High-resolution single-nucleus RNA sequencing of the rhesus macaque primary visual cortex (V1) and visual area V4 from two adult animals.
Summary This study presents a single-nucleus RNA sequencing atlas of the rhesus macaque visual cortex, with a focus on primary visual cortex (V1) and visual area V4. Using snRNA-seq of NeuN+ nuclei from two adult rhesus macaques, we characterized neuronal cell types and identified strong differences in principal neuron composition between the two areas. Multiple transcriptomically distinct Layer 4 subtypes were found to be enriched in V1, showing specific gene expression patterns related to neuronal development and connectivity. Spatial validation by smFISH revealed transcriptional gradients across visual cortical areas that correspond to the dorsal and ventral visual processing streams. Processed data, including Seurat objects, UMAP coordinates, cell type annotations, and marker gene lists, are available on Zenodo (DOI: 10.5281/zenodo.19111601). Custom analysis code is available on Zenodo (DOI: 10.5281/zenodo.19134053).  Overall Design Single-nucleus RNA sequencing was performed on NeuN+ nuclei isolated from visual cortical areas V1 and V4 of two adult rhesus macaques (one male, one female). Libraries were prepared using the 10x Genomics Chromium platform. Data were integrated to identify neuronal subtypes, with a particular focus on Layer 4 principal neurons and area-specific differences. Key findings were validated using multiplexed single-molecule fluorescence in situ hybridization (smFISH) across multiple visual areas (V1, V2, V4, MT and TEO).
Summary This study presents a single-nucleus RNA sequencing atlas of the rhesus macaque visual cortex, with a focus on primary visual cortex (V1) and visual area V4. Using snRNA-seq of NeuN+ nuclei from two adult rhesus macaques, we characterized neuronal cell types and identified strong differences in principal neuron composition between the two areas. Multiple transcriptomically distinct Layer 4 subtypes were found to be enriched in V1, showing specific gene expression patterns related to neuronal development and connectivity. Spatial validation by smFISH revealed transcriptional gradients across visual cortical areas that correspond to the dorsal and ventral visual processing streams. Processed data, including Seurat objects, UMAP coordinates, cell type annotations, and marker gene lists, are available on Zenodo (DOI: 10.5281/zenodo.19111601). Custom analysis code is available on Zenodo (DOI: 10.5281/zenodo.19134053).  Overall Design Single-nucleus RNA sequencing was performed on NeuN+ nuclei isolated from visual cortical areas V1 and V4 of two adult rhesus macaques (one male, one female). Libraries were prepared using the 10x Genomics Chromium platform. Data were integrated to identify neuronal subtypes, with a particular focus on Layer 4 principal neurons and area-specific differences. Key findings were validated using multiplexed single-molecule fluorescence in situ hybridization (smFISH) across multiple visual areas (V1, V2, V4, MT and TEO).