Hi Vlad,

I just met with Max from Biohub and will start to work on getting this dataset curated for cellxgene. In the meantime, is there anything you need from me to get the object hosted on the cell atlas, or will you wait for the cellxgene link to post it?

Thanks,

Aaron

From: Vladimir Kiselev <vk6@sanger.ac.uk>
Date: Wednesday, May 26, 2021 at 7:28 AM
To: Jonah Cool <jcool@chanzuckerberg.com>, Aaron James Wilk <awilk@stanford.edu>
Cc: "cv19caingest@sanger.ac.uk" <cv19caingest@sanger.ac.uk>, Martin Prete <mp33@sanger.ac.uk>, Maximilian Lombardo <mlombardo@chanzuckerberg.com>, Kirtana Veeraraghavan <kveeraraghavan@chanzuckerberg.com>
Subject: Re: [Cv19caingest] Blish lab: New single-cell dataset for COVID-19 cell atlas [EXT]

Hi All,

Please let us know when the links to visualisations are ready and share them with us. We will then add them to the covid19atlas portal.

Many thanks,

Cheers,

Vlad

Vlad Kiselev

CellGen Informatics Team Leader

Wellcome Sanger Institute

Hinxton, Cambridge, CB10 1SA

Phone: +44(0)1223496850

Message: Mattermost or Slack [cellgeni.slack.com]

Web: https://wikiselev.github.io [wikiselev.github.io]

From: Jonah Cool <jcool@chanzuckerberg.com>
Date: Saturday, 22 May 2021 at 03:04
To: Aaron James Wilk <awilk@stanford.edu>
Cc: Vladimir Kiselev <vk6@sanger.ac.uk>, "cv19caingest@sanger.ac.uk" <cv19caingest@sanger.ac.uk>, Martin Prete <mp33@sanger.ac.uk>, Maximilian Lombardo <mlombardo@chanzuckerberg.com>, Kirtana Veeraraghavan <kveeraraghavan@chanzuckerberg.com>
Subject: Re: [Cv19caingest] Blish lab: New single-cell dataset for COVID-19 cell atlas [EXT]

Hi Aaron!

Great to hear from you as always! We would be happy to host the data on cellxgene and can work with Vlad and his team to then have the link reflected on the covid19cellatlas site. We can take a look at the seurat object that you shared and then circle back with some potential questions/amendments that would be helpful or required for us to host the data.

Have a great weekend and thanks for reaching out.

All good things,

Jonah

On Fri, May 21, 2021 at 11:33 AM Aaron James Wilk <awilk@stanford.edu> wrote:

Hi Vlad,

Apologies for the extremely delayed reply. We’ve been in the midst of revising the manuscript and had elected to wait to share the data until we were more confident that the object we’d share would be the final one! Here is a link to a Seurat object for the dataset: https://drive.google.com/file/d/1cG60rcbff-h_3ZoAM2GkJTttIQR4RWb9/view?usp=sharing [drive.google.com] Please let me know if you have any issues downloading it. The manuscript is currently in press at JEM (doi: 10.1084/jem.20210582) but not online yet.

Additionally, it would be wonderful for this dataset to be hosted on the cellxgene platform as well. I can’t recall if that is a completely independent process so I’ve also cc’d Jonah to remind me how to start moving with that.

Thanks so much for your help and don’t hesitate to reach out with any questions or concerns!

Best,

Aaron Wilk

From: Vladimir Kiselev <vk6@sanger.ac.uk>
Date: Thursday, January 7, 2021 at 1:57 AM
To: Aaron James Wilk <awilk@stanford.edu>, "cv19caingest@sanger.ac.uk" <cv19caingest@sanger.ac.uk>
Cc: Martin Prete <mp33@sanger.ac.uk>
Subject: Re: [Cv19caingest] Blish lab: New single-cell dataset for COVID-19 cell atlas [EXT]

Hi Aaron,

Yes, sure, we can add your reference and datasets to the website. Could you please share the datasets with us?

Many thanks,

Cheers,

Vlad

--

Vladimir Kiselev

CellGen Informatics Team Leader

Wellcome Sanger Institute

Wellcome Genome Campus

Hinxton, Cambridge, CB10 1SA

Phone: +44 (0) 1223 496850

Message: Mattermost or Slack [cellgeni.slack.com]

Web: https://wikiselev.github.io [wikiselev.github.io]

From: Aaron James Wilk <awilk@stanford.edu>
Date: Wednesday, 6 January 2021 at 17:17
To: "cv19caingest@sanger.ac.uk" <cv19caingest@sanger.ac.uk>
Subject: [Cv19caingest] Blish lab: New single-cell dataset for COVID-19 cell atlas [EXT]

Hi there,

My name is Aaron Wilk from the Blish lab at Stanford University. Your cell atlas is currently hosting our early COVID-19 scRNA-seq immune profiling work, and I am excited to tell you that we have now posted a preprint expanding that initial work to many more patients across a wider range of disease severity: https://www.biorxiv.org/content/10.1101/2020.12.18.423363v1 [biorxiv.org]

Would you be able to host Seurat .rds and .h5ad for this dataset as well?

Please let me know if you have any questions.

All the best,

Aaron Wilk

-- 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.

-- 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.