Spatial transcriptomic profiling of optic tract gene expression alterations following traumatic brain injury in male cFosTRAP2 mice using the CHIMERA model

STUDY PURPOSE: Optic tract is a white matter region previously known to be susceptible to traumatic brain injury (TBI). We investigated whether TBI leads to differential gene expression in this region upon CHIMERA (Closed Head Impact Model of Engineered Rotational Acceleration) in male cFosTRAP2 mice (aged 3-4 months). A mild TBI was induced using CHIMERA where no skull fracture, structural damage or vascular haemorrhages was caused. DATA COLLECTED: We investigated transcriptomic changes in brain at 7 days after a mild CHIMERA injury (2.1J impact energy) using 10x genomics Visium spatial transcriptomics technology (n=2 Sham, n=2 TBI). Spatial gene expression data was acquired from 2 sections (bregma -1.80mm and -3.2 mm) from each mouse brain and analyzed using the Seurat R package. We obtained transcriptomic information with strong replicate reproducibility for 55-µm circular regions tiling entire brain sections (2 sections/mouse/condition; 4992 sequenced regions/section; ~40,000 RNA-seq datasets) and a subset of data representing CHIMERA TBI responsive regions is presented here. The dataset of greater than 1B reads yielded cell clusters with region-specific dysregulation of genes. Here we present data acquired using Seurat spatial transcriptomics workflow that tabulated fold changes and FDRs for genes that were differentially expressed in thalamic cluster. The fold changes presented in our dataset were derived from pooled Visium data, where spots from all animals within each experimental group were integrated using Seurat prior to clustering and differential expression analysis. Thus, the reported average log2 fold changes reflect group-level (pooled) expression patterns rather than per-animal averages. All raw and processed spatial transcriptomics data, including per-sample Visium outputs, are available through the NCBI Gene Expression Omnibus under accession number GSE282909. This repository includes count matrices, spatial coordinates, and sample-level metadata to enable independent reanalysis. DATA USAGE NOTES: