Subsetting Mouse Whole Cortex and Hippocampus 10x data by brain region?

We want to compare our snRNAseq data cell types to the Mouse Whole Cortex and Hippocampus 10x dataset. We want to do this for the corresponding brain region only.

Has anyone successfully subset the large 10X gene expression matrix by brain region? We generated a list of nuclei barcodes from the brain region of interest using the ‘Table of cell metadata file’, but extracting the rows from the large 10X ‘gene expression matrix’ file has proved challenging.

Any advice is appreciated!


Hi Katherine,

We recognize the challenges in unpacking the large 10x matrices. Sufficient memory should help, but the script outlined here may also be of help: Gene expression matrix.cvs is too large to load it - #17 by jeremyinseattle

If you still have issues, feel free to share more specifics here and we can work it through with you.

In general: how big of a file/matrix is too big for you? (Conversely, what size is preferable?)