This readme.txt file was generated on 2025-2-17 by Madeline K Grunklee and edited 20250301-20250313 by data curator Recommendated citation for the data: Grunklee, M. K., Bartz, J. C., Karwan, D. L., Lichtenberg, S. S., Lurndahl, N. A., Larsen, P. A., Schwabenlander, M. D., Rowden, G. R., Li, E. A., Yuan, Q., & Wolf, T. M. (2025). Supporting Dataset for "RT-QuIC Optimization for Prion Detection in Two Minnesota Soil Types" and "Detection of Chronic Wasting Disease Prions in Soil at an Illegal White-tailed Deer Carcass Disposal Site" [Data set]. Data Repository for the University of Minnesota (DRUM). https://doi.org/10.13020/P2P3-1509 ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset: Supporting Dataset for "RT-QuIC Optimization for Prion Detection in Two Minnesota Soil Types" and "Detection of Chronic Wasting Disease Prions in Soil at an Illegal White-tailed Deer Carcass Disposal Site" 2. Author Information Corresponding Author Contact Information Name: Tiffany M. Wolf Institution: University of Minnesota College of Veterinary Medicine Address: Department of Veterinary Population Medicine, 1988 Fitch Ave, St. Paul, MN 55108 USA Email: wolfx305@umn.edu ORCID: 0000-0003-1740-4442 Lead Author Contact Information Name: Madeline K. Grunklee Institution: University of Minnesota College of Veterinary Medicine Address: Department of Veterinary Population Medicine, 1988 Fitch Ave, St. Paul, MN 55108 USA Email: maddiegrunklee@gmail.com Co-Author Contact Information Name: Jason C. Bartz Institution: Department of Medical Microbiology and Immunology, Creighton University School of Medicine Address: Omaha, Nebraska 68178, USA ORCID: 0000-0003-4081-7886 Name: Diana L. Karwan Institution: University of Minnesota College of Food, Agricultural, and Natural Resource Sciences Address: Department of Forest Resources, 115 Green Hall, 1530 Cleveland Ave. N., St. Paul, Minnesota 55108, USA ORCID: 0000-0002-4529-0369 Name: Stuart S. Lichtenberg Institution: University of Minnesota College of Veterinary Medicine Address: Department of Veterinary and Biomedical Sciences, 301 Veterinary Science Building, 1971 Commonwealth Avenue, St. Paul, Minnesota 55108, USA ORCID: 0000-0002-2445-8927 Name: Nicole A. Lurndahl Institution: University of Minnesota College of Veterinary Medicine Address: Department of Veterinary and Biomedical Sciences, 301 Veterinary Science Building, 1971 Commonwealth Avenue, St. Paul, Minnesota 55108, USA Name: Peter A. Larsen Institution: University of Minnesota College of Veterinary Medicine Address: Department of Veterinary and Biomedical Sciences, 301 Veterinary Science Building, 1971 Commonwealth Avenue, St. Paul, Minnesota 55108, USA Email: plarsen@umn.edu ORCID: 0000-0002-3634-3625 Name: Marc D. Schwabenlander Institution: University of Minnesota College of Veterinary Medicine Address: Department of Veterinary and Biomedical Sciences, 301 Veterinary Science Building, 1971 Commonwealth Avenue, St. Paul, Minnesota 55108, USA Email: schwa239@umn.edu ORCID: 0000-0001-9664-6890 Name: Gage R. Rowden Institution: University of Minnesota College of Veterinary Medicine Address: Department of Veterinary and Biomedical Sciences, 301 Veterinary Science Building, 1971 Commonwealth Avenue, St. Paul, Minnesota 55108, USA ORCID: 0000-0002-7517-0480 Name: E. Anu Li Institution: University of Minnesota College of Food, Agricultural, and Natural Resource Sciences Address: Department of Forest Resources, 115 Green Hall, 1530 Cleveland Ave. N., St. Paul, Minnesota 55108, USA ORCID: 0000-0002-3274-4245 Name: Qi Yuan Institution: Department of Medical Microbiology and Immunology, Creighton University 1 School of Medicine Address: Omaha, Nebraska 68178, USA 3. Date published or finalized for release: 2025-02-17 4. Date of data collection: 2023-01-19 through 2024-01-23 5. Geographic location of data collection (where was data collected?): Minnesota, USA 6. Information about funding sources that supported the collection of the data: This study was funded by the Minnesota Environment and Natural Resource Trust Fund as recommended by the Legislative-Citizen Commission on Minnesota Resources [2020-087 and 2022-217] and the Conservation Science Graduate Program at the University of Minnesota Twin Cities. 