Question: Single cell RNA vs ATAC seq
gravatar for golden
11 weeks ago by
golden0 wrote:

I have a question about single cell RNA seq and ATAC seq. I have some data for single cell RNA seq and the matched data for ATAC seq (not single cell). Are there any papers that combine single cell RNA seq and ATAC seq (not single cell) results? Since the ATAC seq data is high quality, I think it would be great if I could combine the results of these two techniques. Thank you for your help.

rna-seq • 233 views
ADD COMMENTlink modified 8 weeks ago by Biostar ♦♦ 20 • written 11 weeks ago by golden0

Depends on the question you want to answer. If the scRNA-seq data indicate that the population you assayed is heterogeneous then bulk ATAC-seq is probably not too informative since it is an average through the population. Can you give some more details?

ADD REPLYlink written 11 weeks ago by ATpoint34k

Thank you very much for your reply. The scRNA-seq data is FACS sorted, and we can identify all the cell types in the data. Even if the bulk ATAC-seq is average through the population, are there some papers that uses bulk ATAC-seq to further understand scRNA-seq data?

ADD REPLYlink written 10 weeks ago by golden0

It depends on the data. If you scRNA-seq indicates that you have a very heterogeneous population then maybe bulk ATAC-seq is not too informative. If the population(s) you are interested in are large then you still could derive interesting insights from the chromatin data. It really depends.

ADD REPLYlink written 8 weeks ago by ATpoint34k
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