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This is an example showing trial design and results from the in vitro bacterial reverse mutation test of Study #8325064. The The bacterial reverse mutation test uses four different amino acid-requiring strains of Salmonella typhimurium (S. typhimurium) and one strain of Escherichia coli (E. coli) to detect point mutations, which involve substitution, addition or deletion of one or a few DNA base pairs. The principle of this bacterial reverse mutation test is that it detects chemicals that induce mutations which revert mutations present in the S typhimurium and E. coli tester strains and restore the functional capability of the bacteria to synthesize an essential amino acid. The revertant bacteria are detected by their ability to grow in the absence of the amino acid required by the parent tester strain.
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- 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? When "-" in Mean, Std Dev, Fold Inc - 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)
- (GTSTAT = NOT DONE; variety of REASND)
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| | 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. |
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| Name | ou.xpt Observational and Experimental Unit Identifiers |
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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.) | Rowcaps |
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| Row 1: | Shows values collected the values of the experimental unit identifiers and associated observational unit identifiers 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. | | SetA. SetA is the first row of the raw data table, see the row labeled "SetA" in the table, Raw Data for Study 8325064. |
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| | Rows 2-4: | 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. |
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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.) | Dataset2 |
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| Row | STUDYID | ASSAYID | DOMAIN | SETCD (in TX) | SETCD | EUID | OBUID |
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| 1 | 8325064 | Ames | OU | SetA | VC1A | 0_1 | | 2 | 1238325064 | MLAAmes | OU | SetA | A1A | 4_-S9_C31.3_B | VC20_2 |
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| 3 | 1238325064 | MLAAmes | OU | SetA | A1 | 4_-S9_C31.3_B | VC3 |
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| 4 | 123 | MLA | OU | A1 | 4_-S9_C31.3_B | TFT1 |
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| 5 | 123 | MLA | OU | A1 | 4_-S9_C31.3_B | TFT2 |
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| 6 | 123 | MLA | OU | A1 | 4_-S9_C31.3_B | TFT3 |
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| 7 | 123 | MLA | OU | A2 | 4_-S9_C500_B | VC1 |
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| 8 | 123 | MLA | OU | A2 | 4_-S9_C500_B | VC2 |
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| 9 | 123 | MLA | OU | A2 | 4_-S9_C500_B | VC3 |
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| 10 | 123 | MLA | OU | A2 | 4_-S9_C500_B | TFT1 |
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| 11 | 123 | MLA | OU | A2 | 4_-S9_C500_B | TFT2 |
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| A | 0_3 | | 4 | 8325064 | Ames | OU | SetA | A | 0_4 | | 5 | 8325064 | Ames | OU | SetA | A | 0_5 | 6 | 8325064 | Ames | OU | SetF | F | 5_1 | | 7 | 8325064 | Ames | OU | SetF | F | 5_2 | | 8 | 8325064 | Ames | OU | SetF | F | 5_3 | | 9 | 8325064 | Ames | OU | SetG | G |
| | 10 | 8325064 | Ames | OU | SetG | G |
| | 11 | 8325064 | Ames | OU | SetG | G |
| | 12 | 8325064 | Ames | OU | SetR | R |
| | 13 | 8325064 | Ames | OU | SetR | R |
| | 14 | 8325064 | Ames | OU | SetR | R | 12 | 123 | MLA | OU | A2 | 4_-S9_C500_B | TFT3 |
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| title | gt.xpt (similar to LB) |
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| 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. |
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| Row | STUDYID | ASSAYID | DOMAIN | TXSETCD | EUID | OUID | GTSEQ | GTTESTCD | GTTEST | GTORRES | GTORRESU | GTCOLSRT (coll. summ. result type) | GTSTRESC | GTSTRESN | GTSTRESU | GTDTC | GTMETHOD |
