Figure 3
Site-specific gene expression determined from microdissection of the mouse brain. The microdissection samples were collected from ethanol-fixed mouse brain slices. Then, the microdissection samples were lysed by Proteinase K, followed by poly(A) RNA purification by oligo(dT) magnetic beads. Gene expression levels were determined from purified RNA with Smart-seq2. (a) Schematic image of collection points in the mouse brain. Microdissection samples were collected along CTX, CC, and CN. (b) Image of the mouse brain after collection of microdissection samples and Hematoxylin and eosin (HE) staining. All 34 points (X1 to X34) are indicated with different colours according to CTX, CC, and CN-specific gene expression patterns. Cutoff normalized TPM, Thbs4, 0; Snap25, 121; and Mbp, 1297. White means no data from microdissection. (c) Bar charts of normalized expression levels of CTX, CC, and CN-specific genes in individual microdissection points from X1 to X34. (d) The number of protein-coding genes estimated from RNA-seq results. The detected genes of TN were calculated from previously reported data14. Stars indicate p-value <0.005 determined by Welch’s t-test. (e) Bar charts of normalized expression levels of the prefrontal cortex layer-specific genes in individual microdissection points from X1 to X34. In (c) and (e), images on the right are in situ hybridization images acquired from the Allen Mouse Brain Atlas (http://mouse.brain-map.org/).
