spatial gene expression heatmaps  (Spatial Transcriptomics Inc)

Journal: Acta Neuropathologica

Article Title: Perivascular glial reactivity is a feature of phosphorylated tau lesions in chronic traumatic encephalopathy

doi: 10.1007/s00401-025-02854-x

Figure Lengend Snippet: RNA and protein distribution for reactive gliosis markers in CTE lesion sulcus. a Spatial gene expression heatmaps generated from the Visium spatial transcriptomics data illustrates the mRNA distribution for NQO1, CHI3L1, GFAP, AQP4 and FTL (L-ferritin) within a lesion sulcus for CTE case AU6 from the Australia Sports Brain Bank. b Immunohistochemistry was performed for the corresponding protein in (a) on a different lesion sulcus from the same case. The p-tau (AT8) labelling for the same tissue sections is shown at the bottom (c–d) . Scale bar: 200 µm. In all three cases, focal increases in NQO1, CHI3L1, GFAP, AQP4 and FTL (L-ferritin) mRNA and protein expression are seen in cortical layer 1, the white matter and within the lesion area (yellow arrow) where AT8 tau is highly concentrated. The sulcal border is marked with an asterisk

Article Snippet: Fig. 3 RNA and protein distribution for reactive gliosis markers in CTE lesion sulcus. a Spatial gene expression heatmaps generated from the Visium spatial transcriptomics data illustrates the mRNA distribution for NQO1, CHI3L1, GFAP, AQP4 and FTL (L-ferritin) within a lesion sulcus for CTE case AU6 from the Australia Sports Brain Bank. b Immunohistochemistry was performed for the corresponding protein in (a) on a different lesion sulcus from the same case.

Techniques: Gene Expression, Generated, Immunohistochemistry, Expressing

Journal: Nature Neuroscience

Article Title: Early alterations in the MCH system link aberrant neuronal activity and sleep disturbances in a mouse model of Alzheimer’s disease

doi: 10.1038/s41593-023-01325-4

Figure Lengend Snippet: a , Heatmap showing scaled expression of DE genes (in Spatial Transcriptomics) that appear in at least one of four homeostatic plasticity datasets – . Columns represent tissue domains (TD) taken from the SP layer of CA1 region, from multiple tissue slides of 2 App NL-G-F mice and 2 Wt mice at 3.5 months (mouse genotypes are shown as colored bars across the top). Mouse information metadata is available in Supplementary Table . b , Sunburst visualization of Synaptic Gene Ontology (SynGO) enriched ontology terms on the top 200 DE genes (based on p-value), using a one-sided Fisher’s Exact Test, colored by -log10 FDR (False Discovery Rate). c,d,e,f , Spatial Transcriptomics performed on coronal mouse sections of Wt and App NL-G-F brains at 3.5 and 18 months. Tissue domains (TD) from CA1 pyramidal layer and LHA were selected and Pmch and Mchr1 mRNA levels analyzed. Number of TDs in CA1 pyramidal layer: 3.5 months - Wt n = 33, App NL-G-F n = 42 ( Pmch p = 0.0001, Mchr1 p = 0.0318); 18 months - Wt n = 25, App NL-G-F n = 25; Number of TDs in LHA: 3.5 months - Wt n = 418, App NL-G-F n = 383 ( Pmch p = 0.0001); 18 months - Wt n = 280, App NL-G-F n = 365; EdgeR’s quasi-likelihood F-test (*p < 0.05, ****p < 0.0001). Boxplots show medians, interquartile ranges and minimum/maximum values (up to 1.5 x interquartile range) of log2 normalised expression per TD.

Article Snippet: Extended Data Fig. 3 Transcriptional alterations in the App NL-G-F mice. a , Heatmap showing scaled expression of DE genes (in Spatial Transcriptomics) that appear in at least one of four homeostatic plasticity datasets – .

Techniques: Expressing