Figure 4 : LCM-seq is applicable to partly degraded human post-mortem tissues and reveals differential gene expression of spinal MNs and mDA neurons.

From: Laser capture microscopy coupled with Smart-seq2 for precise spatial transcriptomic profiling

Figure 4

(a) Mean number of genes detected in MNs (n=6) and mDA neurons (SNc: n=4; VTA: n=3, mean±s.e.m.). (b) Clustering of MNs (n=6) and mDA neurons (n=7) based on the top 500 variable genes in expression. (c) Top 20 differentially expressed genes between spinal MNs and mDA neurons (adjusted P<0.05, Wald test, DESeq2, sorted by fold change and adjusted P, mean±s.e.m.). (d) A larger number of genes was detected in mDA neurons using Histogene staining than the quick TH antibody staining (P=0.03, Student’s t-test at 0.1 RPKM cutoff, mean±s.e.m.). (e) Comparable mDA neuron marker expression levels were detected between the Histogene and quick TH staining groups. Boxes range from the 25th to the 75th percentile, with the centerline representing the 50th percentile. Outliers are shown as dots. (f) Clustering of SNc (n=4) and VTA (n=3) neurons, using Histogene staining, based on the top 500 variable genes in expression. (g) The top 20 differentially expressed genes between SNc and VTA neurons (adjusted P<0.05, Wald test, DESeq2, sorted by adjusted P, mean±s.e.m.).