This codebook.txt file was generated on 2021-11-12 by wilsonkm ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset Experimental data associated with the study "The Ixodes scapularis symbiont Rickettsia buchneri inhibits growth of pathogenic Rickettsiaceae in tick cells: implications for vector competence" 2. Author Information Principal Investigator Contact Information Name: Benjamin Cull Institution: University of Minnesota Email: cull0122@umn.edu Associate or Co-investigator Contact Information Name: Nicole Y Burkhardt Institution: University of Minnesota Email: burkh032@umn.edu Associate or Co-investigator Contact Information Name: XinRu Wang Institution: University of Minnesota Email: wang8848@umn.edu Associate or Co-investigator Contact Information Name: Cody J Thorpe Institution: University of Minnesota Email: thorp113@umn.edu Associate or Co-investigator Contact Information Name: Jonathan D Oliver Institution: University of Minnesota Email: joliver@umn.edu Associate or Co-investigator Contact Information Name: Timothy J Kurtti Institution: University of Minnesota Email: kurtt001@umn.edu Associate or Co-investigator Contact Information Name: Ulrike G Munderloh Institution: University of Minnesota Email: munde001@umn.edu 3. Date of data collection: 2021 4. Geographic location of data collection (where was data collected?): Department of Entomology, University of Minnesota, St Paul, MN 55108 5. Information about funding sources that supported the collection of the data: Sponsorship: National Institutes of Health (grants R01 AI49424 and R01 AI081690 to UGM); University of Minnesota Agricultural Experiment Station -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: Attribution-NonCommercial 3.0 United States 2. Links to publications that cite or use the data: The Ixodes scapularis symbiont Rickettsia buchneri inhibits growth of pathogenic Rickettsiaceae in tick cells: implications for vector competence. Cull et al. (2021) Frontiers in Veterinary Science doi: 10.3389/fvets.2021.748427 https://www.frontiersin.org/articles/10.3389/fvets.2021.748427/abstract 3. Links to other publicly accessible locations of the data: n/a 4. Links/relationships to ancillary data sets: n/a 5. Was data derived from another source? No 6. Recommended citation for the data: Cull, B., Burkhardt, N. Y., Wang, X. R., Thorpe, C. J., Oliver, J. D., Kurtti, T. J., & Munderloh, U. G. (2021). Experimental data associated with the study "The Ixodes scapularis symbiont Rickettsia buchneri inhibits growth of pathogenic Rickettsiaceae in tick cells: implications for vector competence" [Data set]. Data Repository for the University of Minnesota (DRUM). https://doi.org/10.13020/ZQXG-JF78 --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: Rbuchneri and Rparkeri competition plate reader data.xlsx Short description: Raw data from Rickettsia buchneri and Rickettsia parkeri competition fluorescent plate reader experiment B. Filename: Rparkeri growth with Rb lysate plate reader data.xlsx Short description: Raw data from fluorescent plate reader experiment examining growth of Rickettsia parkeri in the presence of Rickettsia buchneri lysate C. Filename: Rpeacockii vs Rparkeri plate reader data.xlsx Short description: Raw data from Rickettsia peacockii and Rickettsia parkeri competition fluorescent plate reader experiment D. Filename: Ramblyommatis vs Rparkeri plate reader data.xlsx Short description: Raw data from Rickettsia amblyommatis and Rickettsia parkeri competition fluorescent plate reader experiment 2. Relationship between files: contain data collected during the study cited above. 3. Additional related data collected that was not included in the current data package: n/a 4. Are there multiple versions of the dataset? no -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: Methods can be found in 'Cull et al. (2021) Frontiers in Veterinary Science doi: 10.3389/fvets.2021.748427' 2. Methods for processing the data: submitted data are raw collected data, plus the calculated means and standard deviations from 3 replicate wells. 3. Instrument- or software-specific information needed to interpret the data: n/a 4. Standards and calibration information, if appropriate: Raw fluorescent data from IRE11 tick cells infected with fluorescent Rickettsia were adjusted by subtracting fluorescence reads from uninfected cells. 5. Environmental/experimental conditions: Tick cells infected with Rickettsia were incubated at 28 degrees Celsius in a humidified candle jar for 14 days. Fluorescent data were collected daily at room temperature (approx. 22-25 Celsius). 6. Describe any quality-assurance procedures performed on the data: N/A 7. People involved with sample collection, processing, analysis and/or submission: Benjamin Cull, XinRu Wang ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Rbuchneri and Rparkeri competition plate reader data.xlsx ----------------------------------------- Rbuchneri and Rparkeri competition plate reader data.xlsx contains four sheets: 1. Experiment 1 - GFPuv 2. Experiment 1 - mKate 3. Experiment 2 - GFPuv 4. Experiment 2 - mKate 1. Number of variables: FIVE - R. buchneri infection level, R. parkeri challenge dose, day post infection, GFPuv fluorescence, mKate fluorescence 2. Number of cases/rows: 3. Missing data codes: Code/symbol Definition Code/symbol Definition 4. Variable List A. Name: R. buchneri infection level Description: Percentage of IRE11 tick cells infected with Rickettsia buchneri. 