Dear Sir/Madam,
I’m Kang Jin, a PhD student in Biomedical Informatics Department in Cincinnati Children’s Hospital Medical Center. It’s so exciting to see the Covid19 Cell Atlas (https://www.covid19cellatlas.org/) online held by your institute and HCA. Dr. Bruce Aronow and I are exploring immune cells in human lung and their relations with SARS-COV-2 invasion and inflammation.
The upper airway dataset from Vieira Braga et al (https://urldefense.proofpoint.com/v2/url?u=https-3A__pubmed.ncbi.nlm.nih.go… ) is an awesome dataset which is also available on Covid19 Cell Atlas. I can find the single cell data for 10X and Drop-seq in the paper. However, the single data of CD4+ T cells in the Fig.5 (smartSeq) were not available from either GEO or HCA portal. I’m not sure if it’s available in EGAS00001001755<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ebi.ac.uk_ega_stud… >. Could I ask if I can access the data in EGA? If so, what do I need to do to apply for the data? Thanks so much for your help!
Best regards,
Kang
Kang Jin | PhD student
Biomedical Informatics Graduate Program
Cincinnati Children’s | University of Cincinnati
3333 Burnet Avenue, Cincinnati, OH 45229
Hi there,
I am trying to process this data in R, and having some issues reading the h5ad file.
Can you please point me in the right direction?
Thanks
Best,
Kyren Lazarus
Janes Lab
L4L - UCL
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 It is unfortunate that there are no oral samples available for this Atlas, and I am interested in contributing this unpublished data to the COVID19 Cell Atlas.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=…
