UKCIC COVID-19 Paper Figures

This repository contains Jupyter Notebooks used to generate figures for the UKCIC COVID-19 paper. Each notebook corresponds to a specific figure or analysis presented in the publication.

Prerequisites

Follow instruction below to create conda environment:

git clone https://github.com/thjimmylee/UKCIC-COVID19-paper-figures.git
cd UKCIC-COVID19-paper-figures/spatial_decon

conda create --name spacejam --file environment.txt

Set up a virtual environment (recommended)

conda activate spacejam
python3 -m venv venv
source venv/bin/activate  # On Windows: venv\Scripts\activate

Launch Jupyter Notebook

jupyter notebook

Browse through the folders for .ipynb notebooks to reproduce results.

Integrated histopathology, spatial and single cell transcriptomics resolve cellular drivers of early and late alveolar damage in COVID-19

Jimmy Tsz Hang Lee^1,*, Sam N. Barnett^2,*, Kenny Roberts¹, Helen Ashwin³, Luke Milross⁴, Jae-Won Cho⁵, Alik Huseynov², Benjamin Woodhams^1,6, Alexander Aivazidis¹, Tong Li¹, Joaquim Majo⁷, Patricia Chaves Guerrero², Michael Lee², Antonio M. A. Miranda², Zuzanna Jablonska², Vincenzo Arena⁸, Brian Hanley⁹, Michael Osborn⁹, Virginie Uhlmann⁶, Xiao-Ning Xu¹⁰, Gary R McLean^2,11, Sarah A. Teichmann^1,12, Anna M. Randi^2,13, Andrew Filby¹⁴, Paul M. Kaye³, Andrew J. Fisher^4,15,**, Martin Hemberg^5,**, Michela Noseda^2,**, Omer Ali Bayraktar^1,**

^* These authors contributed equally to this work
^** Co-last and co-corresponding authors

¹ Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
² National Heart and Lung Institute, Imperial College London, London, UK
³ York Biomedical Research Institute, Hull York Medical School, University of York, York, UK
⁴ Newcastle University Translational and Clinical Research Institute, Newcastle upon Tyne, UK
⁵ Gene Lay Institute for Immunology and Inflammation, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
⁶ European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL), Cambridge, UK
⁷ Department of Cellular Pathology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
⁸ Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Istituto di Anatomia Patologica, Università Cattolica Del Sacro Cuore, Rome, Italy
⁹ Department of Cellular Pathology, Northwest London Pathology, Imperial College London NHS Trust, London, UK
¹⁰ Department of Infectious Disease, Imperial College London, London, UK
¹¹ London Metropolitan University, London, UK
¹² Department of Physics, Cavendish Laboratory, University of Cambridge, JJ Thomson Ave, Cambridge CB3 0HE, UK
¹³ British Heart Foundation Centre of Research Excellence, Imperial College London, London, UK
¹⁴ Biosciences Institute and Innovation, Methodology and Application Research Theme, Newcastle University, Newcastle upon Tyne, UK
¹⁵ Institute of Transplantation, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK

bioRXiv preprint: URL
doi: https://doi.org/10.1101/2023.12.20.572494

Webportal: COVID19 Multiomic Atlas