QC filtering for 10x Single Cell Gene Expression Flex Fixed RNA Profiling

Question

[yura.grabovska]

I'm analysing some Single Cell Gene Expression Flex Fixed RNA Profiling.

The probe set excludes mitochondrial genes:

table(PercentageFeatureSet(mp1.seurat, pattern = "^MT-", col.name = "pMitochondrial_RNA")$pMitochondrial_RNA)

    0 
10231

It also excludes ribosomal genes:

table(PercentageFeatureSet(mp1.seurat, pattern = "^RP[SL]", col.name = "pRibosomal_RNA")$pRibosomal_RNA)

    0 
10231

My basic QC approach would have been to filter cells with high mitochondrial gene expression and generally low number of features. But in this case I'm not able to pull in mitochondrial genes as a metric.

Has anyone worked with the Flex platform and has some good experience for what QC to run?

[bk11]

Could you check if the Seurat object has GeneID or Ensembl ID? For QC, you can follow the basic QC tutorial of Seurat.

[ATpoint]

Flex definitely includes mitochondrial genes (https://www.10xgenomics.com/support/software/cell-ranger/downloads#probe-set-downloads). Is this mouse or human? Maybe it's just a lowercase issue, like mt- and not MT-.

[yura.grabovska]

@ATpoint that was such a silly mistake on my part. I'm not used to working with mouse data and it shows.