This README.txt file was generated on 2021/06/29 by Islam Abdelhalim Abdelaziz Ali


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GENERAL INFORMATION
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1. Title of Dataset:Islam Abdelhalim Abdelaziz Ali_Data Set


2. Author Information
<create a new entry for each additional author>

First Author Contact Information
    Name:Islam Abdelhalim Abdelaziz Ali
    Faculty:Dentistry
    Email:u3004980@connect.hku.hk



Corresponding Author Contact Information
    Name:Islam Abdelhalim Abdelaziz Ali
    Faculty:Dentistry
    Email:u3004980@connect.hku.hk


Author Contact Information (if applicable)
    Name:
    Faculty:
    Email:


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DATA & FILE OVERVIEW
---------------------


Directory of Files:
   A. Filename: data Set_Study 1       
      Short description: This folder is divided into subfolders (named by the evaluated outcome and employed assay). Each subfoldeer corresponds to an experiment related to thesis Chapter 2. 
                         Each subfolder is further divided to describe the effect of the independendent variables: (a) biofilm age: 3 and 21 days (at the first level) (b) Surface conditioning (Unconditioned, collage, saliva and serum conditioned) (at the second level) 
                         on the dependent variables (Colony forming units, concentration of biofilm matrix proteins and exopolysaccharides)

        
   B. Filename:data Set_Study 2        
      Short description: This folder is divided into subfolders (named by the evaluated outcome and employed assay). Each subfolder corresponds to an experiment related to thesis Chapter 3.
                         Each subfolder includes data of at least three biological experimental replicates of the independent variables : (a) biofilm age (24, 48 and 72h) and (b) bacterial strain (OG1RF, TX 51258, TX 5240, TX 5242)        


        
   C. Filename:data Set_Study 3     
      Short description:This folder is divided into subfolders (named by the evaluated outcome and employed assay). Each subfolder corresponds to an experiment related to thesis Chapter 5.
                        Each subfolder includes data of at least three biological experimental replicates of the independent varibable: Biofilm treatment (No treatment or control  and TC)

   D. Filename:data Set_Study 4      
      Short description:This folder is divided into subfolders (named by the evaluated outcome and employed assay). Each subfolder corresponds to an experiment related to thesis Chapter 6.
                        Each subfolder includes data of at least three biological experimental replicates of the independent varibable: Biofilm treatment (No treatment or control, TC, 1% NaOCl, 2% CHX)
 
Additional Notes on File Relationships, Context, or Content 
(for example, if a user wants to reuse and/or cite your data, 
what information would you want them to know?): N/A              


File Naming Convention:The subfolders at the first level are named as data set_Chapter Number. 
                       The Subfolders at the second level are named as Dependent variable_Method. 
                       At the third level, excel files that contain data of technical replicates are named as Experiment or Exp (1 or 2 or 3)_additional information (e.g. the outcome measured, indpendent variable(s))   

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DATA DESCRIPTION FOR: [data Set_Study 1]
-----------------------------------------
<create sections for each dataset included>


1. Number of variables: 5


2. Number of cases/rows: N/A


3. Missing data codes:
        Code/symbol        Definition
        Code/symbol        Definition


4. Variable List

   
    A. Name: <Colony forming units (CFUs)counts>
       Description: <dependent variable>
                    Calculated in CFUs/ml, then log10 transformed for statistical analysis  

    B. Name: <Concentration of biofilm matrix Proteins>
       Description: <A dependent variable expressed in micrograms/ml>
                     
    C. Name: <Concentration of biofilm exopolysaccharides>
       Description: <dependent variable expressed in micrograms/ml when evaluated with the total carbohydrate assay orin % when quantified with confocal laser scanning microscope (CLSM)>                
    
    D. Name: <Biofilm age>
       Description: <independent variable> 
                    1 = 3-days biofilm, 2 = 21-days biofilm
    
    E. Name: <Type of surface conditioning >
       Description: <independent variable> 
                    1 = Unconditioned, 2 = Collagen, 3= Saliva , 4= Serum

-----------------------------------------
DATA DESCRIPTION FOR: [data Set_Study 2]
-----------------------------------------
<create sections for each dataset included>


1. Number of variables: 8


2. Number of cases/rows: N/A


3. Missing data codes:
        Code/symbol        Definition
        Code/symbol        Definition


4. Variable List
   
    A. Name: <Biomass>
       Description: <dependent variable>
                      
    B. Name: <Biofilm metabolic activity>
       Description: <dependent variable>
                     
    C. Name: <Colony forming units (CFUs)>
       Description: <dependent variable>                
                      Calculated in CFUs/ml, then log10 transformed for statistical analysis

    D. Name: <Concentration of biofilm exopolysaccharides>
       Description: <dependent variable expressed in micrograms/ml when evaluated with phenolic sulfric acid assay or as Biovolume / mm2 when when quantified with CLSM> 
                    
    E. Name: <Concentration of biofilm matrix proteins>
       Description: <dependent variable expressed in micrograms/ml> 
                    
    F. Name: <levels of extracellular DNA (eDNA)>
       Description: <dependent variable> 
    
    G. Name: <Biofilm age>
       Description: <independent variable - 24, 48 and 72h-old biofilm>

    H. Name: <Strain of E. faecalis>
       Description: <independent variable - OG1RF, TX 5128, TX 5240, TX 5242> 

-----------------------------------------
DATA DESCRIPTION FOR: [data Set_Study 3]
-----------------------------------------
<create sections for each dataset included>


