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2023-van Eijs et al-preprint

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mleipold

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Location: Stanford HIMC, CA, USA

Post Wed Apr 26, 2023 3:06 pm

2023-van Eijs et al-preprint

"Highly multiplexed spatial analysis identifies tissue-resident memory T cells as drivers of ulcerative and immune checkpoint inhibitor induced colitis"
Mick J.M. van Eijs, José J.M. ter Linde, Matthijs J.D. Baars, Mojtaba Amini, Miangela M. Laclé, Eelco C. Brand, Eveline M. Delemarre, Julia Drylewicz, Stefan Nierkens, Rik J. Verheijden, Bas Oldenburg, Yvonne Vercoulen, Karijn P.M. Suijkerbuijk, Femke van Wijk
medRxiv, posted April 25, 2023
https://doi.org/10.1101/2023.04.25.23289056

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

- "Data Availability An R markdown file with code used for IMC data processing and analysis has been deposited on Zenodo, publicly accessible via DOI: 10.5281/zenodo.7858216. In compliance with national legislation, upon acceptance of the manuscript data produced in the present study will become available online (DataverseNL) with restrictions."

Zenodo link is a PDF with the code
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mleipold

Guru

Posts: 5796

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Thu Sep 28, 2023 3:45 pm

Re: 2023-van Eijs et al-preprint

Now published:

iScience. 2023, 26, 107891
https://doi.org/10.1016/j.isci.2023.107891

- "Single-cell segmented raw IMC data derived from participants with colitis and serum multiplexed proteomic data have been deposited online in DataVerseNL. In compliance with national legislation, this repository is accessible with restrictions via https://doi.org/10.34894/N84F12 ."
-Imaging mass cytometry data (after single-cell segmentation)
-- segmented_IMC_data.Rda (restricted)
This file contains the raw single-cell segmented channel data for all IMC channels including geometric cell data.
-- IMC_clinical_metadata.csv (restricted)
This file contains clinical metadata for the subjects included in segmented_IMC_data.Rda
-- IMC_clinical_metadata_codebook.csv (unrestricted)
This file contains codebook with description of all parameters included IMC_clinical_metadata.csv

- As mentioned, this is access-restricted. And, the rawest form of the data appears to be the partially-processed RDa, not as TIFFs

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