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ts.xpt (trial summary, study level parameters)
Assumption: Study can have more than one assay type Assumption: ASSAYID value of ALL means it applies to all assays in the study Replaced the ASSAYID values of MNT with MNvit (term used in OECD #487) - is this better? This is not a controlled term so we can use anything but what we use in our IG examples are often used in industry implementations so we should use realistic and best practice values as much as possible. BLEO & CPA - are positive controls, should this be included/where is this captured? — in results for the record / row? Where is TK6 cell type? is this test system (see below) 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 of 10 tobacco products in both the in vitro Micronucleus Assay and the in vitro Neutral Red Uptake
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 Organization Example Sponsor Inc. 8 123 NRU TS 1 SPREFID Sponsor's Study Reference ID NOT APPLICABLE 9 123 NRU TS 1 1 TSTFNAM Test Facility Name Example Tox 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 ... 123 NRU
TS 1 1 STDIR Study Director Dr. R. Smith 123 NRU TS 1 GLPFL GLP Flag Y 123 NRU TS 1 ASTD Assay Standard NIH Publication No. 07-4519 123 NRU TS 1 ASTDV Assay Standard Version 2006-11 123 NRU TS 1 SSTYP Study Type GENOTOXICITY IN VITRO 123 NRU TS 1 SSSTYP Study Sub Type In Vitro Neutral Red Uptake123 NRU TS 1 SPECIES Species Salmonella enterica 123 NRU TS 1 STRAIN Strain/Substrain Salmonella enterica enterica123 NRU TS 1 ?? Test System?? Normal Human Keratinocyte 123 NRU TS 1 REGIME Smoking Regime Traditional combustible 123 NRU TS 1 RUNPRT run-port number?? (always same for whole assay?) 1-1
123 NRU TS 1 SMPLID Sample ID 030001 123 NRU TS 1 SMKFRC Smoke Fraction A 123 TS 1 REPNUM Replicate Number 1
tx.xpt (trial sets)
During CT definition/reviews will decide appropriate TXPARM and TXVAL; For now, we just include good example values based on our experience TXPARMCD/TXPARM = TSPARMCD/TSPARM Row STUDYID ASSAYID DOMAIN SETCD TXSEQ TXPARMCD TXPARM TXVAL 1 123 NRU TX 1-1-A(plate-col-row in the 96-well plate) CSC-10(through SLS-200) PLATENUM. (e.g., 1 or 2) 1 1 2 123 NRU TX 1-1-A CSC-10 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-A CSC-10 INTRVN name of the intervention article Cigarette Smoke Condensate 4 123 NRU TX 1-1-A CSC-10 ITVTYPE(CT e.g, Product, positive control, negative control) type of intervention article PRODUCT 5 123 NRU TX 1-1-A CSC-10 ITVCONC intervention concentration 10 6 123 NRU TX 1-1-A CSC-10 ITVCONCU intervention unit ug/ml 7 123 NRU TX 1-1-B CSC-10 PLATENUM Plate number 1 8 123 NRU TX 1-1-B CSC-10 WELLNUM Number representing the location of the well in the 96-well plate 2-A 9 123 NRU TX 1-1-B CSC-10 INTRVN name of the intervention article Cigarette Smoke Condensate 10 123 NRU TX 1-1-B CSC-10 ITVTYPE type of intervention article PRODUCT 11 123 NRU TX 1-1-B CSC-10 ITVCONC intervention concentration 10 12 123 NRU TX 1-1-B CSC-10 ITVCONCU intervention unit ug/ml ... ... 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 2-A 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
gt.xpt (similar to LB)
Row STUDYID ASSAYID DOMAIN TXCD GTSEQ GTTESTCD GTTEST GTCELLEV(cells evaluated) GTORRES GTORRESU GTSTRESC GTSTRESN GTSTRESU GTDTC GTNOMDY GTELTM GTTPTREF 1 123 NRU GT 1-1-A 1 RELABS Relative Absorbance Reading 100 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 54 123 NRU GT 1-1-D 1 RELABS Relative Absorbance Reading 94.9 ug/ml 100 100 ug/ml 6 123 NRU GT 1-1-E 1 RELABS Relative Absorbance Reading 111 7 123 NRU GT 1-1-F 1 RELABS Relative Absorbance Reading 96.9 8 123 NRU GT 1-1-G 1 RELABS Relative Absorbance Reading 105 9 123 NRU GT 1-1-H 1 RELABS Relative Absorbance Reading 95.2 10 123 NRU GT 1-2-A 1 RELABS Relative Absorbance Reading 83.0
11 123 NRU GT 1-2-B 1 RELABS Relative Absorbance Reading 77.7 ... ... 80 123 NRU GT 1-10-H 1 RELABS Relative Absorbance Reading 0.791 ... ... 160 123 NRU GT 2-10-H 1 RELABS Relative Absorbance Reading 0.780
