Question: How to assess extent of cell-type admixtures from bulk RNA-seq data for a single tissue?
gravatar for nancy
7 months ago by
nancy60 wrote:

We have bulk RNA-seq data from different samples (1 single tissue), treated vs control, (2 to 3 replicates each), and suspect that inherent cell-type heterogeneity is confounding our observations of D.E. We have no prior information on the levels of heterogeneity for these samples, however, looking at FPKM levels of few cell-type specific marker genes indicates a difference of cell composition proportions amongst the different samples.

(This is not a cancer versus normal study)

For the tissue of our interest, there are published single cell RNA-seq data from the various cell types that the authors have kindly made publicly available. This data is also in the form of fpkms.

I want to use the publicly available scRNA-seq data, and see if I can detect different compositions of cells in my bulk RNA-seq data.

Are there any tools that will help me do this? I have come upon CellMix, but our tissue of interest is not whole blood.

Thank you

ADD COMMENTlink modified 7 months ago by YaGalbi1.4k • written 7 months ago by nancy60
gravatar for YaGalbi
7 months ago by
Biocomputing, MRC Harwell Institute, Oxford, UK
YaGalbi1.4k wrote:

Take a look into CIBERSORT.

Similar post on bioconductor

ADD COMMENTlink modified 7 months ago • written 7 months ago by YaGalbi1.4k
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