7. Overview of the data (abstract): These data describe prion detections in soil using real-time quaking-induced conversion (RT-QuIC) assay with various metric calculations common to RT-QuIC. The Soil_Cntrl_Expmts_Data.csv file contains data from a series of control experiments aimed at optimizing and applying RT-QuIC for the detection of chronic wasting disease prions in environmental soil samples. We focused negative control experiments on refining RT-QuIC and sample processing to use on Minnesota native soils, which included limiting background noise from the samples. Starting on 2023-05-08, we used spiked soil control experiments to distinguish true prion signal from background noise and validate detection reliability. Following soil control experiments, the Soil_Test_Samples_Data.csv file describes our sample testing in RT-QuIC collected from our study site, an illegal white-tailed deer (Odocoileus virginianus, WTD) carcass disposal site and a nearby captive WTD farm in Beltrami County, Minnesota. We analyzed study site soil samples for prion presence to assess potential environmental contamination associated with improper carcass disposal practices. -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: CC0 1.0 Universal http://creativecommons.org/publicdomain/zero/1.0/ 2. Links to publications that cite or use the data: Soil_Cntrl_Expmts_Data.csv used in: a. Grunklee M.K., Lichtenberg S.S., Rowden G.R., Karwan D.L., Li E.A., Schwabenlander M.D., Wolf T.M., RT-QuIC Optimization for Prion Detection in Two Minnesota Soil Types, MethodsX [Co-submission; In review] Soil_Test_Samples_Data.csv used in: b. Grunklee M.K., Lurndahl N.A., Lichtenberg S.S., Schwabenlander M.D., Karwan D.L., Wille E.A., Bartz J.C., Yuan Q., Larsen P.A., Wolf T.M., Detection of Chronic Wasting Disease Prions in Soil at an Illegal White-Tailed Deer Carcass Disposal Site, Sci Total Environ. [In review] 3. Was data derived from another source? No 4. Terms of Use: Data Repository for the U of Minnesota (DRUM) By using these files, users agree to the Terms of Use. https://conservancy.umn.edu/pages/policies/#drum-terms-of-use --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: Soil_Cntrl_Expmts_Data.csv Short description: This data includes all control experiments conducted prior to testing study site test samples. I.e. negative soil experiments and inoculation/spiking soil experiments. We described this dataset and outline the full sample/data collection and processing protocols in a.Grunklee et al., In review. We collected this data to inform the sample processing protocol which we then used on the study site soil samples (b.Grunklee et al., In review). All column labels are defined at the end of this readme file. B. Filename: Soil_Test_Samples_Data.csv Short description: This data includes all experiments involved in the testing of the Beltrami County study site soil samples (i.e. those within the dump site, around the CWD+ farm, and immediately around the dump site). We described this dataset and outline the full sample/data collection and processing protocols in b.Grunklee et al. In review. Each plate had at least 1 representative negative control Alfisol or Histosol soil types followed by the study site test soil samples in question. Note: all of these soil samples were initially dried and run in a soil dilution of 10^-1 prior to RT-QuIC analysis per negative soil experimental results (a.Grunklee et al., In review). All column labels are defined at the end of this readme file. 2. Relationship between files: The Soil_Cntrl_Expmts_Data.csv dataset informed our sample processing and analysis protocols for the study site samples contained in the Soil_Test_Samples_Data.csv dataset. Per the results of the Soil_Cntrl_Expmts_Data.csv dataset, we dried and ran study site soil samples in a soil dilution of 10^-1 prior to RT-QuIC analysis (a.Grunklee et al., In review). -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: We collected soil samples from our study site May through September of 2021 as described in a.,b.Grunklee et al., In review. We then tested soil samples using real-time quaking-induced conversion (RT-QuIC) assay 2023-01-19 through 2024-01-23. We calculated various metrics common to RT-QuIC analysis from the assay output in relative fluorescent units (RFU) as described below and in the readme sheets associated with each spreadsheet. These methods are further described in the associated manuscripts (a.,b.Grunklee et al., In review). 