Single-cell spatial transcriptomic profiling of 3xTg-AD mouse brains following fecal microbiota transplantation from stroke and healthy human donors
Description
Single-cell spatial transcriptomics of 3xTg-AD mouse brain after fecal microbiota transplantation (FMT) from human stroke patients or healthy donors. Presymptomatic 3xTg-AD mice received antibiotic pretreatment and oral-gavage FMT at 3 months of age, with brains collected at 6.5 months. FFPE sagittal sections (5 µm) were profiled on the Bruker CosMx Spatial Molecular Imager using the 1,000-plex Mouse Neuroscience panel. 9 sections were collected (n=3 mice per group: naive, healthy-FMT, stroke-FMT). Per-sample flat files include the cell-by-target expression matrix, cell metadata, FOV positions, and segmentation polygons.
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Steps to reproduce
This data displays the raw output from the CosMx transcriptomics platform. We performed single-cell spatial transcriptomic profiling with CosMx™ SMI, following standardized protocols from NanoString University (Bruker Spatial Biology, Inc., Seattle, WA, USA; https://university.nanostring.com/page/document-library). Formalin-fixed, paraffin-embedded sagittal brain sections were mounted onto Superfrost Plus slides and baked overnight at 60 °C. Sections were deparaffinized using sequential xylene and ethanol washes, followed by antigen retrieval and protease digestion at 40 °C for 30 min. Transcript detection was performed using a 1000-plex RNA in situ hybridization panel with ribosomal RNA probes for cell segmentation. Probes were hybridized overnight at 37 °C, followed by stringent washes and application of nuclear and cell segmentation markers, including Histone and GFAP, in addition to rRNA-based segmentation. Flow cells were assembled and loaded onto the CosMx SMI according to the manufacturer’s instructions. Imaging and barcode readout were performed using standard acquisition settings. Cell-typing and segmentation was performed with the InSituType algorithm within AtomX.
Institutions
- University of MissouriMissouri, Columbia