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
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
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
Dear COVID-19 cell atlas,
This is Yuan He, a graduate student from Dr. Alexis Battle’s lab in Johns Hopkins University. Thank you for providing the great platform for researchers to study COVID-19!
We have a question regarding processing of the single cell datasets of *.h5ad files. It said that “Expression values can be in raw counts (which we will re-process) and/or normalised values (which we will serve directly).”. However it’s not clear how the processing was done for each dataset. It would be great if the information about whether the processing was done by your pipeline or by the authors can be included in the website. Also, it would be super helpful if your pipeline of processing could be available!
Thank you very much!