2. Methods for processing the data: We processed the RT-QuIC RFU output data using the following calculations: Time to Threshold: Time measured in hours over course of 48 hour experiment it took to reach maximum relative fluorescence units measurement. MPR: maxpoint ratio (MPR). MPR was measured per well by dividing the maximum relative fluorescent units (RFU) value obtained within 48 hours by the background RFU value (i.e., MPR = maxRFU/backgroundRFU; Rowden et al., 2023). RAF: rate of amyloid formation (RAF). RAF of the reaction was calculated per well as the reciprocal of time required for the fluorescence to reach twice the background fluorescence (Schwabenlander et al., 2024). RAF data lacks the ability to be statistically informative as ideal negative controls should inherently be zero (Rowden et al., 2023). MS: the maximum slope (MS) of relative fluorescence units (RFU) per second from a baseline correction calculation. Across all experiments, the MS of the reaction was measured using a moving window of three reads of baseline corrected relative fluorescence units (RFU; i.e. readings normalized against the background fluorescence) and applying a linear regression to the three values. MS was thus defined as the largest of these values in the reaction time frame. 3. Instrument- or software-specific information needed to interpret the data: We ran all experiments using a BMG FLUOStar® Omega plate reader (BMG Labtech Inc., Cary, NC, USA; https://www.bmglabtech.com/en/fluostar-omega/) and calculated metrics using MARS Data Analysis Software (i.e. software that comes with the purchase of a plate reader). We used GraphPad Prism version 10.2.1 (GraphPad Software, San Diego, CA, USA, 2024; https://www.graphpad.com/features) in a.Grunklee et al., In review and RStudio in the R Software v4.2.3 (R Core Team 2024; https://posit.co/download/rstudio-desktop/) in b.Grunklee et al., In review to manage, curate, interpret, and visualize RT-QuIC data. All files are in .csv format and can be opened using standard spreadsheet software such as Mircosoft Excel. 4. Standards and calibration information, if appropriate: Not applicable. 5. Environmental/experimental conditions: We performed all experiments using BMG FLUOStar® Omega plate readers (BMG Labtech, Ortenberg, Germany) at 42°C, 1600 gain, and recorded readings every 45 minutes with one-minute cycles of double-orbital shaking and resting for 48 hours. 6. Describe any quality-assurance procedures performed on the data: Not applicable. 7. People involved with sample collection, processing, analysis and/or submission: M.K. Grunklee, J.C. Bartz, D.L. Karwan, S.S. Lichtenberg, N. Lurndahl, P.A. Larsen, M.D. Schwabenlander, G.R. Rowden, A.E. Wille, Q. Yuan, T.M. Wolf. ----------------------------------------------------------- DATA-SPECIFIC INFORMATION FOR: Soil_Cntrl_Expmts_Data.csv ----------------------------------------------------------- 1. Number of variables: 17 2. Number of cases/rows: 1376 3. Missing data codes: NA Not applicable 4. Variable List A. Name: Sample ID 1 Description: General study sample ID B. Name: Sample ID 2 Description: Sample ID associated with lab sample inventory C. Name: Run Date Description: Date of experiment start D. Name: Replicate # Description: Replicate # for each sample on plate (8-10 replicates per sample depending on experiment) E. Name: Soil Dilution Description: Concentration dilution applied directly to soil extracts prior to RT-QuIC runs for negative control experimentation (e.g. 10^0, 5^-1, 10^-1, or 10^-2) F. Name: Instrument Number Description: BMG FLUOStar® Omega plate reader's laboratory ID G. Name: Spiked (Y/N) Description: Indicates brain homogenate spike status in inoculation experiments (Y or N) H. Name: Spike Type Description: TL=Thermolysin or PK=Proteinase K. Indicates the organic sequential enzymatic digestion used on the 10% PrPSc+ WTD brain homogenates inoculated in the soil sample. I. Name: Spike Dilution Description: Indicates