Single-cell spatial transcriptomics of an inducible destabilized-domain Cre mouse line to target disease associated microglia

This dataset contains the results from a single-cell spatial transcriptomics experiment performed using Bruker Nanostring CosMx technology on 10µm thick fresh-frozen coronal brain sections from the following groups: 5xFAD hemizygous, Cst7 DD-Cre, Ai14tdTomato double heterozygous (AD, n = 3), and Cst7 DD-Cre/Ai14tdTomato double heterozygous (WT, n = 1) mice treated with TMP, and Cst7 DD-Cre/Ai14tdTomato double heterozygous mice treated with cuprizone (CPZ) and TMP (CPZ, n = 2). The dataset is provided as an .RDS file, which includes raw and corrected counts, along with comprehensive metadata. Metadata includes experimental group, sample ID, cell type annotations, and X-Y coordinates of each cell.
The function of microglia during progression of Alzheimer's disease (AD) can be investigated using mouse models that enable genetic manipulation of microglial subpopulations in a temporal manner. We developed mouse lines that express either Cre recombinase (Cre) for constitut..., , # Single-cell spatial transcriptomics of an inducible destabilized-domain Cre mouse line to target disease associated microglia

Dataset DOI: [10.5061/dryad.15dv41p9d](https://doi.org/10.5061/dryad.15dv41p9d)

## Description of the data and file structure

**Sample preparation:** Isopentane fresh-frozen brain hemispheres were embedded in OCT compound, and 10 μm thick coronal sections prepared on a cryostat. Six hemibrains were mounted directly onto a VWR Superfrost Plus microscope slide and stored at −80°C until fixation. 5xFAD hemizygous, *Cst7* ^DD-Cre^, Ai14^tdTomato^ double heterozygous (*n* = 3), and *Cst7* ^DD-Cre^/Ai14^tdTomato^ double heterozygous (*n* = 1) mice treated with TMP, and *Cst7* ^DD-Cre^/Ai14^tdTomato^ double heterozygous mice treated with cuprizone (CPZ) and TMP (*n* = 2) were used for spatial transcriptomics. Tissues were processed according to the Nanostring CosMx fresh-frozen slide preparation manual for RNA assays.

**Data processing:** Spatial transcriptomics d...,