This codebook.txt file was generated on by ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset: Cell Density of Microcystis Aeruginosa in Three Growth Treatments as calculated from Hemocytometer Measurements at St Anthony Falls Laboratory 2. Author Information Principal Investigator Contact Information Name: Katherine R Tomaska Institution: Saint Anthony Falls Laboratory, University of Minnesota Email:omas098@umn.edu ORCID: Associate or Co-investigator Contact Information Name: Judy Yang Institution: Saint Anthony Falls Laboratory, University of Minnesota Email: judyyang@umn.edu ORCID: https://orcid.org/0000-0001-6272-1266 Associate or Co-investigator Contact Information Name: Guanju Wei Institution: Saint Anthony Falls Laboratory, University of Minnesota Email: wei00235@umn.edu ORCID: 3. Date of data collection: 20210929 - 20211108 4. Geographic location of data collection: Saint Anthony Falls Laboratory, University of Minnesota 5. Information about funding sources that supported the collection of the data: This study was supported by JQ Yang’s startup funds and University of Minnesota’s MnDRIVE Environment seed grant -------------------------- SHARING/ACCESS INFORMATION -------------------------- Recommended citation for the data: Yang, Judy; Tomaska, Katherine R; Wei, Guanju. (2022). Data supporting Inhibition of the Growth of Harmful Algal Bloom-forming Freshwater Cyanobacteria by Clay. Retrieved from the Data Repository for the University of Minnesota, https://doi.org/10.13020/pf7m-2f62. 1. Licenses/restrictions placed on the data: CC0 1.0 Universal 2. Links to publications that cite or use the data: manuscript under consideration 3. Links to other publicly accessible locations of the data: 4. Links/relationships to ancillary data sets: 5. Was data derived from another source? If yes, list source(s): --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: Hemocytometer_Data_Final.xlsx Short description: This file contains the data collected from hemocytometer measurements, as well as data regarding the environmental conditions of growth for the cyanobacteria (including light intensity and pH). The excel spreadsheet is broken down into different columns based on category. The first three columns include the day #, date, and flask number. In total, 9 flasks were used to grow the bacteria. These flasks were separated into three different growth conditions. The next four columns are a record on environmental conditions including light intensity and pH. The next set of columns are a record of dates when a growth solution was added to the flasks. The additional growth solution resulted in a dilution factor that was applied when calculating the overall cell density in each flask. The next column is the average cell count per box. This column represents the average number of cells counted in each 0.004 mm^3 square of the hemocytometer for a given sample. The raw data used to compute this average is located in the last columns, under the “Detailed Hemocytometer count” tab. Finally, the values in the “Average Cell Density” column were calculated by dividing the average cell count per square by the volume of the square (0.004 mm^3) and multiplying by the dilution factor. B. Filename: Code_Cell_counting_final.m Short description: This file contains the MatLab code that was used to process the data within the file Hemocytometer_Data.xlsx. For each date, the MatLab code averages the cell densities of flasks with identical growth conditions. The standard error of the mean for each group of 3 flasks was used to create error bars for the data. The average cell density per treatment type, as well as the error bars associated with these averages, are plotted together. This plot offers a comparison of average cell growth across the three different treatment conditions. C. Filename: Data Deposit_Confocal images (1.66 GB).zip Short description: The confocal imaging shows the physical interactions between cyanobacteria and clay particles. The data set includes 3 folders: 6#_clay solution: Raw data of clay solution experiments 7#_modified clay solution: Raw data of modified clay solution 8#_regular solution: Raw data of regular solution Each folder contains a Nikon confocal microscopy file (.nd2) and twenty output images. 2. Relationship between files: The average cell density in the Hemocytometer_Data.xlsx sheet is read by the MatLab Code file. Error bar calculations based on the data are also calculated in the MatLab code. The confocal imaging is separate from the hemocytometer data. It serves as a visual representation of the quantitative cell density results counted under the microscope. -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: This experiment studied the impacts of three different growth media scenarios on M. aeruginosa growth. Nine flasks were used to grow the bacteria. Therefore, there were 3 flasks for each growth media scenario. The three scenarios included a control with M. aeruginosa grown in BG-11 solution, a scenario where M. aeruginosa was grown ini BG-11 solution with 1% laponite added, and a scenario where M. aeruginosa was grown in a solution modified by laponite and centrifuged. The experimental flasks were placed in an incubator at 24 ℃, shaken