- Cv19caingest - public-lists.sanger.ac.uk

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

5 years, 2 months

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The best translation partner you could trust [EXT]

by Yuki Gao

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5 years, 2 months

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[EXT]

by Karen Hope s

kd

5 years, 2 months

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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>

5 years, 2 months

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Question about publication [EXT]

by Fernando Oneissi Martinez Estrada

Good afternoon: I am finding your Covid19 cell atlas very useful. Can we publish snapshots of the data? What is the best way to use it for publications? I am happy to share our paper draft where I believe some of your data could be very complimentary. If I could extract data for roc curves it would be amazing. Thank you in advance Fernando Martinez

5 years, 3 months

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want to report a problem [EXT]

by Gentleman, Robert C.

Hi Sorry to send to this address but I could not find out where to report problems. I wanted to download and use this file https://urldefense.proofpoint.com/v2/url?u=https-3A__hosted-2Dmatrices-2Dpr… Which is supposed to be an R data set, unfortunately it is not and is corrupted or otherwise not valid (could be they used a very old version of R, but no information is provided on your website). It would be helpful to provide md5 checksums or other tools to help validate downloads etc. Robert

5 years, 3 months

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Normalization [EXT]

by Gerges, Sherif

Hi! I hope this email finds you well! I have a question about the normalized expression for the datasets on covidatlas. How are the data normalized? Are gene expression values comparable across cell types? Best wishes, Sherif -- Sherif Gerges PhD Candidate Harvard Medical School | Broad Institute of Harvard and M.I.T | Analytic & Translational Genetics Unit, MGH Institute for Applied Computational Science | Harvard John A. Paulson School of Engineering and Applied Sciences

5 years, 3 months

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COVID-19 Atlas [EXT]

by Po-Yi Ho

Hey, I am very interested in this website and would like to be added to it. Thank you, Po-Yi -- *Po-Yi Ho, Ph.D.* ORISE Fellow Molecular Epidemiology & Bioinformatics Team Division of Viral Hepatitis, Centers for Disease Control and Prevention (CDC) 1600 Clifton Rd NE, Building 18, Room 4-110, MS H18-4, Atlanta, GA 30329 Tel: 678-559-2413, Email: poyiho.ph(a)gmail.com

5 years, 3 months

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List migraton

by Mark Thompson

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5 years, 5 months

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Ask about T cell dataset in the paper [A cellular census of human lungs identifies novel cell states in health and in asthma] [EXT]

by Jin, Kang

Dear Sir/Madam, I’m Kang Jin, a PhD student in Biomedical Informatics Department in Cincinnati Children’s Hospital Medical Center. It’s so exciting to see the Covid19 Cell Atlas (https://www.covid19cellatlas.org/) online held by your institute and HCA. Dr. Bruce Aronow and I are exploring immune cells in human lung and their relations with SARS-COV-2 invasion and inflammation. The upper airway dataset from Vieira Braga et al (https://urldefense.proofpoint.com/v2/url?u=https-3A__pubmed.ncbi.nlm.nih.go… ) is an awesome dataset which is also available on Covid19 Cell Atlas. I can find the single cell data for 10X and Drop-seq in the paper. However, the single data of CD4+ T cells in the Fig.5 (smartSeq) were not available from either GEO or HCA portal. I’m not sure if it’s available in EGAS00001001755<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ebi.ac.uk_ega_stud… >. Could I ask if I can access the data in EGA? If so, what do I need to do to apply for the data? Thanks so much for your help! Best regards, Kang Kang Jin | PhD student Biomedical Informatics Graduate Program Cincinnati Children’s | University of Cincinnati 3333 Burnet Avenue, Cincinnati, OH 45229

5 years, 7 months

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