Tools for bulk RNA-seq celltype deconvolution
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9 weeks ago
Papyrus ★ 1.3k

Hi all,

I've got some bulk RNA-seq data (mouse brain/hippocampus) and I'm looking for tools to extract celltype composition proportions from the data. I've been looking around and most of the tools focus on using associated single-cell data, which I do not have.

Do you know of any tool which provides celltype predictions (mouse brain) by only inputting bulk RNA-seq (e.g. using internal cell reference datasets)?

If not, is the best strategy to get some public single-cell data to use with my bulk RNA-seq (from what I've read, via MuSiC or CIBERSORTx for example)? In that case, could you recommend (if there exist) databases providing single-cell data with annotated celltypes (instead of raw, unannotated data) which I could use?

If not, what would be the best strategy to achieve this goal?

thanks for your help

composition deconvolution bulk RNA-seq celltypes • 498 views
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9 weeks ago

Do you know of any tool which provides celltype predictions (mouse brain) by only inputting bulk RNA-seq (e.g. using internal cell reference datasets)?

As soon as you search for tools published before 2019, the majority of deconvolution methods will probably be based on bulk RNA-seq alone. See, for example, this review from 2018.

If not, is the best strategy to get some public single-cell data to use with my bulk RNA-seq (from what I've read, via MuSiC or CIBERSORTx for example)?

Dorshizi et al, 2021 demonstrate the use of reference scRNA-seq data sets for brain-specific questions.

In that case, could you recommend (if there exist) databases providing single-cell data with annotated celltypes (instead of raw, unannotated data) which I could use?

  • The Allen Brain Atlas is an incredible resource for transcriptomic (scRNA-seq) data from Mouse and Human data sets. I usually find a tad bit easier to first identify the paper with the corresponding data that I might be interested in and then track down the data on the Allen Brain Atlas servers, but I'm sure you can pick your way through.
  • The scRNAseq package from bioconductor has a range of scRNA-seq data sets ready to load including cell labels
  • the [SingleCell Portal[(https://singlecell.broadinstitute.org/single_cell) may be of help, too.

Apart from that, identifying publications with data sets of interest, e.g. via Pubmed or via GEO, should lead you to promising scRNAseq data set candidates; most of them should be provided with metadata (e.g. cell labels).

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Thanks a lot for the comprehensive answer! I guess I was looking at too-recent methods and missed most of the previous bulk RNA-seq methods. I'll check all the resources you mention!

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Here's another good resource for scRNA-seq atlas data. There is brain data in there along with annotated cell types. https://descartes.brotmanbaty.org/

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Thank you for the info, I'll be sure to check it out!

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