at a rate of 110 rpm, and exposed to approximately 2000 lumens of light in a 12:12 light:dark cycle. We measured cell density three times a week. We performed a cell count under a Nikon Eclipse E400 microscope with a hemocytometer at 40x magnification. To compensate for the reduction in solution volume due to measurements and the evaporation of the bacterial solution, we added additional BG-11+HEPES solution twice during the experiment to keep the volume of solution in each flask at 100 mL. On weeks where the cyanobacterial solution was diluted with BG-11/hepes solution, the cell density measurements were taken before dilution occurs. We calculated the dilution factor for each flask by dividing the volume of the solution by 100mL. In subsequent weeks, this factor was multiplied by the cell density to compensate for the dilution effect due to the added solution. Additionally, the pH of each bacteria solution, as well as the light intensity within the incubator, was recorded at least once a week to ensure steady environmental conditions. The pH was estimated with pH paper. In addition to cell density measurements, the physical interactions between cyanobacteria and clay particles were visualized using a confocal laser scanning microscope (Nikon C2 plus). Each image is around 2048 by 2048 pixels at a resolution of 0.08 um/pixel. We used a 20X objective magnification. A sequence of images was taken at 10-second intervals for 5 minutes. The laser used for excitation has a wavelength of 488 nm (FITC) and the emission wavelength is 525 nm. 2. Methods for processing the data: The raw data includes the hemocytometer data. The number of cells in each 0.004 mm^3 volume square was recorded in a spreadsheet. The overall average cell density of each sample was calculated by dividing the average cell count per square by the volume of the square (0.004 mm^3) and multiplying by the dilution factor. The calculated cell densities for identical growth scenarios were averaged on each date within the Matlab code. The three growth scenarios were plotted together with error bars on MatLab to identify any trends. The error bars were calculated as the standard error of the mean. 3. Instrument- or software-specific information needed to interpret the data: The .nd2 files of the confocal images can be opened by NIS software, which can be downloaded here: https://www.microscope.healthcare.nikon.com/en_EU/products/software/nis-elements/viewer 4. Standards and calibration information, if appropriate: 5. Environmental/experimental conditions: The experimental flasks were placed in an incubator at 24 ℃, shaken at a rate of 110 rpm, and exposed to approximately 2000 lumens of light in a 12:12 light:dark cycle. 6. Describe any quality-assurance procedures performed on the data: We conducted experiments using three replicate samples to improve data quality. 7. People involved with sample collection, processing, analysis and/or submission: Katherine Tomaska (sample collection, processing, analysis, submission) Judy Yang (MatLab code for processing, analysis, submission) William (for the confocal imaging, processing, submission) ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Hemocytometer_Data_Final.xlsx ----------------------------------------- 1. Number of variables: 10 2. Number of cases/rows: 180 3. Missing data codes: Code/symbol Definition Code/symbol Definition 4. Variable List A. Name: Day # Description: Number of days since beginning of experiment (when the stock cyanobacteria was added to corresponding nutrient solutions) B. Name: Date Description: Date of data collection C. Name: Flask # Description: Flask number (1-9) that corresponds to the type of solution Flasks 1 - Stock cyanobacteria solution (not included in analysis) Flasks 2,5,8 - Nutrient Solution Flasks 3,6,9 - Nutrient Solution with 1% Clay Flasks 4,7,10 - Clay-Modified Nutrient Solution D. Name: Light Intensity Lower Description: Light intensity (in lux) at the bottom of the shaker E. Name: Light Intensity Middle Description: Light intensity (in lux) on top of the first row of flasks on the shaker F. Name: Light Intensity Upper Description: Light intensity (in lux) on top of the second row of flasks on the shaker G. Name: pH Description: Approximate pH as measured from pH paper strips H. Name: Volume Description: Volume of the solution in the flask, if applicable I. Name: Volume Added Description: Volume of BG-11 solution added to the original flask to bring the total volume back up to 100mL, if applicable J. Name: Dilution Factor Description: Dilution factor to be applied to the average cell density. Calculated by multiplying the previous day’s conversion factor by (volume added +volume)/ (volume) K. Name: Average Cell Count per Box Description: Average value of all cells under the “detailed hemocytometer count” for a given row. L. Name: Average Cell Density (cells/mm^3) Description: Average cell density of the solution. Calculated by dividing the average cell count by the size of the box (0.004mm^3), and multiplying by the dilution factor. M. Name: Detailed Hemocytometer Count Description: For each row, each box under the detailed hemocytometer count label represents the number of cells counted in one 0.004 mm^3 square.