Using deconvSeq to validate sorted cell sample content

rosedu1 / deconvSeq

deconvolution for RNAseq and bisulfite sequencing

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Using deconvSeq to validate sorted cell sample content #8

Open roni-fultheim opened 3 years ago

roni-fultheim commented 3 years ago

Hi,

I have bulk RNA-seq from islets cell populations (alpha, beta, delta cells etc.), and am interested in analyzing the content of each sample. For example, I would like to know for a sample labeled as sorted alpha cell, how much alpha cells does it truly contain, and if it is contaminated, then with which cell populations. How is that possible using deconvSeq, and do I need to obtain single-cell data?

Thank you

rosedu1 commented 3 years ago

You can obtain the projection matrix, b0, using single-cell data. Then apply that to your bulk rnaseq data.