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://urldefense.proofpoint.com/v2/url?u=https-3A__www.biorxiv.org_content_10.1101_2020.12.18.423363v1&d=DwIGaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=YCVDjNHxAgv8-gpjr0Xb48Y9Vk9U8oXzH6wskU6pf14&m=Tuf8VaxG_jMRurqqcEwfbdAU9FfPVIloKeCctaeVvgE&s=7CEJLbPxGY0aXI5E7DSMZX-k0PUtJqmlirMjWIKnj44&e= 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
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<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://cellgeni.slack.com/> Web: https://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 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
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://urldefense.proofpoint.com/v2/url?u=https-3A__drive.google.com_file_d_1cG60rcbff-2Dh-5F3ZoAM2GkJTttIQR4RWb9_view-3Fusp-3Dsharing&d=DwIGaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=YCVDjNHxAgv8-gpjr0Xb48Y9Vk9U8oXzH6wskU6pf14&m=z_a1-iTiYqv899evDb5Qug-jg0_qplAyOqaIFTT37aY&s=g2vZ4b21foMA71mfGKEWOsnKv0E3MFYgxAsC3KcXyNE&e= 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<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=DwIGaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=YCVDjNHxAgv8-gpjr0Xb48Y9Vk9U8oXzH6wskU6pf14&m=z_a1-iTiYqv899evDb5Qug-jg0_qplAyOqaIFTT37aY&s=wwIp3BbDJkF94qif0jc2XHQLLUmkyRVnZVKqY7fKHUQ&e= > Web: https://urldefense.proofpoint.com/v2/url?u=https-3A__wikiselev.github.io&d=DwIGaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=YCVDjNHxAgv8-gpjr0Xb48Y9Vk9U8oXzH6wskU6pf14&m=z_a1-iTiYqv899evDb5Qug-jg0_qplAyOqaIFTT37aY&s=cHBMNR-gNwlgAj_fwO9tBbv2dLA0WHW4iLUPpKDyipU&e= 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://urldefense.proofpoint.com/v2/url?u=https-3A__www.biorxiv.org_content_10.1101_2020.12.18.423363v1&d=DwIGaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=YCVDjNHxAgv8-gpjr0Xb48Y9Vk9U8oXzH6wskU6pf14&m=z_a1-iTiYqv899evDb5Qug-jg0_qplAyOqaIFTT37aY&s=VnT8fqnO1bwfxZlj9Vq7iki-XOSEk4sIUSfxP0x0vDc&e= 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.
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://urldefense.proofpoint.com/v2/url?u=https-3A__drive.google.com_file_d_1cG60rcbff-2Dh-5F3ZoAM2GkJTttIQR4RWb9_view-3Fusp-3Dsharing&d=DwIFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=YCVDjNHxAgv8-gpjr0Xb48Y9Vk9U8oXzH6wskU6pf14&m=qB8iEfYXSrFKWhCHI9qsU6DjBQVTUMMKvGscqzXefGE&s=bcTfnKmwGE_IRAm52bbtBbeNKrBRL45cm390pnWXLXI&e= 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 <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=DwIFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=YCVDjNHxAgv8-gpjr0Xb48Y9Vk9U8oXzH6wskU6pf14&m=qB8iEfYXSrFKWhCHI9qsU6DjBQVTUMMKvGscqzXefGE&s=mMBfAD_Pb47Sqb0lNLtJSTXxsvNjeMSMd4HMdmi6Rzs&e= >
*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://urldefense.proofpoint.com/v2/url?u=https-3A__www.biorxiv.org_content_10.1101_2020.12.18.423363v1&d=DwIFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=YCVDjNHxAgv8-gpjr0Xb48Y9Vk9U8oXzH6wskU6pf14&m=qB8iEfYXSrFKWhCHI9qsU6DjBQVTUMMKvGscqzXefGE&s=mC8qovg8-zf3fZCE0naOXVzv47eb8lBMDznk_BJab6s&e=
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.
