hello,
i'm reaching out with a couple of questions about the dataset **Gene Expression (snRNAseq - DLPFC, Experiment 2) **(syn53366818).
1- In the Cell Type Objects folder, there isn’t a Seurat object for OPCs, though cell-annotation.full-atlas.csv does contain cell IDs for OPCs. Could you please clarify where I might find the gene expression data for OPCs?
2- There are two Seurat objects for excitatory neurons: cux2+.h5Seurat and cux2-.h5Seurat. Could you help me understand the distinction between these two files?
thank you,
nairuz
Created by Paul Pavlidis ppavlidis Dear @ppavlidis,
1. The OPCs subset of cells is part of the Oligodendroglia object (containing a single Seurat object with both the OPCs and the oligos).
2. Regarding the excitatory neurons, due to limitations with the maximum size of the count matrix under Seurat v4, I had to split the cells into 2 objects. I decided to split by the expression of the CUX2 gene yielding the CUX2+ and CUX2- subsets of excitatory neurons. While the cells are split their subtype annotations are continuous from Exc.1 to Exc.16 spanning both the subsets.
For more details about the analyses performed both for the oligodendroglia (and later oligos and OPCs separately) and the excitatory neurons please see the methods section of [our paper](https://www.nature.com/articles/s41586-024-07871-6) and the code in our [GitHub](https://github.com/naomihabiblab/BEYOND_DLPFC)