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title | Sample from Report Table |
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Image Added The following shows example data for study 123 in a report table. |
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title | Study 123, Report Table |
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The following shows the tabulated data as it is represented in a report for this study. This report includes summary statistics (i.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. , average, standard deviation, coefficient variation) for each plate and an EC50 value for the entire assay. In the table below, the light grey shading for plate 1 are values from wells that do not contain the NHK cells. The dark grey shading represents the column and row location within the 96-well plate, and in this example the applicant chose to use these column and row locations to assign their REFID values in the RELREF dataset and GT dataset. For brevity, the datasets in this example are not comprehensive but are intended to demonstrate a range of proper use.
Neutral Red Cytotoxicity Assay Results (Relative Absorbance Data) |
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| Sample ID | Smoke Regime | Replicate Number | Plate |
Neutral Red Cytotoxicity Assay Results (Relative Absorbance Data) | Run-Port Number | Sample ID | Smoke Fraction | Replicate Number | Plate Number | Well Number |
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| Relative Assay Plate Absorbance Readings |
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| Cigarette Smoke Condensate (µg/mL) | SLS (µg/mL) |
| EC50 (µg/ml) | Well Column: | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 |
| Well Row: | 0 | 10 | 50 | 75 | 100 | 120 | 140 | 160 | 200 | 110 | 200 | 1-1A1001 | 83.56729513.8.57 | 4.44 | 1.76 | 13.7 | 0.547 | .039* | 0.012* | 0.030* | 0.003* | 0.057* | 0.032* | 0.003* | 0.050* | 0.044* | 0.040* |
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| 030001 | Medium | 1 | 1 | B | 0.048* |
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 | 1-1A3C | 0.005* | 98.6 | 77.4 | 57.7 | 35.8 | 8.09 | 7.36 | 3.22 | 0.791 | 6.38 | 0.061 | 1-1A4D | 0.049* | 94.9 | 81.5 | 38.2 | 31.2 | 7.60 | 5.17 | 3.22 | 0.791 | 5.17 | 0.304 | 1-1A5 | 111 | 78.1 | 64.5 | 32.9 | 8.82 | 5.90 | 2.74 | 1.28 | 10.3 | 0.547 | 1-1A6 | 96.6 | 76.2 | 48.0 | 26.8 | 7.84 | 4.20 | 2.74 | 1.52 | 8.09 | 4.93 | 1-1A7G | 0.044* | 105 | 77.9 | 58.2 | 28.3 | 8.09 | 4.68 | 1.76 | 0.547 | 8.57 | 1.76 | 1-1A8 | 95.2 | 74.0 | 47.2 | 24.4 | 8.57 | 3.71 | 3.47 | 0.304 | 11.2 | | H | 0.056* | 0.013* | 0.040* | 0.008* | 0.013* | 0.002* | 0.029* | 0.018* | 0.006* | 0.016* | 0.024* | 0.046* | 0.791 |
| Average |
| 101 | 78.2 | 54.5 | 29.9 | 9.70 | 6.17 | 3.37 | 1.19 | 8.94 | 1.22 |
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| Std. Dev. |
| 6 | 2.9 | 9.4 | 3.6 | 2.95 | 2.19 | 1.12 | 0.72 | 2.72 | 1.58 |
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| Coeff. Var. |
| 5.8 | 3.6 | 17.2 | 11.9 | 30.4 | 35.5 | 33.1 | 61.0 | 30.5 | 129.9 | 1-1
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| *media without cells |
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| 030001 | A1A |
| 93.4 | 74.0 | 56.0 | 35.1 | 11.8 | 8.70 | 5.10 | 1.98 | 5.34 | 1.02 | 1-1A2B |
