Hi all!
I am interested in understanding the % of main cell types composing my bulk RNA-seq data from brain (e.g., astrocytes, microglia, neurons, oligodendrocytes). However, from what I gathered, this appears to be an extremely complicated task. I came across CiberSortX, but I couldn't find a good tutorial for it. There are no accessible instructions about what the input files should look like, how to treat the RNA-seq data, etc. And even the idea of selecting and processing the appropriate dataset (single-cell RNA-seq, or RNA-seq performed on sorted cells) seems a bit daunting.
Has any of you conducted this type of analysis for bulk RNA-seq tissue from brain? Do you know any tutorial or tool that could help me achieve this more easily, or it's not gonna be that easy either way?
Thank you!
2 answers
There are several detailed tutorials available for CiberSortX, but you have to register for the software in order to access them.
For additional info on prepping your bulk RNA-seq data you can also review the Methods section of the CibserSortX paper https://doi.org/10.1038/s41587-019-0114-2.
The PsychEncode consortium performed cell type deconvolution using non-negative least squares (https://www.science.org/doi/10.1126/science.aat8464) and they provide the cell-by-gene expression targets as a resource (http://resource.psychencode.org/). DeconRNAseq implements this for you; though it underperforms its weighted version (MuSiC) which performs competitively with CiberSort (source: https://www.nature.com/articles/s41467-022-28655-4). Check the supplementary material of this paper for their approach to running these alternative (open-source) deconvolution methods.
Log in to answer this question.
-
Using bulk RNA-seq DE results to perform PCA in single cell RNA-seq
written by Oli •
-
How to normalize qPCR results for covariates like cell type markers
written by Sara •
-
Deconvolution cibersortx
written by Nerea •
-
How to calculate cell type frequency between two groups in single cell data
written by Sara •
-
Neuronal markers are expressed in all cell types in 10X single-cell RNASeq
written by viktorfeketa •
-
Cell type deconvolution from Bulk RNA-seq data
written by Anand •
-
Is it wrong to deconvolute bulk RNA seq data of a tissue using scRNAseq data of a different tissue?
written by tushard1987 •
-
Tools for bulk RNA-seq celltype deconvolution
written by Papyrus
-
Using bulk RNA-seq deconvolution as covariates in bulk RNA-seq differential expression analysis
written by telroyjatter
-
Publicly available RNA-seq data of neurons from human
written by flsnike •
Maybe you can try this : https://voineagulab.shinyapps.io/BrainDeconvShiny/
Article at https://www.nature.com/articles/s41467-022-28655-4