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<http://www.sanger.ac.uk/science/groups/cellular-genetics-informatics> Team Leader Wellcome Sanger Institute Hinxton, Cambridge, CB10 1SA Phone: +44(0)1223496850 Message: Mattermost<https://mattermost.sanger.ac.uk/cellgeninf> or Slack<https://cellgeni.slack.com/> Web: https://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<mailto: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=s... [drive.google.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__drive.google.com_file_d_1cG60rcbff-2Dh-5F3ZoAM2GkJTttIQR4RWb9_view-3Fusp-3Dsharing&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=9KyXPtoyUP8edjdvA3wxPg&m=K5ZPsdQyE0rEJ3G0OQbGKwCp5td6zRJhHXhWF3KrFqM&s=-fxLTy7hu5EHV8QxohQfoewblWTzSxF7SAYZXHSyuug&e=> 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<mailto:vk6@sanger.ac.uk>> Date: Thursday, January 7, 2021 at 1:57 AM To: Aaron James Wilk <awilk@stanford.edu<mailto:awilk@stanford.edu>>, "cv19caingest@sanger.ac.uk<mailto:cv19caingest@sanger.ac.uk>" <cv19caingest@sanger.ac.uk<mailto:cv19caingest@sanger.ac.uk>> Cc: Martin Prete <mp33@sanger.ac.uk<mailto: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<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 [cellgeni.slack.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__cellgeni.slack.com_&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=9KyXPtoyUP8edjdvA3wxPg&m=K5ZPsdQyE0rEJ3G0OQbGKwCp5td6zRJhHXhWF3KrFqM&s=WNX25Sk3kgZLGw4c8pv_tBzX8qr4UPjD2NpFGo2uiJk&e=> Web: https://wikiselev.github.io [wikiselev.github.io]<https://urldefense.proofpoint.com/v2/url?u=https-3A__wikiselev.github.io&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=9KyXPtoyUP8edjdvA3wxPg&m=K5ZPsdQyE0rEJ3G0OQbGKwCp5td6zRJhHXhWF3KrFqM&s=lSU7imFibmiTDZzgVcBfUdpemtmzO3AgpFFYzlxuHd4&e=> From: Aaron James Wilk <awilk@stanford.edu<mailto:awilk@stanford.edu>> Date: Wednesday, 6 January 2021 at 17:17 To: "cv19caingest@sanger.ac.uk<mailto:cv19caingest@sanger.ac.uk>" <cv19caingest@sanger.ac.uk<mailto: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]<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.biorxiv.org_content_10.1101_2020.12.18.423363v1&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=9KyXPtoyUP8edjdvA3wxPg&m=K5ZPsdQyE0rEJ3G0OQbGKwCp5td6zRJhHXhWF3KrFqM&s=foYlspKfroCmRjkVWv4XHJ05sHptoF2PuUUJJAzKVgM&e=> 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.
Hi Aaron! I'm a product applications scientist for the cellxgene team. Thanks for sharing a link to your data! Would it be prudent for you, I and my colleague Kirtana to get together sometime next week and chat about the current curation process for cellxgene? Beforehand we can take a look at your data and also provide information more specific to your dataset. Looking forward to your reply, Max On Wed, May 26, 2021 at 10:28 AM Vladimir Kiselev <vk6@sanger.ac.uk> wrote:
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 <http://www.sanger.ac.uk/science/groups/cellular-genetics-informatics> Team Leader
Wellcome Sanger Institute
Hinxton, Cambridge, CB10 1SA
Phone: +44(0)1223496850
Message: Mattermost <https://mattermost.sanger.ac.uk/cellgeninf> or Slack <https://urldefense.proofpoint.com/v2/url?u=https-3A__cellgeni.slack.com_&d=DwIFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=YCVDjNHxAgv8-gpjr0Xb48Y9Vk9U8oXzH6wskU6pf14&m=eKB-yiCkeJ0oIEEjvK10CRSwLnG6NNH-IpLIkFVm2EI&s=G8FerKdyX4L6ekQ1mpfeK3hlI6fHkTp_HWk_aGtHFLM&e= >
*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://urldefense.proofpoint.com/v2/url?u=https-3A__drive.google.com_file_d_1cG60rcbff-2Dh-5F3ZoAM2GkJTttIQR4RWb9_view-3Fusp-3Dsharing&d=DwIFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=YCVDjNHxAgv8-gpjr0Xb48Y9Vk9U8oXzH6wskU6pf14&m=eKB-yiCkeJ0oIEEjvK10CRSwLnG6NNH-IpLIkFVm2EI&s=8o4nCb3ovBoLlMP6LQFbLPYWYWFkzzLrMIYHVauuoLA&e= [drive.google.com] <https://urldefense.proofpoint.com/v2/url?u=https-3A__drive.google.com_file_d_1cG60rcbff-2Dh-5F3ZoAM2GkJTttIQR4RWb9_view-3Fusp-3Dsharing&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=9KyXPtoyUP8edjdvA3wxPg&m=K5ZPsdQyE0rEJ3G0OQbGKwCp5td6zRJhHXhWF3KrFqM&s=-fxLTy7hu5EHV8QxohQfoewblWTzSxF7SAYZXHSyuug&e=> 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 <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 [cellgeni.slack.com] <https://urldefense.proofpoint.com/v2/url?u=https-3A__cellgeni.slack.com_&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=9KyXPtoyUP8edjdvA3wxPg&m=K5ZPsdQyE0rEJ3G0OQbGKwCp5td6zRJhHXhWF3KrFqM&s=WNX25Sk3kgZLGw4c8pv_tBzX8qr4UPjD2NpFGo2uiJk&e=>
Web: https://urldefense.proofpoint.com/v2/url?u=https-3A__wikiselev.github.io&d=DwIFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=YCVDjNHxAgv8-gpjr0Xb48Y9Vk9U8oXzH6wskU6pf14&m=eKB-yiCkeJ0oIEEjvK10CRSwLnG6NNH-IpLIkFVm2EI&s=Y71yepdDOtsz8M2YaX9R5rYBulowH6rH5GjDu1WaOpY&e= [wikiselev.github.io] <https://urldefense.proofpoint.com/v2/url?u=https-3A__wikiselev.github.io&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=9KyXPtoyUP8edjdvA3wxPg&m=K5ZPsdQyE0rEJ3G0OQbGKwCp5td6zRJhHXhWF3KrFqM&s=lSU7imFibmiTDZzgVcBfUdpemtmzO3AgpFFYzlxuHd4&e=>
*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://urldefense.proofpoint.com/v2/url?u=https-3A__www.biorxiv.org_content_10.1101_2020.12.18.423363v1&d=DwIFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=YCVDjNHxAgv8-gpjr0Xb48Y9Vk9U8oXzH6wskU6pf14&m=eKB-yiCkeJ0oIEEjvK10CRSwLnG6NNH-IpLIkFVm2EI&s=dA1TFKLLvaIK608HotDWBjcYYmHRKfUcQqYs2tYHBzY&e= [biorxiv.org] <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.biorxiv.org_content_10.1101_2020.12.18.423363v1&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=9KyXPtoyUP8edjdvA3wxPg&m=K5ZPsdQyE0rEJ3G0OQbGKwCp5td6zRJhHXhWF3KrFqM&s=foYlspKfroCmRjkVWv4XHJ05sHptoF2PuUUJJAzKVgM&e=>
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.
