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

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by Mark Thompson 25 Aug '20

25 Aug '20

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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 02 Jun '20

02 Jun '20

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

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h5ad data [EXT]
by Lazarus, Kyren 01 Jun '20

01 Jun '20

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

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Lung scRNA-data from Vieira Braga et al [EXT]
by Stepan Nersisyan 30 May '20

30 May '20

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

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Human 10x scRNAseq from Oral Cavity [EXT]
by Byrd, Kevin Matthew 11 May '20

11 May '20

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

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Fwd: cell paper vs covid19atlas [EXT]
by Maximilian Haeussler 05 May '20

05 May '20

---------- Forwarded message --------- From: Vladimir Kiselev <vk6(a)sanger.ac.uk> Date: Tue, May 5, 2020 at 4:16 PM Subject: Re: cell paper vs covid19atlas [EXT] To: Maximilian Haeussler <mhaeussl(a)ucsc.edu> Hi Max, Could you please send this question to cv19caingest(a)sanger.ac.uk ? There is a data scientist there who will be able to answer your questions. Cheers, Vlad -- *Vladimir Kiselev* CellGen Informatics <http://www.sanger.ac.uk/science/groups/cellular-genetics-informatics> Team Leader Wellcome Sanger Institute Wellcome Genome Campus Hinxton, Cambridge, CB10 1SA Phone: +44 (0) 1223 496850 Message: Mattermost <https://mattermost.sanger.ac.uk/cellgeninf> or Slack <https://urldefense.proofpoint.com/v2/url?u=https-3A__cellgeni.slack.com_&d=… > Web: https://urldefense.proofpoint.com/v2/url?u=https-3A__genat.uk&d=DwIFaQ&c=D7… [image: cid:image001.png@01D3BF73.275DCF80] <http://www.sanger.ac.uk/> *From: *Maximilian Haeussler <mhaeussl(a)ucsc.edu> *Date: *Tuesday, 5 May 2020 at 15:09 *To: *Vladimir Kiselev <vk6(a)sanger.ac.uk> *Subject: *cell paper vs covid19atlas [EXT] Hi Vlad, is this paper in some way related to your datasets? https://urldefense.proofpoint.com/v2/url?u=https-3A__www.sciencedirect.com_… [sciencedirect.com] <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.sciencedirect.com_…> Is there some overlap in the datasets that you use? If yes, could highlight that on your webpage... best Max -- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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https://www.covid19cellatlas.org [EXT]
by David Gifford 04 May '20

04 May '20

Can you please add me to your email list? Thanks, David Gifford Computer Science, MIT, Professor Biological Engineering, MIT, Professor

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[EXT]
by Claude Bergeron 28 Apr '20

28 Apr '20

Thanks For the support Claude Bergeron Claude.bergeron(a)lrmm.com (514) 2<tel:(514)%20256-6303>95 6303

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data to the COVID-19 Cell Atlas website [EXT]
by Jean-Jacques Fournie 28 Apr '20

28 Apr '20

Dear Colleagues I read with great interest your paper in Nature Medicine, and would like to congratulate you for this important contribution against Covid. As member (and fan) of the HCA, I would like to suggest you to add to the *COVID-19 Cell Atlas *website our cell-sorted human gamma delta T lymphocytes scRNASeq dataset (n=8k cells), freely available at NCBI GEO data sets as *GSE128223*. The (cell, gene) matrix is included and readily downloadable from this site, or else we can directly provide you with if you prefer. Here are 2 important reasons for adding it: 1-It is the only scRNASeq (10xgenomics Chem. 3' V2) resource available for these human T cells, which were TCR purified by state of the art techniques. 2- gamma delta T lymphocytes are abundantly resident in all epithelia and mucosal human tissues and mediate innate immunity resposnes. If interested, read our paper by Pizzolato, G., et al. : Single-cell RNA sequencing unveils the shared and the distinct cytotoxic hallmarks of human TCRVdelta1 and TCRVdelta2 gammadelta T lymphocytes. PNAS (2019): 116, 11906-11915. Best regards, and bravo anyway -- Jean Jacques Fournié, PhD Team noLymits Cancer Research Center of Toulouse CRCT-UMR1037 Inserm-Université Toulouse 3-ERL5294 CNRS Oncopole de Toulouse, 2 Avenue Hubert Curien, CS 53717 31037 TOULOUSE CEDEX 1 - FRANCE office: +335 8274 1590 mobile: +336 1990 0602 website: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.crct-2Dinserm.fr&d=…

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[EXT]
by Adelina M.Túlio Túlio 26 Apr '20

26 Apr '20

ceder matéria para Curitiba ■ Paraná ■Brasil CEP 81280-330

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