COVID_19_UK_CIC_Spatial

Understanding the immune response to SARS-CoV-2 is critical to our ability to control the coronavirus pandemic. Spatial transcriptomics will be performed on COVID-19 post-mortem tissues in collaboration with the UK - Coronavirus Immunology Consortium (UK-CIC). UK-CIC encompasses a concerted effort by the UK's world-leading immunology community to deliver a co-ordinated and agile national research programme to increase our understanding of how the immune system interacts with SARS-CoV-2. UK-CIC is led by Professor Paul Moss (University of Birmingham) and brings together 20 UK immunology centres of excellence, with support from the British Society for Immunology.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 1 Publication

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001015404	We provide a single-nuclei RNA-sequencing (snRNA-seq) dataset derived from four COVID-19 patients, generated using the 10x Chromium Next GEM Single Cell v3.1 kit. For our study, these were integrated with snRNA-seq data with 12 publicly available sc/snRNA-seq datasets, comprising organ donor lung samples (n=89) and COVID-19 lung tissue samples (n=51). Additionally, we provide a spatial transcriptomic dataset characterizing different histopathological stages of diffuse alveolar damage, across a cohort of 33 COVID-19 patients. This was generated using the Nanostring Whole Transcriptome Assay (WTA) with regions of interest (ROIs) sized 400 µm² each. This integrated multi-omics analysis of snRNA-seq, histology, and spatial transcriptomics data, is available for exploration and download via our web portal: https://covid19-multiomicatlas.cellgeni.sanger.ac.uk/.	Illumina NovaSeq 6000	4

Publications	Citations
Integrated histopathology, spatial and single cell transcriptomics resolve cellular drivers of early and late alveolar damage in COVID-19. Lee JTH, Barnett SN, Roberts K, Ashwin H, Milross L, Cho JW, Huseynov A, Woodhams B, Aivazidis A, Li T, Majo J, Chaves P, Lee M, Miranda AMA, Jablonska Z, Arena V, Hanley B, Osborn M, Uhlmann V, Xu XN, McLean GR, Teichmann SA, Randi AM, Filby A, Kaye PM, Fisher AJ, Hemberg M, Noseda M, Bayraktar OA. Nat Commun 16: 2025 1979	0

Publications

Citations

Integrated histopathology, spatial and single cell transcriptomics resolve cellular drivers of early and late alveolar damage in COVID-19.
Lee JTH, Barnett SN, Roberts K, Ashwin H, Milross L, Cho JW, Huseynov A, Woodhams B, Aivazidis A, Li T, Majo J, Chaves P, Lee M, Miranda AMA, Jablonska Z, Arena V, Hanley B, Osborn M, Uhlmann V, Xu XN, McLean GR, Teichmann SA, Randi AM, Filby A, Kaye PM, Fisher AJ, Hemberg M, Noseda M, Bayraktar OA. Nat Commun 16: 2025 1979