Whole-brain spatial organization of hippocampal single-neuron projectomes

Mapping hippocampal single-neuron projections is essential for understanding brain-wide circuit organization and diverse functions of the hippocampus, a brain structure underlying episodic memory and cognition. Here, we reconstructed 10,100 single-neuron projectomes of the mouse hippocampus, identified rostral and caudal axon pathways that preferentially innervated cortical vs. subcortical areas, and classified 43 projectome subtypes with distinct axon targeting patterns. Notably, the soma locations along hippocampal longitudinal and transverse axes determined the number of their target areas and the spatial distribution and complexity of their axon arbors within the targets. We defined selective hippocampal subdomains based on spatial transcriptomic profiles and found that many projectome subtypes were enriched in specific subdomains. Next, we defined the wiring diagram for hippocampal neurons exclusively projecting to hippocampal formation (HPF) and those projecting to both intra- and..., In brief, male mice (C57BL/6J, 11 weeks old) were perfused with artificial cerebrospinal fluid at -4℃. Brain tissue blocks were cut from left brain hemisphere, embedded in OCT (4583#, Sakura), frozen with dry ice and stored in -80℃ fridge. Brain sections (10-μm thick) for Stereo-seq were cut from brain tissue blocks in a pre-cooled cryochamber at -20℃ (Thermo Fisher Cryostar NX50) at various bregma coordinates (100-μm interval). The sections were carefully placed on a pre-cooled Stereo-seq chip (-20℃) and moved from one end to the other with a finger gently pressed under the chip. The temperature of the finger kept the section close to the chip, reducing bubbles and wrinkles. The RNA RIN value of total RNA extracted from adjacent brain sections were above 9, indicating qualified brain sections for spatial transcriptome experiments. Brain sections covering hippocampus (Bregma -0.9 – -4.4 mm) were laid on Stereo-seq chips for mRNA collection and followed by gene sequencing., , # Whole-brain spatial organization of hippocampal single-neuron projectomes

Code and data for mouse hippocampal single-neuron projectome and spatial transcriptome analysis and visualization.

## Description of the data and file structure

The neuronal data is represented as tree-structured swc files following specifications as: . All the swcs are registered to the Allen Template Brain CCF 2017 (Wang, Quanxin, et al. \"The Allen mouse brain common coordinate framework: a 3D reference atlas.\" Cell 181.4 (2020): 936-953) with brain regions following Allen naming conventions, e.g. HPF: Hippocampal formation; HIP: Hippocampal region; CA1: Field CA1; CA3: Field CA3; DG: Dentate gyrus; SUB: Subiculum.

We organize the repository following research article figure groups; at the same time, we provide description for our data and scripts below for easy and independent access to our resources. The projectome data are mainly presented in: 1. readable tabular and JSON files, with description liste...