| 102 | 75.2 | 53.3 | 35.1 | 11.8 | 7.74 | 5.58 | 3.66 | 5.34 | 1.02 |
1-1 | A3C |
| 107 | 79.0 | 55.0 | 26.5 | 10.1 | 6.06 | 3.66 | 1.74 | 7.02 | 0.780 |
1-1 | A4D |
| 104 | 80.2 | 55.3 | 29.8 | 8.94 | 3.90 | 3.66 | 1.50 | 6.30 | 0.780 | 1-1A5E |
| 101 | 75.7 | 54.1 | 26.7 | 4.86 | 4.38 | 1.26 | 1.02 | 6.30 | 1.02 |
1-1 | A6F |
| 110 | 85.7 | 67.7 | 26.0 | 5.34 | 4.62 | 3.42 | 1.50 | 6.30 | 0.540 | 1-1A7G |
| 104 | 77.8 | 64.9 | 27.7 | 8.22 | 3.18 | 2.46 | 1.02 | 6.30 | 0.780 |
1-1 | A8H |
| 103 | 71.6 | 58.9 | 25.5 | 9.42 | 4.14 | 3.90 | 1.26 | 4.38 | 0.780 |
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| Average |
| 103 | 77.4 | 58.1 | 29.0 | 8.82 | 5.34 | 3.63 | 1.71 | 5.91 | 0.840 |
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| Std. Dev. |
| 5 | 4.4 | 5.3 | 4.0 | 2.63 | 1.97 | 1.37 | 0.86 | 0.83 | 0.170 |
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| Coeff. Var. |
| 4.6 | 5.6 | 9.2 | 13.6 | 29.8 | 36.9 | 37.6 | 50.0 | 14.1 | 20.2 |
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title | ts.xpt (trial summary, study level parameters) |
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- 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?
- TK6, human keratinocyte, is this "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 |
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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 using the in vitro Neutral Red Uptake assay | 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 Applicant's Organization | Example Applicant Inc. | 8 | 123 | NRU | TS | 1 | SPREFID | Sponsor's Applicant's Study Reference ID | NOT APPLICABLE | 9 | 123 | NRU | TS | 1 | 1 | TSTFNAM | Test Facility Name | Example Tox Testing 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 | 12 | 123 | NRU | TS | 1 | 1 | STDIR | Study Director | Dr. R. Smith | 13 | 123 | NRU | TS | 1 | GLPFL | GLP Flag | Y | 14 | 123 | NRU | TS | 1 | ASTD | Assay Standard | NIH Publication No. 07-4519 | 15 | 123 | NRU | TS | 1 | ASTDV | Assay Standard Version | 2006-11 | 16 | 123 | NRU | TS | 1 | SSTYP | Study Type | GENOTOXICITY IN VITRO | 17 | 123 | NRU | TS | 1 | SSSTYP | Study Sub Type | In Vitro Neutral Red Uptake | 18 | 123 | NRU | TS | 1 | SPECIES | Species | Salmonella enterica | 19 | 123 | NRU | TS | 1 | ?? | Test System?? | TK6 Normal Human Keratinocyte | Expand |
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- 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.)
Row | STUDYID | ASSAYID | DOMAIN | SETCD | | TXSEQ | TXPARMCD | TXPARM | TXVAL |
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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-A | CSC-10 | STRAIN | Strain/Substrain | Salmonella enterica enterica | 8 | 123 | NRU | TX | 1-1-A | CSC-10 | REGIME | Smoking Regime | Traditional combustible | 9 | 123 | NRU | TX | 1-1-A | CSC-10 | RUN | Assay run number | 1 | 10 | 123 | NRU | TX | 1-1-A | CSC-10 | PORT | Port ID | 1 | 11 | 123 | NRU | TX | 1-1-A | CSC-10 | SMPLID | Sample ID | 030001 | 12 | 123 | NRU | TX | 1-1-A | CSC-10 | SMKFRC | Smoke Fraction | A | 13 | 123 | NRU | TX | 1-1-A | CSC-10 | REPNUM | Replicate Number | 1 | 1 | 123 | NRU | TX | 1-1-B | CSC-10 | PLATENUM. (e.g., 1 or 2) | 1 | 1 | 2 | 123 | NRU | TX | 1-1-B | 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-B | CSC-10 | INTRVN | name of the intervention article | Cigarette Smoke