Sure thing! Perhaps sometime early Tuesday? I’m free all morning (PDT). Best, Aaron From: Maximilian Lombardo <mlombardo@chanzuckerberg.com> Date: Wednesday, May 26, 2021 at 3:24 PM To: Aaron James Wilk <awilk@stanford.edu> Cc: Jonah Cool <jcool@chanzuckerberg.com>, Vladimir Kiselev <vk6@sanger.ac.uk>, "cv19caingest@sanger.ac.uk" <cv19caingest@sanger.ac.uk>, Martin Prete <mp33@sanger.ac.uk>, Kirtana Veeraraghavan <kveeraraghavan@chanzuckerberg.com> Subject: Re: [Cv19caingest] Blish lab: New single-cell dataset for COVID-19 cell atlas [EXT] Hi Aaron! I'm a product applications scientist for the cellxgene team. Thanks for sharing a link to your data! Would it be prudent for you, I and my colleague Kirtana to get together sometime next week and chat about the current curation process for cellxgene? Beforehand we can take a look at your data and also provide information more specific to your dataset. Looking forward to your reply, Max On Wed, May 26, 2021 at 10:28 AM Vladimir Kiselev <vk6@sanger.ac.uk<mailto:vk6@sanger.ac.uk>> wrote: 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<http://www.sanger.ac.uk/science/groups/cellular-genetics-informatics> Team Leader Wellcome Sanger Institute Hinxton, Cambridge, CB10 1SA Phone: +44(0)1223496850 Message: Mattermost<https://mattermost.sanger.ac.uk/cellgeninf> or Slack<https://urldefense.proofpoint.com/v2/url?u=https-3A__cellgeni.slack.com_&d=DwIGaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=YCVDjNHxAgv8-gpjr0Xb48Y9Vk9U8oXzH6wskU6pf14&m=1vWDBran6jDBIBp1bgMCPq28SAhdYXDodsuCaw2I8zs&s=aAOALFQu_gjk5MDEy_cLh-NfQlHzyU57YA3qU02MfIw&e= > Web: https://urldefense.proofpoint.com/v2/url?u=https-3A__wikiselev.github.io&d=DwIGaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=YCVDjNHxAgv8-gpjr0Xb48Y9Vk9U8oXzH6wskU6pf14&m=1vWDBran6jDBIBp1bgMCPq28SAhdYXDodsuCaw2I8zs&s=AgIjTcCGpw-MxdIfu8GuftI16DiraqxmawA4ohFhG9o&e= From: Jonah Cool <jcool@chanzuckerberg.com<mailto:jcool@chanzuckerberg.com>> Date: Saturday, 22 May 2021 at 03:04 To: Aaron James Wilk <awilk@stanford.edu<mailto:awilk@stanford.edu>> Cc: Vladimir Kiselev <vk6@sanger.ac.uk<mailto:vk6@sanger.ac.uk>>, "cv19caingest@sanger.ac.uk<mailto:cv19caingest@sanger.ac.uk>" <cv19caingest@sanger.ac.uk<mailto:cv19caingest@sanger.ac.uk>>, Martin Prete <mp33@sanger.ac.uk<mailto:mp33@sanger.ac.uk>>, Maximilian Lombardo <mlombardo@chanzuckerberg.com<mailto:mlombardo@chanzuckerberg.com>>, Kirtana Veeraraghavan <kveeraraghavan@chanzuckerberg.com<mailto: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<mailto: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://urldefense.proofpoint.com/v2/url?u=https-3A__drive.google.com_file_d_1cG60rcbff-2Dh-5F3ZoAM2GkJTttIQR4RWb9_view-3Fusp-3Dsharing&d=DwIGaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=YCVDjNHxAgv8-gpjr0Xb48Y9Vk9U8oXzH6wskU6pf14&m=1vWDBran6jDBIBp1bgMCPq28SAhdYXDodsuCaw2I8zs&s=NkbxTNSe5qB3LWVRUV0s0EDfHu2H6NMKhcvEfYpTT6I&e= [drive.google.