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_conten…
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,
Dear COVID-19 Cell Atlas maintainer,
I downloaded haniffa21.processed.h5ad from you website twice as follows
$ wget https://covid19.cog.sanger.ac.uk/submissions/release1/haniffa21.processed.h… )
And both times
$ md5sum haniffa21.processed.h5ad
while you provide md5 checksum
Since all other files of COVID-19 PBMC Ncl-Cambridge-UCL release 1.0 matched your md5 checksums perfectly, I suspect you provide wrong checksum for haniffa21.processed.h5ad
Daniil Sarkisyan, Bioinformatician
Department of Immunology, genetics and pathology, BMC B11:406b
mobile: +46 70 885 9883, email: daniil.sarkisyan(a)igp.uu.se
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No problem at all and I too am excited to see the data on the covid19atlas,
which is an awesome community resource. I'm cc'ing that team here to
hopefully help with the modifications that you've pointed out.
All good things,
On Tue, Apr 6, 2021 at 11:55 AM Tsang, John (NIH/NIAID) [E] <
> Hi Jonah,
> Thanks so much! It has been such a pleasure working with you and Pablo on
> this and we are very grateful for your support. Excited that our dataset is
> now on the human covid19 atlas site!
> I noticed a couple of minor items that would benefit from small textual
> changes if possible:
> 1) title of the dataset -> "Blood PBMCs from COVID-19 patients over time"
> would be a better title as most of our patients were not fatal.
> 2) lab name - there are quite a few labs in the Laboratory of Immune
> Systems Biology (as it's a department). Easiest to put "Tsang Lab" like the
> others would be most consistent.
> Thanks again!
> *From:* Jonah Cool <jcool(a)chanzuckerberg.com>
> *Sent:* Tuesday, April 6, 2021 2:40 PM
> *To:* Tsang, John (NIH/NIAID) [E] <john.tsang(a)nih.gov>; Lau, William
> (NIH/NIAID) [E] <lauwill(a)mail.nih.gov>
> *Subject:* your data on covid19cellatlas
> John & William,
> Hope all is well and you've been getting lots of positive feedback on the
> paper. I wanted to quickly confirm that your data is now available (think
> it has been for a few days, actually:)) on the covid19cellatlas site
> <https://www.covid19cellatlas.org/index.patient.html> under the "patient"
> Thanks again for working with us on this and looking forward to connecting
> again soon.
> All good things,