Hi Ni,

Nice to hear from you, hope you are well. I didn’t know you were at the other end of this 😊

We have the H5AD file for all of the data but Gary just needs to amend some of the annotation and then we can pass this onto you (sometime today). Would a link to our google drive be OK for you to pick it up?

We were hoping to add to our manuscript that the data will become available on the covid-19 cell atlas, hope this is ok?

Many thanks,

Emily

Emily Stephenson

Haniffa Lab

M3.121 Leech Building

Faculty of Medical Sciences

Newcastle University

NE2 4HH

From: Ni Huang <nh3@sanger.ac.uk>
Date: Wednesday, 6 January 2021 at 14:48
To: Emily Stephenson <Emily.Stephenson2@newcastle.ac.uk>, "cv19caingest@sanger.ac.uk" <cv19caingest@sanger.ac.uk>
Cc: M A Haniffa <m.a.haniffa@newcastle.ac.uk>, Michael Mather <Michael.Mather@newcastle.ac.uk>, Gary Reynolds <gary.reynolds@newcastle.ac.uk>
Subject: Re: [Cv19caingest] Data Upload [EXT]

⚠ External sender. Take care when opening links or attachments. Do not provide your login details.

Hi Emily,

Thanks for submitting data to the portal. Take CZI-organised datasets as an example, we make them fully browsable but not downloadable yet. You could provide the data as an H5AD, which is most convenient, or we can do the conversion if necessary. There is a guide on data format here [docs.google.com]. Please let me know of any further questions.

Many thanks,

From: Emily Stephenson <Emily.Stephenson2@newcastle.ac.uk>
Date: Monday, 4 January 2021 at 11:41
To: "cv19caingest@sanger.ac.uk" <cv19caingest@sanger.ac.uk>
Cc: M A Haniffa <m.a.haniffa@newcastle.ac.uk>, Michael Mather <Michael.Mather@newcastle.ac.uk>, Gary Reynolds <gary.reynolds@newcastle.ac.uk>
Subject: [Cv19caingest] Data Upload [EXT]

Good Morning,

If it is possible, we would like to upload our COVID-19 patient data to the COVID-19 Cell Atlas web portal.

Please let us know how we can begin this process. The data is currently unpublished.

Many thanks and best wishes,