Cell cycle genes for D. melanogaster and C. elegans (for scRNA-seq analysis)
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7 weeks ago
predeus ★ 1.7k

Hello all,

It's pretty common to do cell cycle correction when analyzing scRNA-seq data, especially for some tasks (e.g. trajectory inference).

In Seurat, there's a built-in list of gene names (cc.genes or cc.genes.updated.2019) that define S and G2/M phases in human. In mouse I guess it's relatively easy to get similar list using standard orthology databases or just lowercasing it if you're feeling lazy.

However, I can't find the similar lists for other model animals. I'm sure they are quite different so simple blasting would not be ideal.

Any suggestions would be welcome.

cycle-correction single-cell regression scRNA-seq bias • 417 views
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Just as a side note -- the scran package also comes with a list of both human and mouse reference genes:

library(scran)
mm.pairs <- readRDS(system.file("exdata", "mouse_cycle_markers.rds", 
    package="scran"))
hs.pairs <- readRDS(system.file("exdata", "human_cycle_markers.rds", 
    package="scran"))

# Using Ensembl IDs to match up with the annotation in 'mm.pairs'.
assignments <- cyclone(sce.416b, mm.pairs, gene.names=rowData(sce.416b)$ENSEMBL)

The OSCA reference has more ideas on how to treat the cell cycle issue in general.

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Thank you!

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