This DATSETNAMEreadme.txt file was generated on 2021-02-23 by Amber Ide GENERAL INFORMATION 1. Title of Dataset: Phosphatidylserine exposure promotes increased adhesion in Dictyostelium Copine A mutants 2. Author Information A. Principal Investigator Contact Information Name: Cynthia Damer Institution: Central Michigan University Address: 1200 S Franklin St, Mount Pleasant MI 48859 Email: damer1ck@cmich.edu B. Associate or Co-investigator Contact Information Name: Amber Ide Institution: Central Michigan University Address: 1200 S Franklin St, Mount Pleasant MI 48859 Email: ide1ad@cmich.edu 3. Date of data collection (single date, range, approximate date) 2018-2021 4. Geographic location of data collection. Bioscience Building, Central Michigan University Mount Pleasant MI USA 5. Information about funding sources that supported the collection of the data: National Institute of Health 2R15GM078089-02 Internal Faculty Research and Creative Endeavors Grant Central Michigan University National Science Foundation 1337647 Graduate Student Research Grant SHARING/ACCESS INFORMATION 1. Licenses/restrictions placed on the data: 2. Links to publications that cite or use the data: 3. Links to other publicly accessible locations of the data: 4. Links/relationships to ancillary data sets: 5. Was data derived from another source? NO A. If yes, list source(s): 6. Recommended citation for this dataset: DATA & FILE OVERVIEW 1. File List: 1. Phagocytosis 1um FITC bead- Flow cytometry data of 1 um FITC bead phagocytosis 2. GFP-Bacteria phagocytosis data- Cell and GFP-bacteria counts from microscopy images 3. LatA adhesion data- Flow cytometry data from treating cells with LatA 4. Proteinase K Adhesion data- Flow cytometry data from treating cells with different concentrations of proteinase k 5. Annexin V-APC data- Flow cytometry data from treating cells with Annexin V-APC 6. Unlabeled Annexin V data-Flow cytometry data from treating cells with unlabeled Annexin V and FITC beads 7. Polybia MP1 data- Cell counts of cells treated with different concentrations of polybia MP1. 8. S1_raw_images- Raw images of SibA and Actin western blots. 2. Relationship between files, if important: 3. Additional related data collected that was not included in the current data package: 4. Are there multiple versions of the dataset? NO A. If yes, name of file(s) that was updated: i. Why was the file updated? ii. When was the file updated? METHODOLOGICAL INFORMATION 1. Description of methods used for collection/generation of data: Methods used: Flow cytometry, fluorescence microscopy, cell counting, BioRad Chemidoc imager 2. Methods for processing the data: 1. Phagocytosis of 1 um FITC bead data- Took the Cell Mean FITC-A data, averaged together and calculated standard error. 2. GFP-bacteria phagocytosis data-Calculated the total average of bacteria per cell from each trial and standard error: Averaged the the number of cells and the number of bacteria associated with each cell together and calculated total average from 6 images per condition. Images taken at 40X. 3. LatA adhesion data- Took the Cell Mean FITC-A data from each trial, normalized the cell fluorescence to the average mean cell fluorescence within each trial, and calculated standard error. 4. Proteinase K adhesion data- Used Cells 2 Mean FITC-A fluorescence to normalize data; Mean cell fluorescence was normalized to the average mean cell fluorescence for each cell type within each trial, and calculated standard error. 5. Annexin V-APC data- Used AV Mean APC-A fluorescence and normalized data: Data normalized to the average mean cell fluorescence for all cell types and conditions within each trial and calculated standard error. 6. Unlabeled Annexin V data- Used Cells 2 Mean FITC-A and normalized data: Mean cell fluorescence was normalized to the average of all samples within each trial and calculated standard error. 7. Polybia MP1 data- Counted live cells using a hemocytometer and cells counts at each concentration were normalized to the cells counts for 0 um concentration for each cell type in each trial and calculated standard error. 8. S1_raw_images- Colorimetric and chemiluminescence images of SibA and Actin Western Blots. Methods: Transferred stain free gel to PVDF membrane and added rabbit polyclonal anti-SibA antibody or mouse anti-actin antibody to membrane. Added secondary HRP-Conjugated antibody to blots. Added chemiluminescence to blots and imaged using BioRad Chemidoc imager. X lanes indicate lanes not included in data. Order of which lanes were loaded: 1st lane is molecular weight marker, 2nd lane is NC4A2 cells, 3rd lane is cpnA- cells, 4th lane is NC4A2 cells with proteinase K treatment, 5th lane is cpnA- cells with proteinase K treatment. 