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__drive.google.com_file_d_1cG60rcbff-2Dh-5F3ZoAM2GkJTttIQR4RWb9_view-3Fusp-3Dsharing&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=9KyXPtoyUP8edjdvA3wxPg&m=K5ZPsdQyE0rEJ3G0OQbGKwCp5td6zRJhHXhWF3KrFqM&s=-fxLTy7hu5EHV8QxohQfoewblWTzSxF7SAYZXHSyuug&e=> 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<mailto:vk6@sanger.ac.uk>> Date: Thursday, January 7, 2021 at 1:57 AM To: Aaron James Wilk <awilk@stanford.edu<mailto:awilk@stanford.edu>>, "cv19caingest@sanger.ac.uk<mailto:cv19caingest@sanger.ac.uk>" <cv19caingest@sanger.ac.uk<mailto:cv19caingest@sanger.ac.uk>> Cc: Martin Prete <mp33@sanger.ac.uk<mailto: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<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 [cellgeni.slack.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__cellgeni.slack.com_&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=9KyXPtoyUP8edjdvA3wxPg&m=K5ZPsdQyE0rEJ3G0OQbGKwCp5td6zRJhHXhWF3KrFqM&s=WNX25Sk3kgZLGw4c8pv_tBzX8qr4UPjD2NpFGo2uiJk&e=> Web: https://urldefense.proofpoint.com/v2/url?u=https-3A__wikiselev.github.io&d=DwIGaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=YCVDjNHxAgv8-gpjr0Xb48Y9Vk9U8oXzH6wskU6pf14&m=1vWDBran6jDBIBp1bgMCPq28SAhdYXDodsuCaw2I8zs&s=AgIjTcCGpw-MxdIfu8GuftI16DiraqxmawA4ohFhG9o&e= [wikiselev.github.io]<https://urldefense.proofpoint.com/v2/url?u=https-3A__wikiselev.github.io&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=9KyXPtoyUP8edjdvA3wxPg&m=K5ZPsdQyE0rEJ3G0OQbGKwCp5td6zRJhHXhWF3KrFqM&s=lSU7imFibmiTDZzgVcBfUdpemtmzO3AgpFFYzlxuHd4&e=> From: Aaron James Wilk <awilk@stanford.edu<mailto:awilk@stanford.edu>> Date: Wednesday, 6 January 2021 at 17:17 To: "cv19caingest@sanger.ac.uk<mailto:cv19caingest@sanger.ac.uk>" <cv19caingest@sanger.ac.uk<mailto: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://urldefense.proofpoint.com/v2/url?u=https-3A__www.biorxiv.org_content_10.1101_2020.12.18.423363v1&d=DwIGaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=YCVDjNHxAgv8-gpjr0Xb48Y9Vk9U8oXzH6wskU6pf14&m=1vWDBran6jDBIBp1bgMCPq28SAhdYXDodsuCaw2I8zs&s=Nk2WAWVXWEHkCySooywXEBCPejHEME6hvij9SKix87c&e= [biorxiv.org]<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.biorxiv.org_content_10.1101_2020.12.18.423363v1&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=9KyXPtoyUP8edjdvA3wxPg&m=K5ZPsdQyE0rEJ3G0OQbGKwCp5td6zRJhHXhWF3KrFqM&s=foYlspKfroCmRjkVWv4XHJ05sHptoF2PuUUJJAzKVgM&e=> 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.
Cool! I just sent out an invite for Tuesday at 10AM PDT. Looking forward to the chat and have a great weekend! Max On Wed, May 26, 2021 at 7:39 PM Aaron James Wilk <awilk@stanford.edu> wrote:
Sure thing! Perhaps sometime early Tuesday? I’m free all morning (PDT).
Best,
Aaron
*From: *Maximilian Lombardo <mlombardo@chanzuckerberg.com> *Date: *Wednesday, May 26, 2021 at 3:24 PM *To: *Aaron James Wilk <awilk@stanford.edu> *Cc: *Jonah Cool <jcool@chanzuckerberg.com>, Vladimir Kiselev < vk6@sanger.ac.uk>, "cv19caingest@sanger.ac.uk" <cv19caingest@sanger.ac.uk>, Martin Prete <mp33@sanger.ac.uk>, Kirtana Veeraraghavan < kveeraraghavan@chanzuckerberg.com> *Subject: *Re: [Cv19caingest] Blish lab: New single-cell dataset for COVID-19 cell atlas [EXT]
Hi Aaron!
I'm a product applications scientist for the cellxgene team.
Thanks for sharing a link to your data! Would it be prudent for you, I and my colleague Kirtana to get together sometime next week and chat about the current curation process for cellxgene? Beforehand we can take a look at your data and also provide information more specific to your dataset.
