Analyze striatal 10x data by Seurat in R

How To Allen Brain Cell (ABC) Atlas
1

Hi thanks for the incredible resource!
I am a single cell beginner and was trying to find the 10x v3 data that’s disected from striatum and analyze in R by Seurat.
Could you help to locate the files?
Does the matrix files under this link :
ttps://data.nemoarchive.org/biccn/grant/u19_zeng/zeng/transcriptome/scell/10x_v3/mouse/process ed/analysis/10X_cells_v3_AIBS/
contain all the v3 data including other brain regions?
Could you suggest a good way to isolate striatum data and analyze in R？
Is it plausible to use the h5ad file that’s uploaded in AWS?

Thanks a lot!
Ling

2

Hi Ling,

Thanks for your question! The whole mouse brain atlas dataset does indeed include cells obtained from the striatum. I’d recommend following these tutorial notebooks for examples of how to subset the data to meet your specific needs. Hopefully this helps!

Thanks,
Ray