is <200 mg/dL. The value <200 may not be used in the normal range variables LBORNRHI or LBSTNRHI; however, a sponsor may decide, e.g., to enter "0" into LBORNRLO and "199" in LBORNRHI. The sponsor must define the appropriate value for all of the normal range variables.
Row 13:Shows the use of LBUSCHFL to indicate that the test result was obtained from an unscheduled blood collection. In this case, the subject was moribund and a blood sample was taken prior to sacrifice.
Rows 1, 6:Use records in the SUPPLB dataset example to show biological significance assigned by the investigator for test results.
Dataset2
RowSTUDYIDASSAYIDDOMAINTXSETCDEUIDOUIDGTSEQGTTESTCDGTTESTGTORRESGTORRESUGTCOLSRT (coll. summ. result type)GTSTRESCGTSTRESNGTSTRESUGTDTCGTMETHOD
18325064AmesGTSETA A0_11RPPRevertant Numbers Per Plate26COLONIES
2626COLONIES
2015-08-03

INSTRUMENT COUNTED

28325064AmesGTSETA A0_22RPPRevertant Numbers Per Plate35COLONIES
3535

2015-08-03		INSTRUMENT COUNTED
38325064AmesGTSETA A0_33RPPRevertant Numbers Per Plate39COLONIES
3939

2015-08-03		INSTRUMENT COUNTED
48325064AmesGTSETA A0_44RPPRevertant Numbers Per Plate35COLONIES
3535

2015-08-03

INSTRUMENT COUNTED

58325064AmesGTSETA A0_55RPPRevertant Numbers Per Plate30COLONIES
3030
2015-08-03INSTRUMENT COUNTED
68325064AmesGTSETA AALL6RPPRevertant Numbers Per Plate33.0COLONIESMEAN33.033.0


78325064AmesGTSETA AALL7RPPRevertant Numbers Per Plate5.0COLONIESSTANDARD DEVIATION5.05.0

INSTRUMENT COUNTED

88325064AmesGTSETF
5_11RPPRevertant Numbers Per Plate8

88

MANUALLY COUNTED
98325064AmesGTSETF
5_11









108325064AmesGTSETF 
5_22RPPRevertant Numbers Per Plate10

1010

MANUALLY COUNTED
118325064AmesGTSETF 
5_33RPPRevertant Numbers Per Plate12

1212

MANUALLY COUNTED
128325064AmesGTSETF
ALL6RPPMEANMean of Revertant Numbers Per Plate

10.0




10.0


10.0





138325064AmesGTSETF 
ALL7RPPSTDDVStandard Deviation of Revertant Numbers Per Plate2.0

2.02.0


148325064AmesGTSETF 
ALL8RPPFDINCFold Increase of Revertant Numbers Per Plate0.3

0.30.3


158325064AmesGTSETF 

9CYTOTOXCytotoxicityVery thin background bacterial lawn

V




8325064AmesGTSETI
5_11RPPRevertant Numbers Per Plate1104

11041104



8325064AmesGTSETI
5_22RPPRevertant Numbers Per Plate1037

10371037



8325064AmesGTSETI
5_33RPPRevertant Numbers Per Plate971

971971



8325064AmesGTSETI
ALL6RPPMEANMean of Revertant Numbers Per Plate

1037.3




1037.3


1037.3






8325064AmesGTSETI
ALL7RPPSTDDVStandard Deviation of Revertant Numbers Per Plate66.5

66.566.5



8325064AmesGTSETI
ALL8RPPFLDINCFold Increase of Revertant Numbers Per Plate31.4

31.431.4