Looking forward to your reply,
Max
On Wed, May 26, 2021 at 10:28 AM Vladimir Kiselev <vk6@sanger.ac.uk> wrote:
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 <http://www.sanger.ac.uk/science/groups/cellular-genetics-informatics> Team Leader
Wellcome Sanger Institute
Hinxton, Cambridge, CB10 1SA
Phone: +44(0)1223496850
Message: Mattermost <https://mattermost.sanger.ac.uk/cellgeninf> or Slack <https://urldefense.proofpoint.com/v2/url?u=https-3A__cellgeni.slack.com_&d=DwIFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=YCVDjNHxAgv8-gpjr0Xb48Y9Vk9U8oXzH6wskU6pf14&m=g3JZ3-sny-5HzMZ_iRHMXQD5vS0edhmnPBE7pLX_MZM&s=6sTXDwHeAVOf1_G6YN_Tmk8tr4z8owvHdXkywj7fWcA&e= >
*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://urldefense.proofpoint.com/v2/url?u=https-3A__drive.google.com_file_d_1cG60rcbff-2Dh-5F3ZoAM2GkJTttIQR4RWb9_view-3Fusp-3Dsharing&d=DwIFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=YCVDjNHxAgv8-gpjr0Xb48Y9Vk9U8oXzH6wskU6pf14&m=g3JZ3-sny-5HzMZ_iRHMXQD5vS0edhmnPBE7pLX_MZM&s=XSkwktlUkZ4R2Kz-nXq1QcLYdTe8D1vlEgAJ4CMpno0&e= [drive.google.com] <https://urldefense.proofpoint.com/v2/url?u=https-3A__drive.google.com_file_d_1cG60rcbff-2Dh-5F3ZoAM2GkJTttIQR4RWb9_view-3Fusp-3Dsharing&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=9KyXPtoyUP8edjdvA3wxPg&m=K5ZPsdQyE0rEJ3G0OQbGKwCp5td6zRJhHXhWF3KrFqM&s=-fxLTy7hu5EHV8QxohQfoewblWTzSxF7SAYZXHSyuug&e=> 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 <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 [cellgeni.slack.com] <https://urldefense.proofpoint.com/v2/url?u=https-3A__cellgeni.slack.com_&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=9KyXPtoyUP8edjdvA3wxPg&m=K5ZPsdQyE0rEJ3G0OQbGKwCp5td6zRJhHXhWF3KrFqM&s=WNX25Sk3kgZLGw4c8pv_tBzX8qr4UPjD2NpFGo2uiJk&e=>
Web: https://urldefense.proofpoint.com/v2/url?u=https-3A__wikiselev.github.io&d=DwIFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=YCVDjNHxAgv8-gpjr0Xb48Y9Vk9U8oXzH6wskU6pf14&m=g3JZ3-sny-5HzMZ_iRHMXQD5vS0edhmnPBE7pLX_MZM&s=jwtlJG2JgH_p_VC_HyYGF7tBFhQDDaw9fZU8O1ynXkU&e= [wikiselev.github.io] <https://urldefense.proofpoint.com/v2/url?u=https-3A__wikiselev.github.io&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=9KyXPtoyUP8edjdvA3wxPg&m=K5ZPsdQyE0rEJ3G0OQbGKwCp5td6zRJhHXhWF3KrFqM&s=lSU7imFibmiTDZzgVcBfUdpemtmzO3AgpFFYzlxuHd4&e=>
*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://urldefense.proofpoint.com/v2/url?u=https-3A__www.biorxiv.org_content_10.1101_2020.12.18.423363v1&d=DwIFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=YCVDjNHxAgv8-gpjr0Xb48Y9Vk9U8oXzH6wskU6pf14&m=g3JZ3-sny-5HzMZ_iRHMXQD5vS0edhmnPBE7pLX_MZM&s=cs5EdPfUXJxTGrPtgFD8tFKEUomiIIFkwRijThOMSKQ&e= [biorxiv.org] <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.biorxiv.org_content_10.1101_2020.12.18.423363v1&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=9KyXPtoyUP8edjdvA3wxPg&m=K5ZPsdQyE0rEJ3G0OQbGKwCp5td6zRJhHXhWF3KrFqM&s=foYlspKfroCmRjkVWv4XHJ05sHptoF2PuUUJJAzKVgM&e=>
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.
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<http://www.sanger.ac.uk/science/groups/cellular-genetics-informatics> Team Leader Wellcome Sanger Institute Hinxton, Cambridge, CB10 1SA Phone: +44(0)1223496850 Message: Mattermost<https://mattermost.sanger.ac.uk/cellgeninf> or Slack<https://urldefense.proofpoint.com/v2/url?u=https-3A__cellgeni.slack.com_&d=DwIGaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=YCVDjNHxAgv8-gpjr0Xb48Y9Vk9U8oXzH6wskU6pf14&m=-1rJuyoh_qPljVgz1MB2EOceGvpkGExyh61cxCDRsWE&s=tGcpwQmeaWFbT2bi_DdUBFNQ8uPdWm78bd-GOP1rcMU&e= > Web: https://urldefense.proofpoint.com/v2/url?u=https-3A__wikiselev.github.io&d=DwIGaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=YCVDjNHxAgv8-gpjr0Xb48Y9Vk9U8oXzH6wskU6pf14&m=-1rJuyoh_qPljVgz1MB2EOceGvpkGExyh61cxCDRsWE&s=NSlHzt7IJmfwMWH8iYUxsb8uP-hygRJa66TQEOifR1w&e= 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<mailto: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://urldefense.proofpoint.com/v2/url?u=https-3A__drive.google.com_file_d_1cG60rcbff-2Dh-5F3ZoAM2GkJTttIQR4RWb9_view-3Fusp-3Dsharing&d=DwIGaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=YCVDjNHxAgv8-gpjr0Xb48Y9Vk9U8oXzH6wskU6pf14&m=-1rJuyoh_qPljVgz1MB2EOceGvpkGExyh61cxCDRsWE&s=oIpJ3QUB0EQmExbKi7mSoOmf5YFKgcCWdK8Ou56XhNk&e= [drive.google.