Fig. 5: CA1i Gene Expression Signature: Layer 2 and Layer 3.
From: Laminar organization of pyramidal neuron cell types defines distinct CA1 hippocampal subregions
a New HGEA Level 82 showing CA1 layer delineation. b Deconvolved confocal image of CA1 coronal section corresponding to HGEA Level 82. Dorsoventral and mediolateral orientation shown by crosshairs. White boxed area expanded in c. Scale bar, 400 µm. c Expanded images of white boxed areas (2, 3, and 4) in b showing the distribution of Lrmp, Ndst4, Trib2, and Peg10 transcripts within layers 2 and 3. White dashed lines delineate the boundary of the pyramidal cell layer. d Violin plot of log-normalized gene expression for Lrmp, Ndst4, Trib2, and Peg10 within the CA1i region at HGEA Level 82. e-h (Left) Individual labeling of each gene marker on CA1 DAPI nuclei (gray) from c and (right) full distribution spatial heatmap of log-normalized gene expression within individual cellular ROIs plotted to the dorsoventral (Y axis) and mediolateral (X axis) anatomical position within the CA1i region. In CA1i ROIs, layer 2 shifts to the superficial layer and the emerging layer 3 occupies the deep pyramidal layer. A total of 1879 CA1i pyramidal cells were analyzed in this image. Representative RNAscope data from one biologically independent mouse (HGEA Level 82); comparable laminar gene expression patterns were observed across five mice total. Source data are provided as a Source Data file.
