Clinical cohort for cancer sequenced using scRNA-Seq

Question

[Nitin Narwade]

Just curious about the availability of single-cell RNA-Seq data with clinical attributes. All the transcriptomic data I found for the patients which have clinical parameters is bulk RNA-Seq.

So is there any patient cohort (I might have missed in my search) for cancer that has phenotypic data, such as metastasis status, tumor grade, survival status, etc., and is sequenced at single cell level? If anyone knows about it could you please share the resource link?

Thank you in advance :)

Regards,
Nitin N.

[GenoMax]

A search brings up the following:

http://tisch.comp-genomics.org/

https://ngdc.cncb.ac.cn/cancerscem/

https://github.com/shooshtarilab/TMExplorer

Sequence data would likely be not be available in public space

[Nitin Narwade]

Thank you so much for sharing this information.

Actually, I already have the scRNA-Seq dataset for tumors in general, I am looking specifically for the scRAN-Seq data where they have clinical information associated with the samples.

I will try to explain why I am looking for this,

Generally, if I want to perform survival analysis or regression for metastasis score/tumor grade, I am using bulk RNA-Seq data from GEO, cBioPortal, etc. I categorize the patients into high and low groups based on my marker gene expression and then perform the analysis. Now the problem with this analysis is, as it is bulk RNA-Seq, we are sequencing the whole tumor and not the specific cell type. The marker I am working with has high expression in fibroblasts and I am working with cancer cells. and therefore I want to do the same analysis in only cancer cells and not in fibroblasts. And that is the reason why I am looking for the scRNA-Seq data which has survival status, metastasis score, tumor grade, etc.

I am sorry if I was not very clear before.

Thanks and Regards,

Nitin N.

Answer 1

[Radu Tanasa]

Here is an example: https://www.ebi.ac.uk/gxa/sc/experiments/E-MTAB-8559/results/tsne

I'm pretty sure you can find many others as well!