1. Number of variables: 10


2. Number of cases/rows: N/A


3. Missing data codes:
        Code/symbol        Definition
        Code/symbol        Definition


4. Variable List

    A. Name: <Planktonic growth>
       Description: <dependent variable determined by measuring the optical density of bacteria>
                      
    B. Name: <Biofilm metabolic activity>
       Description: <dependent variable>
                     
    C. Name: <Colony forming units (CFUs)>
       Description: <dependent variable>                
                      Calculated in CFUs/ml, then log10 transformed for statistical analysis

    D. Name: <Biomass>
       Description: <dependent variable> 
                    
    E. Name: <Concentration of biofilm exopolysaccharides>
       Description: <dependent variable expressed in micrograms/ml when evaluated with the chemical phenol sulfric acid assay> 
                    
    F. Name: <Attached bacterial cells>
       Description: <dependent variable expressed as Biovolume / mm2 when quantified with CLSM> 
    
    G. Name: <Red blood cells (RBCs) hemolysis >
       Description: <dependent variable>

    H. Name: <Diameter of proteolytic zone around bacterial colonies>
       Description: <dependent variable> 

    I. Name: <delta delta CT value>
       Description: <dependent variable, indicates gene expression in bacteria> 

    J. Name: <Treatment>
       Description: <independent variable, Control (no treatment) and TC concentrations (0.47, 0.94 , 1.88 mM)>

-----------------------------------------
DATA DESCRIPTION FOR: [data Set_Study 4]
-----------------------------------------
<create sections for each dataset included>


1. Number of variables: 5


2. Number of cases/rows: N/A


3. Missing data codes:
        Code/symbol        Definition
        Code/symbol        Definition


4. Variable List
   
    A. Name: <biofilm metabolic activity>
       Description: <dependent variable determined after different treatment durations, and at 10days after removal of treatment>
                      
    B. Name: <Colony forming units (CFUs)>
       Description: <dependent variable calculated as CFU/ml, then log10 transformed for statistical analysis. Determined after long term treatmenta and 10days after removal of treatment>
                     
    C. Name: <Biofilm dead cells>
       Description: <dependent variable epxressed as % when quantified with CLSM>                
                      
    D. Name: <concentration of Biofilm exopolysaccharides>
       Description: <dependent variable expressed in micrograms/ml> 

    E. Name: <Treatment>
       Description: <independent variable, Deionized water (Control), TC concentrations (0.5, 0.75, 1%), 1% NaOCl, 2% CHX>
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METHODOLOGICAL INFORMATION
--------------------------

1. Software-specific information:Image Processing software
<create a new entry for each qualifying software program>

Name:CellC cell counting software
Version:Windows compitable version v1.2
System Requirements:MCR installer
Open Source? (Y/N): Y 

(if available and applicable)
Executable URL: N/A
Source Repository URL: N/A
Developer:Institute of Signal Processing, Tampere University of Technology, Tampere, Finland
Product URL:https://sites.google.com/site/cellcsoftware/Home
Software source components:N/A


Additional Notes(such as, will this software not run on 
certain operating systems?):The CellC cell counting software has MATLAB-compatible version that requires MATLAB R2007a or higher and Image Processing Toolbox 5.0 for operation


2. Software-specific information:Image Processing software
<create a new entry for each qualifying software program>
Name:Imaris Biteplane Scientific software
Version:version v 7.5.2
System Requirements:refer to the following website to check the minimum, recommended and high-end system requirments https://imaris.oxinst.com/support/system-requirements
Open Source? (Y/N):N 

(if available and applicable)
Executable URL: N/A
Source Repository URL: N/A
Developer:Biteplane (Oxford Instrument company)
Product URL:https://imaris.oxinst.com/packages
Software source components:N/A


Additional Notes(such as, will this software not run on 
certain operating systems?):N/A

3. Equipment-specific information: Microplate Reader 
<create a new entry for each qualifying piece of equipment>

Manufacturer:Molecular Devices, LLC,San Jose, CA, USA
Model: SpectraMax M2

(if applicable)
Embedded Software / Firmware Name:N/A
Embedded Software / Firmware Version:N/A
Additional Notes:N/A

4. Equipment-specific information: Confocal laser Scanning Electron Microscope (CLSM)
<create a new entry for each qualifying piece of equipment>

Manufacturer:Olympus, Tokyo, Japan
Model:Fluoview FV 1000

(if applicable)
Embedded Software / Firmware Name:N/A
Embedded Software / Firmware Version:N/A
Additional Notes:N/A

5. Equipment-specific information: Scanning Electron Microscope (SEM)
<create a new entry for each qualifying piece of equipment>

Manufacturer:Hitachi, Tokyo, Japan
Model:SU1510 VARIABLE PRESSURE SEM

(if applicable)
Embedded Software / Firmware Name: N/A
Embedded Software / Firmware Version: N/A
Additional Notes:N/A

6. Equipment-specific information: Real Time PCR system
<create a new entry for each qualifying piece of equipment>

Manufacturer: Applied Biosystems, Foster City, CA, USA
Model:Step One plus

(if applicable)
Embedded Software / Firmware Name: N/A
Embedded Software / Firmware Version: N/A
Additional Notes:N/A