Cv19caingest November 2020

cv19caingest@sanger.ac.uk

4 participants
4 discussions

by Ksenia Sokolova

Hello, I had a question about the pre-processing of the datasets hosted on the covid19cellatlas.org<http://covid19cellatlas.org>. I am sorry if I reached out on a wrong address, and I would be grateful if you could forward me to the right person. Specifically, I am interested in the information on the normalization/processing of the raw expression values, used to generate the .h5ad files for the healthy donors. I noted on the data ingestion information that the raw counts are always pre-processed, but no information on what that processing is or for what datasets that affected. So, I would be grateful if you could clarify this. Sincerely yours, Ksenia Sokolova

3 years, 11 months

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3 years, 11 months

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by Karen Hope s

3 years, 11 months

Imaging mass cytometry data as part of the COVID-19 cell atlas? [EXT]

by Andre Rendeiro

Hello, We've recently generated spatially-resolved single-cell data of post-mortem lung tissue of COVID-19 patients and other lung infections (https://urldefense.proofpoint.com/v2/url?u=https-3A__www.medrxiv.org_conten… ). Would there be interest in adding this dataset to the COVID-19 portal of the HCA? We already provide a h5ad file with the single-cell data (https://urldefense.proofpoint.com/v2/url?u=https-3A__zenodo.org_record_4139… ), but perhaps this could help researchers having a one-stop place for COVID-19 single cell data? Of importance, our features do not represent gene expression but protein abundance for 36 selected proteins, so this is in contrast to most other datasets which I believe are scRNA-seq. Best wishes, Andre -- *André Rendeiro, Ph.D. *Postdoctoral Associate, Elemento Lab Englander Institute for Precision Medicine Institute for Computational Biomedicine *Weill Cornell Medicine *1305 York Ave., Y13.13 New York, NY (USA) 10021 afr4001(a)med.cornell.edu <mailto:afr4001@med.cornell.edu>

3 years, 11 months

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Cv19caingest November 2020