Fig. 4: CA1d Gene Expression Signature: Layer 1 and Layer 2.
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 image of white box area in b showing the distribution of Lrmp, Ndst4, Trib2, and Peg10 transcripts within layers 1 and 2. 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 CA1d 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 CA1d region. Note the increased expression of Lrmp in the superficial and Ndst4 in the deep pyramidal layer. Dashed lines delineate the pyramidal layer. A total of 1,501 CA1d 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.