Condensate | 4 | 123 | NRU | TX | 1-1-B | CSC-10 | ITVTYPE(CT e.g, Product, positive control, negative control) | type of intervention article | PRODUCT | 5 | 123 | NRU | TX | 1-1-B | CSC-10 | ITVCONC | intervention concentration | 10 | 6 | 123 | NRU | TX | 1-1-B | CSC-10 | ITVCONCU | intervention unit | ug/ml | 7 | 123 | NRU | TX | 1-1-B | CSC-10 | STRAIN | Strain/Substrain | Salmonella enterica enterica | 8 | 123 | NRU | TX | 1-1-B | CSC-10 | REGIME | Smoking Regime | Traditional combustible | 9 | 123 | NRU | TX | 1-1-B | CSC-10 | RUN | Assay run number | 1 | 10 | 123 | NRU | TX | 1-1-B | CSC-10 | PORT | Port ID | 1 | 11 | 123 | NRU | TX | 1-1-B | CSC-10 | SMPLID | Sample ID | 030001 | 12 | 123 | NRU | TX | 1-1-B | CSC-10 | SMKFRC | Smoke Fraction | A | 13 | 123 | NRU | TX | 1-1-B | CSC-10 | REPNUM | Replicate Number | 1 | 14 | 123 | NRU | TX | 1-1-B | CSC-10 | ITVCONC | intervention concentration | 10 | 15 | 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 | 10-H | 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 |
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| EC50 (µg/ml). Effective concentration at 50% cytotoxicity. (using a specific sigmoidal equation = model). |
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Dataset wrap |
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Certain data (Absorbance Reading and Background Corrected Absorbance Reading) are not shown in the sample report table above but are included here for completeness of the NRU assay. Rowcaps |
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Rows 1-3: | Show the experimental unit data for GTREFID 1-3-B. | Rows 4-6: | Show the experimental unit data for GTREFID 1-3-C. | Rows 7-9: | Show the data for the entire trial set, GTREFID=1-3. | Rows 10-12: | Show the experimental unit data for GTREFID 1-10-G | Rows 13-15: | Show the data for the entire trial set, GTREFID=1-10 | Rows 16-18: | Show the experimental unit data for GTREFID 2-10-G. | Rows 19-21: | Show the data for the entire trial set, GTREFID=2-10 | Row 22: | Shows the data for the entire assay, GTREFID=123NRU. |
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Dataset2 |
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Row | STUDYID | DOMAIN | GTSEQ | GTREFID | GTTESTCD | GTTEST | GTORRES | GTORRESU | GTCOLSRT | GTSTRESC | GTSTRESN | GTSTRESU |
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1 | 123 | GT | 1 | 1-3-B | ABSORB | Absorbance Reading | 1.7 |
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| 1.7 | 1.7 |
| 2 | 123 | GT | 2 | 1-3-B | BKCABS | Background Corrected Absorbance Reading | 1.6 |
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| 1.6 | 1.6 |
| 3 | 123 | GT | 3 | 1-3-B | RELABS | Relative Absorbance Reading | 77.7 |
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| 77.7 | 77.7 |
| 4 | 123 | GT | 4 | 1-3-C | ABSORB | Absorbance Reading | 1.8 |
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| 1.8 | 1.8 |
| 5 | 123 | GT | 5 | 1-3-C | BKCABS | Background Corrected Absorbance Reading | 1.7 |
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| 1.7 | 1.7 |
| 6 | 123 | GT | 6 | 1-3-C | RELABS | Relative Absorbance Reading | 77.4 |
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| 77.4 | 77.4 |
