Single-cell spatial transcriptomics of ACAN cKO in WT and 5xFAD mice

This dataset comprises results from one single-cell spatial experiment conducted on mouse brains. This experiment was performed using the Bruker Nanostring CosMx technology on 10 µm coronal brain sections from 8-month-old female WT, WT ACAN cKO, 5xFAD, and 5x ACAN cKO mice. The dataset is provided as two separate RDS files split by flowcell which include raw and corrected counts for the RNA data, along with comprehensive metadata. Metadata includes mouse genotype, sample ID, cell type annotations, and X-Y coordinates of each cell., Sample preparation: Isopentane fresh-frozen brain hemispheres were embedded in optimal cutting temperature (OCT) compound (Tissue-Tek, Sakura Fintek, Torrance, CA), and 10 µm thick coronal sections were prepared using a cryostat (CM1950, LeicaBiosystems, Deer Park, IL). Six hemibrains were mounted onto each VWR Superfrost Plus microscope slide (Avantor, 48311-703) and kept at -80°C until fixation. For transcriptomic analysis, n=3 mice per genotype were used for both the 5xFAD and 5xFAD ACAN cKO groups, while n=4 for WT and n=2 for WT ACAN cKO. Tissues were processed according to the Nanostring CosMx fresh-frozen slide preparation manual for RNA assay (NanoString University). Data processing: Spatial transcriptomics datasets were filtered using the AtoMx RNA Quality Control module to flag outlier negative probes (control probes targeting non-existent sequences to quantify non-specific hybridization), lowly-expressing cells, FOVs, and target genes. Datasets were then normal..., # Single-cell spatial transcriptomics of ACAN cKO in WT and 5xFAD mice Dataset DOI: [10.5061/dryad.z612jm6pw](10.5061/dryad.z612jm6pw) ## Description of the data and file structure Due to the large file size, the R object has been split by flowcell into two separate files (5xACANcKO_RNA_slide1.rds and 5xACANcKO_RNA_slide2.rds). The two files should be loaded into the R workspace and combined using the merge() function. For merging and downstream analysis, we recommend using a high performance computing system and at least 64GB of RAM for optimal performance. Data were analyzed using the R package Seurat. Sample metadata are stored in `[e-mail]`. ### Files and variables Single-cell spatial transcriptomics dataset Rownames of metadata (accessed using rownames(`[e-mail]`) contain unique identifiers for each single cell, formatted as `c_[slide][fov][cell]`. Additional metadata columns are described below: * fov: Field Of View (FOV) the cell is in * Area: Number of pi...,本数据集包含一项针对小鼠大脑的单细胞空间实验结果。该实验采用布鲁克（Bruker）纳米斯特林（Nanostring）CosMx技术，对8月龄雌性野生型（WT）、WT ACAN条件性敲除（ACAN cKO）、5xFAD以及5x ACAN cKO小鼠的10 μm冠状脑切片进行检测。数据集以两个独立的RDS文件形式提供，按流动槽（flowcell）拆分，包含RNA数据的原始计数与校正计数，以及完整的元数据。元数据涵盖小鼠基因型、样本ID、细胞类型注释以及每个细胞的X-Y坐标。 样本制备：将新鲜异戊烷冷冻的大脑半球嵌入最优切片温度（Optimal Cutting Temperature, OCT）包埋剂（Tissue-Tek，Sakura Fintek，美国加利福尼亚州托伦斯市），使用冷冻切片机（CM1950，徕卡生物系统（LeicaBiosystems），美国伊利诺伊州迪尔帕克市）制备10 μm厚的冠状脑切片。每个VWR Superfrost Plus显微镜载玻片（Avantor，48311-703）上挂载6个半脑样本，并置于-80℃保存直至固定。转录组学分析中，5xFAD组与5xFAD ACAN cKO组每组均使用n=3只小鼠，WT组n=4只，WT ACAN cKO组n=2只。样本处理遵循纳米斯特林CosMx新鲜冷冻切片RNA检测手册（纳米斯特林大学，NanoString University）进行。 数据处理：空间转录组数据集通过AtoMx RNA质量控制模块进行过滤，以标记异常阴性探针（靶向非存在序列的对照探针，用于量化非特异性杂交信号）、低表达细胞、视野（Field Of View, FOV）以及靶基因。随后对数据集进行标准化…… # 野生型与5xFAD小鼠ACAN条件性敲除的单细胞空间转录组学 数据集DOI：[10.5061/dryad.z612jm6pw](10.5061/dryad.z612jm6pw) ## 数据与文件结构说明 由于文件体积较大，该R对象已按流动槽拆分为两个独立文件（5xACANcKO_RNA_slide1.rds与5xACANcKO_RNA_slide2.rds）。需将两个文件加载至R工作区，并使用merge()函数进行合并。为实现合并与下游分析，我们推荐使用高性能计算系统，且至少配备64GB内存以获得最优性能。数据分析采用R包Seurat完成。样本元数据存储于`[e-mail]`中。 ### 文件与变量 单细胞空间转录组数据集 元数据的行名（通过rownames(`[e-mail]`)获取）包含每个单细胞的唯一标识符，格式为`c_[slide][fov][cell]`。下文将介绍其他元数据列： * fov：细胞所在的视野（Field Of View, FOV） * Area：像素数……