2023-Nyirenda et al-preprint

[mleipold]

"Spatially resolved single-cell atlas of the lung in fatal Covid19 in an African population reveals a distinct cellular signature and an interferon gamma dominated response"
James Nyirenda, Olympia Hardy, Joao Luiz Silva Filho, Vanessa Herder, Charalampos Attipa, Charles Ndovi, Memory Siwombo, Takondwa Namalima, Leticia Suwedi, Watipenge Nyasulu, Thokozile Ngulube, Deborah Nyirenda, Leonard Mvaya, Joseph Phiri, Dennis Chasweka, Chisomo Eneya, Chikondi Makwinja, Chisomo Phiri, Frank Ziwoya, Abel Tembo, Kingsley Makwangwala, Stanely Khoswe, Peter Banda, Ben Morton, Orla Hilton, Sarah Lawrence, Monique Frere dos Reis, Gisely Cardoso Melo, Marcus Vinicious Guimaros de Lecerda, Fabio Trindande Maranhao Costa, Wuelta Marcelo Monteiro, Luiz Carlos de Lima Fereirra, Carla Johnson, Dagmara Mcguinness, Kondwani Jambo, Michael J Haley, Benjamin Kumwenda, Massimo Palmarini, Kayla G Barnes, Donna M Denno, Wieger Voskuijl, Steve Kamiza, Kevin Couper, Matthias Marti, Thomas D Otto, Christopher A Moxon
bioRxiv, posted November 17, 2023
https://doi.org/10.1101/2023.11.16.566964

- will update when/if this is peer-reviewed and published

- no IMC accession given

- reuses IMC data from:
2023-Filho et al-preprint
2021-Rendeiro et al- Nature

[mleipold]

Now published:

Nat Med. 2024
https://doi.org/10.1038/s41591-024-03354-3

- "Data availability

scRNA-seq: Raw data and processed count matrices are deposited at the EBI ArrayExpress (accession number E-MTAB-13544). Fully processed RDS objects of the scRNA-seq analysis and IMC can be found through the GitHub repository (https://github.com/olympiahardy/COSMIC_ ... ovid_Atlas) and through the following Zenodo records: https://doi.org/10.5281/zenodo.13898422 (ref. 72) and https://doi.org/10.5281/zenodo.13899297 (ref. 73)."

Ref 72: https://doi.org/10.5281/zenodo.13898422
- as far as I can tell, these are only the RNA
- "Imaging Mass Cytometry Analysis This Zenodo record can be accessed using the DOI here: 10.5281/zenodo.13899297 . The GitHub repository can be accessed here: https://github.com/joaolsf/Spatial_Sing ... lawi_COVID"

Ref 73: https://zenodo.org/records/13899297
- "Here, there are scripts containing pre-processing, image denoise, cell segmentation, single-cell and spatial statistics analysis as well as visualisation plots for the Imaging Mass Cytometry of the post-mortem lung sections."

**** so, as far as I can tell, there are no raw IMC TIFF or MCD files available