The cerebral cortex is organized into functional areas and two hypotheses have arisen to elucidate their generation: the protomap and the protocortex. The protomap suggests that progenitors have intrinsic programs inducing the regionalization from early stages. The protocortex proposes that extrinsic factors such as afferences from thalamic neurons induce cortical regionalization. Although it has been shown that a clear protomap is present at early corticogenesis stages and that, on the contrary, postnatal thalamic afferences are required for proper somatosensory cortex development, what happens in between remains unclear. We wanted to study whether cortical regionalization is transcriptionally encoded at the end of corticogenesis. To do so, we coupled a novel multiplexing method to single-nuclei RNA sequencing in order to collect high-throughput spatial transcriptomics data of the murine cortex at E16. We employed ordinal regression and deep neural network models to predict and study the spatial distribution of nuclei, according to their gene expression profile. Our results show that at E16 cortical spatial organisation is still not discrete but rather follows a 4- cardinal point pattern, as during early stages. We also observe that differentiated neurons present specific spatial transcriptional programs, increasing their spatial resolution when compared to progenitors.