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...,