This README.txt file was generated on <20211104> by <WONG Tsz Lam Matthew>

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GENERAL INFORMATION
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1. Title of Dataset:Dataset regarding PhD project titled "Protein tyrosine kinase 7 (PTK7) promotes metastasis in hepatocellular carcinoma under SOX9 regulation and TGF-beta signalling"


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

First Author Contact Information
    Name:WONG, Tsz Lam Matthew
    Faculty:Medicine
    Email:matmat94@connect.hku.hk



Corresponding Author Contact Information
    Name:Dr. MA, Kwai Yee Stephanie
    Faculty:Medicine
    Email:stefma@hku.hk


Author Contact Information (if applicable)
    Name:N/A
    Faculty:N/A
    Email:N/A


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DATA & FILE OVERVIEW
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Directory of Files:
   A. Filename: Animal models       
      Short description:Representative images and analyses regarding all in vivo studies performed in the project      


        
   B. Filename:Bioinformatics        
      Short description:Datasets and correponding analyses regarding the identification of pathways associated with protein of interest
                        Also includes validation on various animal models.         


        
   C. Filename:Functional        
      Short description:Representative images and analyses regarding functional assays performed on HCC cell lines with PTK7 expression manipulated


   D. Filename:IHC
      Short description:Images of patient tissue sections represented by TMA and corresponding scoring of PTK7 staining intensity


   E. Filename:Others
      Short description:Readings and analyses regarding ChIP and luciferase reporter assays


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?):              


File Naming Convention:File name self-explanatory


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DATA DESCRIPTION FOR: TMA/Summary of expression and clinical info
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<create sections for each dataset included>


1. Number of variables:PTK7 expression (tumour/non-tumour) & SOX9 expression (tumour/non-tumour) 


2. Number of cases/rows: A total of 159 patients represented by 3 TMAs


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


4. Variable List



    A. Name: PTK7 expression
       Description: Defined as H(High) or L(Low)


    B. Name: SOX9 expression
       Description: Defined as H(High), M(Medium) or L(Low)

    C. Name:TNM 
       Description: TNM stages ranging from 1 to 4

    D. Name: OS
       Descrtipion:The overall survival of patients by months

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METHODOLOGICAL INFORMATION
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#
# Software: If specialized software(s) generated your data or
# are necessary to interpret it, please provide for each (if
# applicable): software name, version, system requirements,
# and developer. 
#If you developed the software, please provide (if applicable): 
#A copy of the software’s binary executable compatible with the system requirements described above. 
#A source snapshot or distribution if the source code is not stored in a publicly available online repository.
#All software source components, including pointers to source(s) for third-party components (if any)

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

Name:GSEA 
Version:4.0.1
System Requirements:64-bit Windows
Open Source? (Y/N): Y

(if available and applicable)
Executable URL:
Source Repository URL:
Developer:
Product URL:
Software source components:


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


2. Equipment-specific information:Confocal microscope
<create a new entry for each qualifying piece of equipment>

Manufacturer:ZEISS
Model:LSM 880

(if applicable)
Embedded Software / Firmware Name:ZEN (blue version)
Embedded Software / Firmware Version:3.2
Additional Notes: