READ ME File For 'Dataset for Doctoral Thesis, Investigating the role of MHC class I molecules in immune evasion by transmissible tumour cells'

Dataset DOI: 10.5258/SOTON/D3092

ReadMe Author: Kathryn Anne Hussey, University of Southampton ORCID ID 0000-0002-8882-1502

This dataset supports the thesis entitled 'Investigating the role of MHC class I molecules in immune evasion by transmissible tumour cells'
AWARDED BY: Univeristy of Southampton
DATE OF AWARD: 2024

DESCRIPTION OF THE DATA
IHC-Analysis_Macros
Macros used for semi-automated image analysis of immunohistochemistry Devil Facial Tumour Disease samples to generate expression scores. 'IHC-Profiler_ImageJ-Macro_...' files need to be run in ImageJ software with the IHC Profiler plugin installed (referenced in the thesis). '..._Fiji_Macro_...' files need to be run in Fiji software. 

IHC-Images
Images taken at 200x magnification of immunohistochemistry staining of DFT1 and DFT2 tumours. Files (.tif) are labelled with the Tasmanian devil name, tumour number (if applicable), and primary antibody used for staining. Images were used for semi-automated image analysis to generate expression scores for strength of staining.

NGS_Devil-Host-MHCI-Sequencing(1)
Illumina sequencing files generated from MHC class I sequencing of Devil Facial Tumour Disease tumour cells and hosts (4906-gamma & A-M). Files are labelled with the sample/Tasmanian devil name, replicate number (1-3), and forward (R1) or reverse (R2) reads. Files are in a zipped format (.fastq.gz) and need to be unzipped to a .fastq format for analysis.

NGS_Devil-Host-MHCI-Sequencing(2)
Illumina sequencing files generated from MHC class I sequencing of Devil Facial Tumour Disease tumour cells and hosts (N-W). Files are labelled with the sample/Tasmanian devil name, replicate number (1-3), and forward (R1) or reverse (R2) reads. Files are in a zipped format (.fastq.gz) and need to be unzipped to a .fastq format for analysis.

NGS-Analysis_Scripts
Scripts and assocaited files for processing and analysis of Illumina sequencing files (.fastq) for MHC class I sequencing of Devil Facial Tumour Disease tumour cells and hosts. Scripts were run in the numbered order in the .zip folder, using packages detailed in the thesis.

Tasmanian-Devil-Biopsies-Metadata
.csv file, containing metadata for all Tasmanian devil samples (tumour and ear biopsies) used in the creation of this thesis, collected between 2006-2022. Spreadsheet includes information on sample collection, tumour measurements, and immunohistochemistry analysis generated for this thesis.


This dataset contains:
IHC-Analysis_Macros.zip
IHC-Images.zip
NGS_Devil-Host-MHCI-Sequencing(1).zip
NGS_Devil-Host-MHCI-Sequencing(2).zip
NGS-Analysis_Scripts.zip
Tasmanian-Devil-Biopsies-Metadata.csv

Date of data collection: 2019 - 2023

Related projects/Funders:
PhD project funded by The Gerald Kerkut Charitable Trust, and the University of Southampton Presidential Scholarship

Related publication:
Hussey, K., Caldwell, A., Kreiss, A., Skødt, K., Gastaldello, A., Pye, R., Hamede, R., Woods, G.M. and Siddle, H.V. (2022) ‘Expression of the Nonclassical MHC Class I, Saha-UD in the Transmissible Cancer Devil Facial Tumour Disease (DFTD)’, Pathogens, 11(3), 351. https://doi.org/10.3390/pathogens11030351

Date that the file was created: May, 2024