1 = uninfected 2 = 25% 3 = 50% 4 = 75% 5 = >95% B. Name: R. parkeri challenge dose Description: Approximate number of R. parkeri used to challenge each tick cell. 1 = uninfected (UI) 2 = 10:1 (Rp10 / MOI 10) 3 = 100:1 (Rp100 / MOI 100) 4 = 1000:1 (Rp1000 / MOI 1000) C. Name: day post infection Description: Day of experiment following infection with R. parkeri Values = day 1 - 14 D. Name: GFPuv fluorescence Description: Fluorescence measurement at excitation/emission 395/509 corresponding to Rb-GFPuv replication, values adjusted to fluorescence from uninfected IRE11. E. Name: mKate fluorescence Description: Fluorescence measurement at excitation/emission 588/633 corresponding to Rp-mKate replication, values adjusted to fluorescence from uninfected IRE11. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Rparkeri growth with Rb lysate plate reader data.xlsx ----------------------------------------- Rparkeri growth with Rb lysate plate reader data.xlsx contains two sheets: 1. Rp growth with Rb lysate 2. Rp-challenge Rb lysate 1. Number of variables: FOUR - treatment, R. parkeri challenge dose, days post infection, mKate fluorescence 2. Number of cases/rows: 3. Missing data codes: Code/symbol Definition Code/symbol Definition 4. Variable List A. Name: Treatment Description: Details of treatment applied to cells before infection with R. parkeri Sheet1: 1 = untreated 2 = cell free Rb 1/10 (1 in 10 dilution of R. buchneri lysate) 3 = cell free Rb (R. buchneri lysate) 4 = IRE11-Rb cell lysate (lysate of IRE11 cells infected with R. buchneri) 5 = IRE11 cell lysate (lysate of uninfected IRE11 cells) Sheet2: 1 = untreated 2 = Rb/Rp d1 (lysate of R. buchneri after 1 day challenge with R. parkeri) 3 = Rb/Rp d2 (lysate of R. buchneri after 2 days challenge with R. parkeri) 4 = Rb/Rp d3 (lysate of R. buchneri after 3 days challenge with R. parkeri) 5 = Rb/Rp d5 (lysate of R. buchneri after 5 days challenge with R. parkeri) 6 = Rb/Rp d7 (lysate of R. buchneri after 7 days challenge with R. parkeri) B. Name: R. parkeri challenge dose Description: Approximate number of R. parkeri used to challenge each tick cell. 1 = uninfected (UI) 2 = 10:1 (Rp10 / MOI10) 3 = 100:1 (Rp100 / MOI100) 4 = 1000:1 (Rp1000 / MOI1000) C. Name: day post infection Description: Day of experiment following infection with R. parkeri Values = day 1 - 14 D. Name: mKate fluorescence Description: Fluorescence measurement at excitation/emission 588/633 corresponding to Rp-mKate replication, values adjusted to fluorescence from uninfected IRE11. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Rpeacockii vs Rparkeri plate reader data.xlsx ----------------------------------------- Rpeacockii vs Rparkeri plate reader data.xlsx contains four sheets: 1. Experiment 1 - mKate 2. Experiment 1 - GFPuv 3. Experiment 2 - mKate 4. Experiment 2 - GFPuv 1. Number of variables: FIVE - R. peacockii infection level, R. parkeri challenge dose, day post infection, GFPuv fluorescence, mKate fluorescence 2. Number of cases/rows: 3. Missing data codes: Code/symbol Definition Code/symbol Definition 4. Variable List A. Name: R. peacockii infection level Description: Percentage of IRE11 tick cells infected with Rickettsia peacockii. 1 = uninfected 2 = 25% 3 = 50% 4 = 75% 5 = >95% B. Name: R. parkeri challenge dose Description: Approximate number of R. parkeri used to challenge each tick cell. 1 = uninfected (UI) 2 = 10:1 (Rp10 / MOI 10) 3 = 100:1 (Rp100 / MOI 100) 4 = 1000:1 (Rp1000 / MOI 1000) C. Name: day post infection Description: Day of experiment following infection with R. parkeri Values = day 1 - 14 D. Name: GFPuv fluorescence Description: Fluorescence measurement at excitation/emission 395/509 corresponding to R. peacockii-GFPuv replication, values adjusted to fluorescence from uninfected IRE11. E. Name: mKate fluorescence Description: Fluorescence measurement at excitation/emission 588/633 corresponding to Rp-mKate replication, values adjusted to fluorescence from uninfected IRE11. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Ramblyommatis vs Rparkeri plate reader data.xlsx ----------------------------------------- Ramblyommatis vs Rparkeri plate reader data.xlsx contains four sheets: 1. Experiment 1 - mKate 2. Experiment 2 - mKate 1. Number of variables: FOUR - R. amblyommatis infection level, R. parkeri challenge dose, day post infection, mKate fluorescence 2. Number of cases/rows: 3. Missing data codes: Code/symbol Definition Code/symbol Definition 4. Variable List A. Name: R. amblyommatis infection level Description: Percentage of IRE11 tick cells infected with Rickettsia amblyommatis. 1 = uninfected 2 = 25% 3 = >95% B. Name: R. parkeri challenge dose Description: Approximate number of R. parkeri used to challenge each tick cell. 1 = uninfected (UI) 2 = 10:1 (Rp10 / MOI 10) 3 = 1000:1 (Rp1000 / MOI 1000) C. Name: day post infection Description: Day of experiment following infection with R. parkeri Values = day 1 - 14 D. Name: mKate fluorescence Description: Fluorescence measurement at excitation/emission 588/633 corresponding to Rp-mKate replication, values adjusted to fluorescence from uninfected IRE11.