Gene expression of striosome and matrix compartments in the dorsal striatum of Nr4a1-eGFP mice

Striatal spiny projection neurons (SPNs) in the striosome (or patch) and matrix compartments possess distinct connectivity and functionally. To identify distinct genetic architecture of those two SPN subpopulations, we isolated GFP-positive striosomes and nearby GFP-negative matrix from 3-month-old Nr4a1-eGFP transgenic mice using laser-capture microdissection. The isolated striosomes and matrix tissues were then subjected to batch RNA sequencing. The resulting datasets would be useful to compare the gene expression patterns between striosome and matrix SPNs.