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__drive.google.com_file_d_1cG60rcbff-2Dh-5F3ZoAM2GkJTttIQR4RWb9_view-3Fusp-3Dsharing&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=9KyXPtoyUP8edjdvA3wxPg&m=K5ZPsdQyE0rEJ3G0OQbGKwCp5td6zRJhHXhWF3KrFqM&s=-fxLTy7hu5EHV8QxohQfoewblWTzSxF7SAYZXHSyuug&e=> 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<mailto:vk6@sanger.ac.uk>> Date: Thursday, January 7, 2021 at 1:57 AM To: Aaron James Wilk <awilk@stanford.edu<mailto:awilk@stanford.edu>>, "cv19caingest@sanger.ac.uk<mailto:cv19caingest@sanger.ac.uk>" <cv19caingest@sanger.ac.uk<mailto:cv19caingest@sanger.ac.uk>> Cc: Martin Prete <mp33@sanger.ac.uk<mailto: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<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 [cellgeni.slack.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__cellgeni.slack.com_&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=9KyXPtoyUP8edjdvA3wxPg&m=K5ZPsdQyE0rEJ3G0OQbGKwCp5td6zRJhHXhWF3KrFqM&s=WNX25Sk3kgZLGw4c8pv_tBzX8qr4UPjD2NpFGo2uiJk&e=> Web: https://urldefense.proofpoint.com/v2/url?u=https-3A__wikiselev.github.io&d=DwIGaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=YCVDjNHxAgv8-gpjr0Xb48Y9Vk9U8oXzH6wskU6pf14&m=-1rJuyoh_qPljVgz1MB2EOceGvpkGExyh61cxCDRsWE&s=NSlHzt7IJmfwMWH8iYUxsb8uP-hygRJa66TQEOifR1w&e= [wikiselev.github.io]<https://urldefense.proofpoint.com/v2/url?u=https-3A__wikiselev.github.io&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=9KyXPtoyUP8edjdvA3wxPg&m=K5ZPsdQyE0rEJ3G0OQbGKwCp5td6zRJhHXhWF3KrFqM&s=lSU7imFibmiTDZzgVcBfUdpemtmzO3AgpFFYzlxuHd4&e=> From: Aaron James Wilk <awilk@stanford.edu<mailto:awilk@stanford.edu>> Date: Wednesday, 6 January 2021 at 17:17 To: "cv19caingest@sanger.ac.uk<mailto:cv19caingest@sanger.ac.uk>" <cv19caingest@sanger.ac.uk<mailto: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://urldefense.proofpoint.com/v2/url?u=https-3A__www.biorxiv.org_content_10.1101_2020.12.18.423363v1&d=DwIGaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=YCVDjNHxAgv8-gpjr0Xb48Y9Vk9U8oXzH6wskU6pf14&m=-1rJuyoh_qPljVgz1MB2EOceGvpkGExyh61cxCDRsWE&s=rfcElXxo8qb_HGViGc2CF6hn5Sf1ugdUX7S3JGgLGvU&e= [biorxiv.org]<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.biorxiv.org_content_10.1101_2020.12.18.423363v1&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=9KyXPtoyUP8edjdvA3wxPg&m=K5ZPsdQyE0rEJ3G0OQbGKwCp5td6zRJhHXhWF3KrFqM&s=foYlspKfroCmRjkVWv4XHJ05sHptoF2PuUUJJAzKVgM&e=> 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.
Hi Aaron, Vladimir is on annual leave this week. We can add Blish Lab’s new dataset without the cellxgene link and we’ll update that later. I’ll need a title, an object and a source link (pre-print or published article). That’s pretty much it. I think: * the object is https://drive.google.com/file/d/1cG60rcbff-h_3ZoAM2GkJTttIQR4RWb9/view?usp=s... [drive.google.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__drive.google.com_file_d_1cG60rcbff-2Dh-5F3ZoAM2GkJTttIQR4RWb9_view-3Fusp-3Dsharing&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=9KyXPtoyUP8edjdvA3wxPg&m=K5ZPsdQyE0rEJ3G0OQbGKwCp5td6zRJhHXhWF3KrFqM&s=-fxLTy7hu5EHV8QxohQfoewblWTzSxF7SAYZXHSyuug&e=> * source would be https://doi.org/10.1084/jem.20210582 Main thing missing is a title. We already have another object for Blish Lab (Peripheral Blood Mononuclear Cells) so I guess the link to the team will remain the same. Please, confirm that and I’ll upload the object (RDS) and add the entry for this new dataset. Kind regards, Martin.- From: Aaron James Wilk <awilk@stanford.edu> Date: Tuesday, 1 June 2021 at 18:34 To: Vladimir Kiselev <vk6@sanger.ac.uk>, Jonah Cool <jcool@chanzuckerberg.com> 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 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<http://www.sanger.ac.uk/science/groups/cellular-genetics-informatics> Team Leader Wellcome Sanger Institute Hinxton, Cambridge, CB10 1SA Phone: +44(0)1223496850 Message: Mattermost<https://mattermost.sanger.ac.uk/cellgeninf> or Slack [cellgeni.slack.