| 7 | 123 | GT | 7 | 1-3 | RELABS | Relative Absorbance Reading | 78.2 | % | MEAN | 78.2 | 78.2 | % | 8 | 123 | GT | 8 | 1-3 | RELABS | Relative Absorbance Reading | 2.9 | % | STANDARD DEVIATION | 2.9 | 2.9 | % | 9 | 123 | GT | 9 | 1-3 | RELABS | Relative Absorbance Reading | 3.6 |
| COEFFICIENT OF VARIANCE | 3.6 | 3.6 |
| 10 | 123 | GT | 10 | 1-10-G | ABSORB | Absorbance Reading | 0.7 |
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| 0.7 | 0.7 |
| | 123 | GT | 11 | 1-10-G | BKCABS | Background Corrected Absorbance Reading | 0.6 |
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| 0.6 | 0.6 |
| 12 | 123 | GT | 12 | 1-10-G | RELABS | Relative Absorbance Reading | 8.57 |
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| 8.57 | 8.57 |
| 13 | 123 | GT | 13 | 1-10 | RELABS | Relative Absorbance Reading | 8.94 | % | MEAN | 8.94 | 8.94 |
| 14 | 123 | GT | 14 | 1-10 | RELABS | Relative Absorbance Reading | 2.72 | % | STANDARD DEVIATION | 2.72 | 2.72 |
| 15 | 123 | GT | 15 | 1-10 | RELABS | Relative Absorbance Reading | 30.5 |
| COEFFICIENT OF VARIANCE | 30.5 | 30.5 |
| 16 | 123 | GT | 16 | 2-10-G | ABSORB | Absorbance Reading | 0.9 |
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| 17 | 123 | GT | 17 | 2-10-G | BKCABS | Background Corrected Absorbance Reading | 0.8 |
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| 18 | 123 | GT | 18 | 2-10-G | RELABS | Relative Absorbance Reading | 6.30 |
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| 6.30 | 6.30 |
| 19 | 123 | GT | 19 | 2-10 | RELABS | Relative Absorbance Reading | 5.91 | % | MEAN | 5.91 | 5.91 |
| 20 | 123 | GT | 20 | 2-10 | RELABS | Relative Absorbance Reading | 0.83 | % | STANDARD DEVIATION | 0.83 | 0.83 |
| 21 | 123 | GT | 21 | 2-10 | RELABS | Relative Absorbance Reading | 14.1 |
| COEFFICIENT OF VARIANCE | 14.1 | 14.1 |
| 22 | 123 | GT | 22 | 123NRU | | Effective Concentration of 50 Percent Cytotoxicity | 123 | ug/ml |
| 123 | 123 |
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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 | Expand |
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title | gt.xpt (similar to LB) |
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Image RemovedImage Removed |
Row | STUDYID | ASSAYID | DOMAIN | TXSETCD | GTSEQ | GTTESTCD | GTTEST | GTORRES | GTORRESU | GTSTRESC | GTSTRESN | GTSTRESU |
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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 |
4 | 123 | NRU | GT | 1-1-D | 1 | RELABS | Relative Absorbance Reading | 94.9 | ug/ml | 100 | 100 | ug/ml |
5 | 123 | NRU | GT | 1-1-E | 1 | RELABS | Relative Absorbance Reading | 111 | ug/ml | 111 | 111 | ug/ml |
123 | NRU | GT | 1-1-F | 1 | RELABS | Relative Absorbance Reading | 96.9 | ug/ml | 96.9 | 96.9 | ug/ml | 123 | NRU | GT | 1-1-G | 1 | RELABS | Relative Absorbance Reading | 105 | ug/ml | 105 | 105 | ug/ml | 123 | NRU | GT | 1-1-H | 1 | RELABS | Relative Absorbance Reading | 95.2 | ug/ml | 95.2 | 95.2 | ug/ml | 10 | 123 | NRU | GT | 1-2-A | 1 | RELABS | Relative Absorbance Reading | 83.0 | ug/ml | 83.0 | 83.0 | ug/ml |
11 | 123 | NRU | GT | 1-2-B | 1 | RELABS | Relative Absorbance Reading | 77.7 | ug/ml | 77.7 | 77.7 | ug/ml |
... | ... | 80 | 123 | NRU | GT | 1-10-H | 1 | RELABS | Relative Absorbance Reading | 0.791 | ug/ml | 0.791 | 0.791 | ug/ml |
... | ... | 160 | 123 | NRU | GT | 2-10-H | 1 | RELABS | Relative Absorbance Reading | 0.780 | ug/ml | 0.780 | 0.780