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

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>

4 years, 1 month

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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

4 years, 1 month

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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

4 years, 1 month

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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

4 years, 1 month

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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

4 years, 2 months

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List migraton

by Mark Thompson

This list has been successfully migrated to the new Sanger mailman list server https://public-lists.sanger.ac.uk <https://public-lists.sanger.ac.uk/> There are no alterations to how this list is configured, please continue to send and receive messages as before. To login and mange your account please create a new account using the ‘Sign up’ button in the top right of the window.

4 years, 3 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

4 years, 6 months

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h5ad data [EXT]

by Lazarus, Kyren

Hi there, I am trying to process this data in R, and having some issues reading the h5ad file. Can you please point me in the right direction? Thanks Best, Kyren Lazarus Janes Lab L4L - UCL

4 years, 6 months

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Lung scRNA-data from Vieira Braga et al [EXT]

by Stepan Nersisyan

Hello! I've downloaded .h5ad file of nasal scRNA-seq published in Vieira Braga et al (2019) and I really need count-level data for my downstream analysis. However, I cannot find information on total number of reads mapped to each cell (which I can find as "n_counts" for majority of other datasets), so I cannot restore count matrix. Is there any way to get this data too? Thank you very much, it will really help me to finalize my research. Best regards, Stepan Nersisyan, Researcher, Faculty of Biology and Biotechnology, Higher School of Economics, Moscow, Russia

4 years, 6 months

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Human 10x scRNAseq from Oral Cavity [EXT]

by Byrd, Kevin Matthew

Hi, I am a lead PI from a group at UNC with Human V3 10x scRNAseq from the oral cavity, specifically from the hard palate/gingiva from 4 healthy human volunteers (2M/2F). It is unfortunate that there are no oral samples available for this Atlas, and I am interested in contributing this unpublished data to the COVID19 Cell Atlas. This work was funded through the industry, so it would not necessarily need to publish if incorporated. Happy to have a zoom call or continue this conversation over email. Best, Kevin M. Byrd, DDS, PhD The University of North Carolina at Chapel Hill Office: 3606 Koury Oral Health Sciences; CB #7455 Research Instructor, Oral & Craniofacial Health Sciences Resident, Graduate Training Program in Periodontology Chapel Hill, NC 27599-7525 Cell Phone: 260-249-4724

4 years, 7 months

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