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__cellgeni.slack.com_&d=DwMGaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=xVM0Oj0byXJqPMlhvbopPQeNDkgpFF7SJ9Qqo_aizig&m=lKsEU9Bd6rtqTfZCkUGZS3DXC1qAc6ZkHRqIuLdnYoY&s=quvLvlGreFDL8J9uzAcrDb6epi9urz9C-YHJx0_vb2Y&e=> Web: https://wikiselev.github.io [wikiselev.github.io]<https://urldefense.proofpoint.com/v2/url?u=https-3A__wikiselev.github.io&d=DwMGaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=xVM0Oj0byXJqPMlhvbopPQeNDkgpFF7SJ9Qqo_aizig&m=lKsEU9Bd6rtqTfZCkUGZS3DXC1qAc6ZkHRqIuLdnYoY&s=BwM-FT6a-8hxo3GQzUp2JgtdFeXRr35XI0VKurGCWWI&e=> 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<mailto: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=s... [drive.google.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__drive.google.com_file_d_1cG60rcbff-2Dh-5F3ZoAM2GkJTttIQR4RWb9_view-3Fusp-3Dsharing&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=9KyXPtoyUP8edjdvA3wxPg&m=K5ZPsdQyE0rEJ3G0OQbGKwCp5td6zRJhHXhWF3KrFqM&s=-fxLTy7hu5EHV8QxohQfoewblWTzSxF7SAYZXHSyuug&e=> 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<mailto:vk6@sanger.ac.uk>> Date: Thursday, January 7, 2021 at 1:57 AM To: Aaron James Wilk <awilk@stanford.edu<mailto:awilk@stanford.edu>>, "cv19caingest@sanger.ac.uk<mailto:cv19caingest@sanger.ac.uk>" <cv19caingest@sanger.ac.uk<mailto:cv19caingest@sanger.ac.uk>> Cc: Martin Prete <mp33@sanger.ac.uk<mailto: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<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 [cellgeni.slack.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__cellgeni.slack.com_&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=9KyXPtoyUP8edjdvA3wxPg&m=K5ZPsdQyE0rEJ3G0OQbGKwCp5td6zRJhHXhWF3KrFqM&s=WNX25Sk3kgZLGw4c8pv_tBzX8qr4UPjD2NpFGo2uiJk&e=> Web: https://wikiselev.github.io [wikiselev.github.io]<https://urldefense.proofpoint.com/v2/url?u=https-3A__wikiselev.github.io&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=9KyXPtoyUP8edjdvA3wxPg&m=K5ZPsdQyE0rEJ3G0OQbGKwCp5td6zRJhHXhWF3KrFqM&s=lSU7imFibmiTDZzgVcBfUdpemtmzO3AgpFFYzlxuHd4&e=> From: Aaron James Wilk <awilk@stanford.edu<mailto:awilk@stanford.edu>> Date: Wednesday, 6 January 2021 at 17:17 To: "cv19caingest@sanger.ac.uk<mailto:cv19caingest@sanger.ac.uk>" <cv19caingest@sanger.ac.uk<mailto: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]<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.biorxiv.org_content_10.1101_2020.12.18.423363v1&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=9KyXPtoyUP8edjdvA3wxPg&m=K5ZPsdQyE0rEJ3G0OQbGKwCp5td6zRJhHXhWF3KrFqM&s=foYlspKfroCmRjkVWv4XHJ05sHptoF2PuUUJJAzKVgM&e=> 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.
Hi Martin, Am I correct in understanding that if Aaron and Max generate the hosted cellxgene link then all that you need is that link along with the basic lab info? Basically, it would save the time of submitting the object and other details, right? Asking only to try and streamline work for Aaron and you as well! Best, Jonah On Wed, Jun 2, 2021 at 2:21 AM Martin Prete <mp33@sanger.ac.uk> wrote:
Hi Aaron,
Vladimir is on annual leave this week. We can add Blish Lab’s new dataset without the cellxgene link and we’ll update that later.
I’ll need a title, an object and a source link (pre-print or published article). That’s pretty much it. I think:
- the object is https://urldefense.proofpoint.com/v2/url?u=https-3A__drive.google.com_file_d_1cG60rcbff-2Dh-5F3ZoAM2GkJTttIQR4RWb9_view-3Fusp-3Dsharing&d=DwIFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=YCVDjNHxAgv8-gpjr0Xb48Y9Vk9U8oXzH6wskU6pf14&m=HCbLS-MOlRcexmQt0tb2xpS9vgwni40C0gwAXjkn3DM&s=yREM8xgAmUqWMAsu5-sUArXSRpGPMi9qGGmjvmv4M6c&e= [drive.google.com] <https://urldefense.proofpoint.com/v2/url?u=https-3A__drive.google.com_file_d_1cG60rcbff-2Dh-5F3ZoAM2GkJTttIQR4RWb9_view-3Fusp-3Dsharing&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=9KyXPtoyUP8edjdvA3wxPg&m=K5ZPsdQyE0rEJ3G0OQbGKwCp5td6zRJhHXhWF3KrFqM&s=-fxLTy7hu5EHV8QxohQfoewblWTzSxF7SAYZXHSyuug&e=> - source would be https://urldefense.proofpoint.com/v2/url?u=https-3A__doi.org_10.1084_jem.20210582&d=DwIFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=YCVDjNHxAgv8-gpjr0Xb48Y9Vk9U8oXzH6wskU6pf14&m=HCbLS-MOlRcexmQt0tb2xpS9vgwni40C0gwAXjkn3DM&s=8rXt33BrGmiyTm0o6oCBRSEZ7gViJmYsjVL1KIJE_VI&e=
Main thing missing is a title. We already have another object for Blish Lab (Peripheral Blood Mononuclear Cells) so I guess the link to the team will remain the same.
Please, confirm that and I’ll upload the object (RDS) and add the entry for this new dataset.