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| 1 | 8325064 | Ames | GT | SETA | A | 0_1 | 1 | RPP | Revertant Numbers Per Plate | 26 | COLONIES |
| 26 | 26 | COLONIES |
2015-08-03 | INSTRUMENT COUNTED | | 2 | 8325064 | Ames | GT | SETA | A | 0_2 | 2 | RPP | Revertant Numbers Per Plate | 35 | COLONIES |
| 35 | 35 |
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2015-08-03 | INSTRUMENT COUNTED | | 3 | 8325064 | Ames | GT | SETA | A | 0_3 | 3 | RPP | Revertant Numbers Per Plate | 39 | COLONIES |
| 39 | 39 |
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2015-08-03 | INSTRUMENT COUNTED | | 4 | 8325064 | Ames | GT | SETA | A | 0_4 | 4 | RPP | Revertant Numbers Per Plate | 35 | COLONIES |
| 35 | 35 |
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2015-08-03 | INSTRUMENT COUNTED | | 5 | 8325064 | Ames | GT | SETA | A | 0_5 | 5 | RPP | Revertant Numbers Per Plate | 30 | COLONIES |
| 30 | 30 |
| 2015-08-03 | INSTRUMENT COUNTED | | 6 | 8325064 | Ames | GT | SETA | A | ALL | 6 | RPP | Revertant Numbers Per Plate | 33.0 | COLONIES | MEAN | 33.0 | 33.0 |
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| | 7 | 8325064 | Ames | GT | SETA | A | ALL | 7 | RPP | Revertant Numbers Per Plate | 5.0 | COLONIES | STANDARD DEVIATION | 5.0 | 5.0 |
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| INSTRUMENT COUNTED | | 8 | 8325064 | Ames | GT | SETF |
| 5_1 | 1 | RPP | Revertant Numbers Per Plate | 8 |
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| 8 | 8 |
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| MANUALLY COUNTED | | 9 | 8325064 | Ames | GT | SETF |
| 5_1 | 1 |
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| | 10 | 8325064 | Ames | GT | SETF |
| 5_2 | 2 | RPP | Revertant Numbers Per Plate | 10 |
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| 10 | 10 |
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| MANUALLY COUNTED | | 11 | 8325064 | Ames | GT | SETF |
| 5_3 | 3 | RPP | Revertant Numbers Per Plate | 12 |
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| 12 | 12 |
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| MANUALLY COUNTED | | 12 | 8325064 | Ames | GT | SETF |
| ALL | 6 | RPPMEAN | Mean of Revertant Numbers Per Plate | 10.0
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| 10.0
| 10.0
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| | 13 | 8325064 | Ames | GT | SETF |
| ALL | 7 | RPPSTDDV | Standard Deviation of Revertant Numbers Per Plate | 2.0 |
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| 2.0 | 2.0 |
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| | 14 | 8325064 | Ames | GT | SETF |
| ALL | 8 | RPPFDINC | Fold Increase of Revertant Numbers Per Plate | 0.3 |
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| 0.3 | 0.3 |
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| | 15 | 8325064 | Ames | GT | SETF |
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| 9 | CYTOTOX | Cytotoxicity | Very thin background bacterial lawn |
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| 8325064 | Ames | GT | SETISETG |
| 5_1 | 1 | RPP | Revertant Numbers Per Plate | 1104 |
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| 1104 | 1104 |
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| 8325064 | Ames | GT | SETI |
| 5_2 | 2 | RPP | Revertant Numbers Per Plate | 1037 |
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| 1037 | 1037 |
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| 8325064 | Ames | GT | SETI |
| 5_3 | 3 | RPP | Revertant Numbers Per Plate | 971 |
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| 971 | 971 |
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| 8325064 | Ames | GT | SETI |
| ALL | 6 | RPPMEAN | Mean of Revertant Numbers Per Plate | 1037.3
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| 1037.3
| 1037.3
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| 8325064 | Ames | GT | SETI |
| ALL | 7 | RPPSTDDV | Standard Deviation of Revertant Numbers Per Plate | 66.5 |
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| 66.5 | 66.5 |
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| 8325064 | Ames | GT | SETI |
| ALL | 8 | RPPFLDINC | Fold Increase of Revertant Numbers Per Plate | 31.4 |
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| 31.4 | 31.4 |
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