Hello!
I've downloaded .h5ad file of nasal scRNA-seq published in Vieira Braga et
al (2019) and I really need count-level data for my downstream analysis.
However, I cannot find information on total number of reads mapped to each
cell (which I can find as "n_counts" for majority of other datasets), so I
cannot restore count matrix. Is there any way to get this data too? Thank
you very much, it will really help me to finalize my research.
Best regards,
Stepan Nersisyan,
Researcher, Faculty of Biology and Biotechnology, Higher School of
Economics, Moscow, Russia
Hi,
I am a lead PI from a group at UNC with Human V3 10x scRNAseq from the oral cavity, specifically from the hard palate/gingiva from 4 healthy human volunteers (2M/2F). It is unfortunate that there are no oral samples available for this Atlas, and I am interested in contributing this unpublished data to the COVID19 Cell Atlas. This work was funded through the industry, so it would not necessarily need to publish if incorporated. Happy to have a zoom call or continue this conversation over email.
Best,
Kevin M. Byrd, DDS, PhD
The University of North Carolina at Chapel Hill
Office: 3606 Koury Oral Health Sciences; CB #7455
Research Instructor, Oral & Craniofacial Health Sciences
Resident, Graduate Training Program in Periodontology
Chapel Hill, NC 27599-7525
Cell Phone: 260-249-4724
Dear Colleagues
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
techniques.
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
Team noLymits
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
website: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.crct-2Dinserm.fr&d=…
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!
Best,
Yuan