3. Instrument- or software-specific information needed to interpret the data: 1. Flow cytometer- Beckman Coulter CytoFlex Flow Cytometer, 488 nm laser and FITC detector (525/40) for beads, and with the 638 nm laser and APC detector (660/20) for Annexin V-APC 2. Fluorescent microscope- Leica DMi 8 microscope 3. R software- R version 3.6.1 4. BioRad ChemiDoc Touch Imaging System 4. Standards and calibration information, if appropriate: 5. Environmental/experimental conditions: 6. Describe any quality-assurance procedures performed on the data: 7. People involved with sample collection, processing, analysis and/or submission: Amber Ide and Elise Wight DATA-SPECIFIC INFORMATION FOR: Phagocytosis 1um FITC Bead 1. Number of variables: 3 variables 2. Number of cases/rows: 3 trials 3. Variable List: Variable names: Cell type, Buffer, time Description: Cell- NC4A2 and cpnA- cells Buffer- Sorensen's buffer and Sorensen's buffer with Sodium azide Time- Cell samples taken out at 5 minute intervals from 0-30 minutes Units: Mean Cell fluorescence (FITC), time in minutes 4. Missing data codes: 5. Specialized formats or other abbreviations used: NC4A2 is wildtype DATA-SPECIFIC INFORMATION FOR: GFP-Bacteria phagocytosis data 1. Number of variables: 4 variables 2. Number of cases/rows: 5 trials with Buffer, 3 trials with Sodium azide 3. Variable List: Variable names: Cell type and buffer Description: Cell type- NC4A2 and cpnA- cells Buffer- Sorensen's buffer or Sorensen's buffer with sodium azide Units: Average number of bacteria per cell 4. Missing data codes: 5. Specialized formats or other abbreviations used: NC4A2 is wild type DATA-SPECIFIC INFORMATION FOR: LatA adhesion data 1. Number of variables: 4 variables 2. Number of cases/rows: 4 trials 3. Variable List: Variable names: Cell type and Buffer with LatA Description: Cell type- NC4A2 and cpnA- cells Buffer with LatA- Sorensen's buffer with LatA and Sorensen's buffer with LatA and sodium azide Units: Mean cell fluorescence (FITC) 4. Missing data codes: 5. Specialized formats or other abbreviations used: NC4A2 is wild type LatA is Latrunculin A DATA-SPECIFIC INFORMATION FOR: Proteinase K adhesion data < 1. Number of variables: 5 variables 2. Number of cases/rows: 3 trials 3. Variable List: Variables: Cell type and Proteinase K concentration Descriptions: Cell type- NC4A2 and cpnA- cells Proteinase K concentrations: 0, 100, and 500 ug Units: Mean cell fluorescence (FITC), micrograms (ug) < 4. Missing data codes: < 5. Specialized formats or other abbreviations used: NC4A2 is wild type DATA-SPECIFIC INFORMATION FOR: AnnexinV-APC data < 1. Number of variables: 4 variables 2. Number of cases/rows: 6 trials 3. Variable List: Variable names: Cell type and Annexin V Descriptions: Cell type- NC4A2 and cpnA- cells Annexin V- Annexin V and annexing V with calcium ionophore Units: Mean cell fluorescence (APC) 4. Missing data codes: < 5. Specialized formats or other abbreviations used: NC4A2 is wild type, AV is Annexin V DATA-SPECIFIC INFORMATION FOR: Unlabeled Annexin V data 1. Number of variables: 5 variables 2. Number of cases/rows: three trials 3. Variable List: Variable names: cell type, conditions Descriptions: Cell type-NC4A2 and cpnA- cells Conditions: control=Beads alone with cells, BSA= BSA and beads with cells, Annexin V= Annexin V and beads with cells Units: Mean cell fluorescence (FITC) < 4. Missing data codes: < 5. Specialized formats or other abbreviations used: NC4A2 is wild type, BSA is bovine serum albumin DATA-SPECIFIC INFORMATION FOR: Polybia MP1 data < 1. Number of variables: 5 variables 2. Number of cases/rows: 3 trials 3. Variable List: Variable names: Cell type and polybia Description: Cell type- NC4A2, cpnA-, NC4A2/GFP-CpnA, and cpnA-/GFP-CpnA polybia- Cell samples shaking with 0-5 um polybia Units: Cell count, micromolar (um) < 4. Missing data codes: < 5. Specialized formats or other abbreviations used: NC4A2 is wild type, micromolar (um) DATA-SPECIFIC INFORMATION FOR: S1_raw_images 1. Number of variables: 4 variables per blot 2. Number of cases/rows: 1 trial 3. Variable List: Variable names: Cell type, condition Description: Cell- NC4A2 and cpnA- cells Condition- Proteinase K added to cells or no proteinase K added to cells Units: kDa 4. Missing data codes: 5. Specialized formats or other abbreviations used: NC4A2 is wildtype, PK is proteinase K, X indicates lanes not included in data, MWM indicates molecular weight marker