Journal: bioRxiv
Article Title: OmicGlaze: Spatial Multi-Omic Mapping of Traumatic Brain Injury
doi: 10.64898/2026.03.30.715462
Figure Lengend Snippet: A A focal blunt injury was induced in the upper right hemisphere of the mouse brain. Serial coronal sections were obtained at the mid-hippocampal level, with adjacent sections allocated for histological analysis (hematoxylin and eosin staining and Nissl staining), spatial RNA sequencing (spatial RNA-seq), and spatial ATAC sequencing (spatial ATAC-seq). B Image of a Nissl-stained section adjacent to the TBI_03 sample used for sequencing, illustrating tissue morphology. The left side corresponds to the uninjured hemisphere, and the right side to the injured hemisphere. C Zoomed-in view of the isocortex on the uninjured side of panel B. Scale bar represents 250 µm. D Zoomed-in view of the isocortex on the injured side of panel B. Scale bar represents 250 µm. E Spatial distribution of the number of detected genes per spot in the Control_01 sample. Each dot represents a 55-micron spot on the Visium slide (11 x 11 mm 2 ). F - H Spatial distribution of the number of detected genes per spot in the TBI_01, TBI_02, and TBI_03 samples. I Spatial region annotation of the TBI_03 sample, highlighting 14 anatomical regions. Abbreviations: CNU, cerebral nuclei; CTX_ISO, isocortex; CTX_OLF, olfactory cortex; CTX_RSP, retrosplenial area; CTX_SP, cortical subplate; HPF_CA_PYR, hippocampal formation cornu ammonis pyramidal layer; HPF_DG_GCL, hippocampal formation dentate gyrus granule cell layer; HPF_other, the polymorphic layer and molecular layer of hippocampus; HY, hypothalamus; LM, leptomeninges; TH, thalamus; VS, ventricular systems. J Unsupervised clustering of the integrated dataset comprising Control_01, TBI_01, TBI_02, and TBI_03 samples, colored by brain regions as defined in panel I. K Heatmap showing the expression levels of the top five marker genes for each of the 14 annotated regions in Control_01. Each row represents one gene and each column under the same color represents one region. Selected marker genes are labeled on the plot: Adora2a (marker for CNU region), Apod (fiber tracts), Satb2 (CTX_ISO region), Dlk1 (HY region), Synop2 (TH region), Hopx ( HPF_other region), Nrep (CTX_RSP region), Ttr (VS region), and Gpr151 (habenula region).
Article Snippet: We used Visium V2 CytAssist Spatial Gene Expression Reagent Kits (10X Genomics, #1000523) to profile mRNAs from tissue slices.
Techniques: Staining, RNA Sequencing, Sequencing, Control, Olfactory, Expressing, Marker, Labeling
