CPM Comparability Between Aged–Adult scRNA-seq and Imputed MERFISH Data

General
1

Hello,

I am interested in comparing gene expression between adult and aged mice in specific brain regions using the following two datasets:

  • 10x-scRNAseq-aged-adult

  • MERFISH-C57BL6J-638850 with Imputed Genes + Reconstructed Coordinates

Since the 10x scRNA-seq dataset does not contain spatial information, I am considering using the MERFISH dataset to identify region-specific marker genes. I would then use these markers to infer the anatomical origins of cells in the 10x scRNA-seq dataset and investigate age-related changes in gene expression within specific brain regions.

I have a few questions:

  1. Are the CPM values directly comparable between these two datasets, particularly for genes imputed in the MERFISH dataset?

  2. Are there differences in normalization or expression scaling that should be considered when comparing these datasets?

  3. If direct comparison of CPM values is not appropriate, would it be reasonable to use MERFISH for identifying region-specific markers and then perform adult-versus-aged comparisons entirely within the 10x scRNA-seq dataset?

I would greatly appreciate any guidance on this approach.

Thank you!