the concentration of 10% PrPSc+ WTD brain homogenate spiked into soil sample (i.e. NA, 0, or 10^-3-10^-5) J. Name: Time to Threshold Description: Time measured in hours over course of 48 hour experiment it took to reach maximum relative fluorescence units measurement. K. Name: MPR Description: maxpoint ratio (MPR). MPR was measured per well by dividing the maximum relative fluorescent units (RFU) value obtained within 48 hours by the background RFU value (i.e., MPR = maxRFU/backgroundRFU; Rowden et al., 2023). L. Name: RAF Description: rate of amyloid formation (RAF). RAF of the reaction was calculated per well as the reciprocal of time required for the fluorescence to reach twice the background fluorescence (Schwabenlander et al., 2024). RAF data lacks the ability to be statistically informative as ideal negative controls should inherently be zero (Rowden et al., 2023). M. Name: MS Description: the maximum slope (MS) of relative fluorescence units (RFU) per second from a baseline correction calculation. Across all experiments, the MS of the reaction was measured using a moving window of three reads of baseline corrected relative fluorescence units (RFU; i.e. readings normalized against the background fluorescence) and applying a linear regression to the three values. MS was thus defined as the largest of these values in the reaction time frame. N. Name: Run Time (Hours) Description: All 48 hours in control experiments unless otherwise noted O. Name: Soil Wet/Dry Description: Dry or Wet status indicates if the soil sample was oven dried prior to sample extraction and experimentation P. Name: Plate ID Description: Plate ID in code to locate raw data files Q. Name: Comment Description: Comments ---------------------------------------------------------- DATA-SPECIFIC INFORMATION FOR: Soil_Test_Samples_Data.csv ---------------------------------------------------------- 1. Number of variables: 14 2. Number of cases/rows: 2560 3. Missing data codes: NA Not applicable 4. Variable List A. Name: Sample ID 1 Description: General study sample ID B. Name: Sample ID 2 Description: Sample ID associated with lab sample inventory C. Name: Replicate # Description: Replicate # for each sample on plate (8 replicates per sample in each experiment) D. Name: Collection Date Description: Date of field soil sample collection E. Name: Run Date Description: Date of experiment start F. Name: Instrument Number Description: BMG FLUOStar® Omega plate reader's laboratory ID G. Name: Time to Threshold Description: Time measured in hours over course of 48h experiment it took to reach maximum relative fluorescence units measurement. H. Name: MPR Description: maxpoint ratio (MPR). MPR was measured per well by dividing the maximum relative fluorescent units (RFU) value obtained within 48 hours by the background RFU value (i.e., MPR = maxRFU/backgroundRFU; Rowden et al., 2023). I. Name: RAF Description: rate of amyloid formation (RAF). RAF of the reaction was calculated per well as the reciprocal of time required for the fluorescence to reach twice the background fluorescence (Schwabenlander et al., 2024). RAF data lacks the ability to be statistically informative as ideal negative controls should inherently be zero (Rowden et al., 2023). J. Name: MS Description: the maximum slope (MS) of relative fluorescence units (RFU) per second from a baseline correction calculation. Across all experiments, the MS of the reaction was measured using a moving window of three reads of baseline corrected relative fluorescence units (RFU; i.e. readings normalized against the background fluorescence) and applying a linear regression to the three values. MS was thus defined as the largest of these values in the reaction time frame. K. Name: Run Time (Hours) Description: All test samples ran on or after 7/7/2023 were ran for 72 hours (unless otherwise noted). This raw data can be requested. However, data was fully analyzed using only 48 hour data. L. Name: Soil Order Description: Note all test soil samples were Alfisols unless otherwise noted (e.g. 041* is in the Histosol soil area and DK003 is in the Entisol soil area) M. Name: Plate ID Description: Plate ID in code to locate raw data files N. Name: Comment Description: Comments