This README.txt file was generated on <20200825> by <Ho Julian>

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GENERAL INFORMATION
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1. Title of Dataset: Supporting data for "Zika virus infection downregulates MHC class I presentation"


2. Author Information

    Name: Ho Julian

    Faculty: Li Ka Shing Faculty of Medicine

    Email: u3507221@connect.hku.hk


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DATA & FILE OVERVIEW
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# Directory of Files in Dataset: List and define the different 
# files included in the dataset. This serves as its table of 
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Directory of Files:
   A. Filename: HMC3 surface MHC-I + other markers' expression FACS
      Short description: FACS results from ZIKV-infected HMC3 of MHC and functional markers' expressions (also including plaque assay results)

      
   B. Filename: U251 surface MHC-I FACS         
      Short description: FACS results from ZIKV-infected U251 of MHC-I (also including plaque assay results)
      

   C. Filename: HMC3 LEGENDplex         
      Short description: Cytokine and growth factor bead-based multiplex results of ZIKV-infected HMC3    

        
   D. Filename: HMC3 MHC-I degradation mechanism FACS
      Short description: FACS results of intracellular staining of MHC-I of ZIKV-infected HMC3 and effect of MG132 proteosomal inhibition


   E. Filename: A549 & A549 RIG-I KO surface MHC-I FACS       
      Short description: FACS results from ZIKV-infected A549 and A549 RIG-I KO cells of MHC-I (also including plaque assay results)        


   F. Filename: Thesis figures Prism
      Short description: Prism files of figures used in the thesis



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?): HMC3 and A549 cells were infected at MOI = 2


#
# File Naming Convention: Define your File Naming Convention 
# (FNC), the framework used for naming your files systematically 
# to describe what they contain, which could be combined with the
# Directory of Files. 
#

File Naming Convention: Based on the date (naming with date of infection) and the nature of experiment


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DATA DESCRIPTION FOR: HMC3 surface MHC-I + other markers' expression FACS
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<create sections for each dataset included>


1. Number of sub-data: 6

2. Number of cases/rows: N/A


3. Missing data codes: N/A


4. Variable List


    A. Name: protein expression level
       Description: HLA-A,B,C, HLA-DR, CD40, CD68, CD80, IBA1

    B. Name: time point
       Description: 1dpi, 2dpi 

    C. Name: infection/treatment condition
       Description: mock, IFN-g, ZIKV-infected


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DATA DESCRIPTION FOR: U251 surface MHC-I FACS
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<create sections for each dataset included>


1. Number of sub-data: 7


2. Number of cases/rows: N/A


3. Missing data codes: N/A


4. Variable List

    A. Name: protein expression level
       Description: HLA-A,B,C

    B. Name: time point
       Description: 1dpi, 2dpi 

    C. Name: infection/treatment condition
       Description: mock, IFN-a, ZIKV-infected


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DATA DESCRIPTION FOR: HMC3 LEGENDplex   
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<create sections for each dataset included>


1. Number of sub-data: 7


2. Number of cases/rows: N/A


3. Missing data codes: N/A


4. Variable List


    A. Name: cytokine/growth factor
       Description: Biolegend LEGENDplex Antivirus and Neuroinflammation panels (also one experimental replicate of Microglia/Macrophage panel)

    B. Name: time point
       Description: 1 dpi and 2 dpi

    C. Name: infection/treatment condition
       Description: mock, IFN-g, ZIKV-infected (some included IL-12 treatment)
    

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DATA DESCRIPTION FOR:   HMC3 MHC-I degradation mechanism FACS
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<create sections for each dataset included>


1. Number of sub-data: 3


2. Number of cases/rows: N/A


3. Missing data codes: N/A


4. Variable List


    A. Name: protein expression level
       Description: intracell and cell surface HLA-A,B,C

    B. Name: time point
       Description: 36 hpi and 48 hpi

    C. Name: infection condition
       Description: mock, ZIKV-infected 

    D. Name: drug condition
       Description: DMSO, MG132, Bafilomycin A1 and BFA



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DATA DESCRIPTION FOR:   A549 & A549 RIG-I KO surface MHC-I FACS
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<create sections for each dataset included>


1. Number of sub-data: 7


2. Number of cases/rows: N/A


3. Missing data codes: N/A


4. Variable List


    A. Name: protein expression level
       Description: HLA-A,B,C

    B. Name: time point
       Description: 1 dpi and 2 dpi

    C. Name: infection/treatment condition
       Description: mock, IFN-a, ZIKV-infected 

    D. Name: cell line
       Description: A549 Dual cell or A549 Dual RIG-I KO cell


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DATA DESCRIPTION FOR:   Thesis figures Prism
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<create sections for each dataset included>


1. Number of sub-data: 5


2. Number of cases/rows: N/A


3. Missing data codes: N/A


4. Variable List: N/A


   

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METHODOLOGICAL INFORMATION
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1. Software-specific information: FlowJo_v10.6.1
For the use of analysing FACS data



2. Equipment-specific information: 

Manufacturer: Invitrogen
Model: Attune NxT Flow Cytometer