Bridging Function, Connectivity, and Transcriptomics of Mouse Cortical Neurons

小鼠皮层神经元的桥接功能、连接性和转录组学 大脑的多功能和强大的功能特性反映在神经元的活动模式中， 计算，以及由于学习、稳态可塑性和其他过程而导致的它们随时间的演变。的 脑回路由大量的细胞类型组成，这可以通过以下特征来定义： 基因表达的模式，以及这些电路的复杂连接，预计将密切相关。 与其功能特性有关。 然而，这些关系的确切性质远不清楚。细胞类型本身的概念，特别是 当在细粒度的水平上考虑时，在任何给定的大脑区域中有一百种或更多的细胞类型， 在社区积极开展研究。一个中心问题是转录组学定义的细胞类型是否以及如何 为更广泛的电路特性提供特定的基础，例如解剖学中所表达的特性-定义为 神经元的位置，形态，连接-或在体内神经元活动的功能类型。 拟议的项目将通过调查分子和解剖学之间的联系来解决这个问题 细胞类型的电路和功能在小鼠初级视觉皮层（V1）。我们将连接的类型 通过多重荧光原位杂交检测转录组类型的体内功能性视觉反应 （mFISH）。将在V1的整个皮层深度进行神经活动的钙成像，共同配准 通过对该组织进行mFISH成像，将确定神经元的转录组类型， 每个神经元的功能与其类型之间的联系。 与此同时，我们将使用一个独特的功能连接组学数据集，该数据集已经在艾伦研究所获得， 其中电子显微镜（EM）图像与来自V1的体内成像数据共配准。这些数据将 允许我们将每个神经元的功能特性映射到其形态类型和连接性 特征，在EM体积中解决。形态学类型反过来又能让我们比较 使用我们早期的PatchSeq数据集，使用转录组类型的数据集，其中 获得单个神经元的形态学、内在电生理学和转录组学。 这些数据和分析将免费与科学界分享。我们将提供一个基于Web的 资源通过艾伦研究所细胞类型卡门户网站，跨转录组，形态， 这些数据集中的连通性和功能类型。 因此，本项目将揭示转录组类型，皮层回路结构及其与转录组之间的关系。 这是一项重要的研究，同时也为这一领域今后的广泛研究提供了重要资源。

Bridging Function, Connectivity, and Transcriptomics of Mouse Cortical Neurons The versatile and powerful functional properties of the brain are reflected in the neuronal activity patterns and computations, and their evolution over time due to learning, homeostatic plasticity, and other processes. The composition of brain circuits out of a large number of cell types, which may be defined by the characteristic patterns of gene expression, and the intricate connectivity of these circuits are expected to be intimately related to their functional properties. However, the exact nature of these relationships is far from clear. The concept of a cell type itself, especially when considered at a fine-grained level, with a hundred or more cell types in any given brain area, is under active research in the community. A central question is whether and how transcriptomically-defined cell types provide specific underpinnings for broader circuit properties, such as those expressed in anatomy – defined by neuron’s location, morphology, connectivity – or in the functional types of neuronal activity in vivo. The proposed project will address this question by investigating the links between molecular and anatomical cell types to circuits and function in the mouse primary visual cortex (V1). We will connect the types of functional visual responses in vivo with transcriptomic types via multiplexed fluorescence in-situ hybridization (mFISH). Calcium imaging of neural activity will be carried out across the full cortical depth in V1, co-registered with mFISH imaging of that tissue, and the transcriptomic types of the neurons will be determined, establishing links between each neuron’s function and its type. In parallel, we will use a unique functional connectomics dataset already obtained at the Allen Institute, in which Electron Microscopy (EM) images are co-registered with in vivo imaging data from V1. These data will permit us to map the functional properties of each neuron to its morphological type and connectivity characteristics, resolved in the EM volume. The morphological type will, in turn, allow us to compare this dataset with the transcriptomic types, using our earlier PatchSeq dataset, where triple-modality data of morphology, intrinsic electrophysiology, and transcriptomics was obtained for individual neurons. These data and analyses will be freely shared with the scientific community. We will provide a web-based resource through the Allen Institute Cell Type Cards portal, linking across transcriptomic, morphological, connectivity, and functional types in these datasets. Thus, this project will uncover the relations between transcriptomic types, cortical circuit structure, and its function, while providing a major resource for a broad spectrum of future studies in this area.