Kind regards,
Martin.-
*From: *Aaron James Wilk <awilk@stanford.edu> *Date: *Tuesday, 1 June 2021 at 18:34 *To: *Vladimir Kiselev <vk6@sanger.ac.uk>, Jonah Cool < jcool@chanzuckerberg.com> *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 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 <http://www.sanger.ac.uk/science/groups/cellular-genetics-informatics> Team Leader
Wellcome Sanger Institute
Hinxton, Cambridge, CB10 1SA
Phone: +44(0)1223496850
Message: Mattermost <https://mattermost.sanger.ac.uk/cellgeninf> or Slack [cellgeni.slack.com] <https://urldefense.proofpoint.com/v2/url?u=https-3A__cellgeni.slack.com_&d=DwMGaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=xVM0Oj0byXJqPMlhvbopPQeNDkgpFF7SJ9Qqo_aizig&m=lKsEU9Bd6rtqTfZCkUGZS3DXC1qAc6ZkHRqIuLdnYoY&s=quvLvlGreFDL8J9uzAcrDb6epi9urz9C-YHJx0_vb2Y&e=>
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*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://urldefense.proofpoint.com/v2/url?u=https-3A__drive.google.com_file_d_1cG60rcbff-2Dh-5F3ZoAM2GkJTttIQR4RWb9_view-3Fusp-3Dsharing&d=DwIFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=YCVDjNHxAgv8-gpjr0Xb48Y9Vk9U8oXzH6wskU6pf14&m=HCbLS-MOlRcexmQt0tb2xpS9vgwni40C0gwAXjkn3DM&s=yREM8xgAmUqWMAsu5-sUArXSRpGPMi9qGGmjvmv4M6c&e= [drive.google.com] <https://urldefense.proofpoint.com/v2/url?u=https-3A__drive.google.com_file_d_1cG60rcbff-2Dh-5F3ZoAM2GkJTttIQR4RWb9_view-3Fusp-3Dsharing&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=9KyXPtoyUP8edjdvA3wxPg&m=K5ZPsdQyE0rEJ3G0OQbGKwCp5td6zRJhHXhWF3KrFqM&s=-fxLTy7hu5EHV8QxohQfoewblWTzSxF7SAYZXHSyuug&e=> 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 <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 [cellgeni.slack.com] <https://urldefense.proofpoint.com/v2/url?u=https-3A__cellgeni.slack.com_&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=9KyXPtoyUP8edjdvA3wxPg&m=K5ZPsdQyE0rEJ3G0OQbGKwCp5td6zRJhHXhWF3KrFqM&s=WNX25Sk3kgZLGw4c8pv_tBzX8qr4UPjD2NpFGo2uiJk&e=>
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*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://urldefense.proofpoint.com/v2/url?u=https-3A__www.biorxiv.org_content_10.1101_2020.12.18.423363v1&d=DwIFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=YCVDjNHxAgv8-gpjr0Xb48Y9Vk9U8oXzH6wskU6pf14&m=HCbLS-MOlRcexmQt0tb2xpS9vgwni40C0gwAXjkn3DM&s=4bAjAeCoxOmypmDNrfgA15G5GXXybiAoYXOmpZVXmW0&e= [biorxiv.org] <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.biorxiv.org_content_10.1101_2020.12.18.423363v1&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=9KyXPtoyUP8edjdvA3wxPg&m=K5ZPsdQyE0rEJ3G0OQbGKwCp5td6zRJhHXhWF3KrFqM&s=foYlspKfroCmRjkVWv4XHJ05sHptoF2PuUUJJAzKVgM&e=>
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 <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.google.com_maps_search_215-2BEuston-2BRoad-2C-2BLondon-2C-2BNW1-2B2BE-3Fentry-3Dgmail-26source-3Dg&d=DwIFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=YCVDjNHxAgv8-gpjr0Xb48Y9Vk9U8oXzH6wskU6pf14&m=HCbLS-MOlRcexmQt0tb2xpS9vgwni40C0gwAXjkn3DM&s=KBT-e3Gd3eKvN7sKwr3dnq_JlK3459lBuaFLvIXxwbM&e= >.
-- 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 <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.google.com_maps_search_215-2BEuston-2BRoad-2C-2BLondon-2C-2BNW1-250D-250A-2B2BE-3Fentry-3Dgmail-26source-3Dg&d=DwIFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=YCVDjNHxAgv8-gpjr0Xb48Y9Vk9U8oXzH6wskU6pf14&m=HCbLS-MOlRcexmQt0tb2xpS9vgwni40C0gwAXjkn3DM&s=2gR-6yI7ZNNyS8J7OWqny53pt4781OUM6x7awWBmsIA&e= >.
-- 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 <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.google.com_maps_search_215-2BEuston-2BRoad-2C-2BLondon-2C-2BNW1-2B2BE-3Fentry-3Dgmail-26source-3Dg&d=DwIFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=YCVDjNHxAgv8-gpjr0Xb48Y9Vk9U8oXzH6wskU6pf14&m=HCbLS-MOlRcexmQt0tb2xpS9vgwni40C0gwAXjkn3DM&s=KBT-e3Gd3eKvN7sKwr3dnq_JlK3459lBuaFLvIXxwbM&e= >.
participants (5)
-
Aaron James Wilk -
Jonah Cool -
Martin Prete -
Maximilian Lombardo -
Vladimir Kiselev