z score gene expression heatmap  (Revvity)

Journal: Biological Psychiatry Global Open Science

Article Title: Regional Molecular Changes in Chronic Lipopolysaccharide-Induced Neuroinflammation

doi: 10.1016/j.bpsgos.2025.100515

Figure Lengend Snippet: Circulating inflammatory cytokines and brain tissue expression of inflammatory and apoptotic markers. Serum concentrations of IL-1β (A) , TNF-α (B) , and IL-6 (C) in the ST- and LT-LPS and CON groups. (D–K) Heatmaps of real-time polymerase chain reaction results showing the effect of ST- and LT-LPS treatment on the mRNA expression of inflammatory markers in the Hyp, Pfc, Str, Hip, Mdb, Ctx, and Cbm. (G–I, K) Heatmaps of the sagittal plane of the rat brain showing upregulated or downregulated mRNA expression in the different brain regions as a result of LPS administration. LPS (1 mg/kg, i.p.; ST, n = 8; LT, n = 9) and saline (0.1 mL, i.p.; ST, n = 10; LT, n = 10) were administered once off (ST; n = 18) and once a week for 4 weeks (LT; n = 19). Data are presented as mean ± SD relative to the housekeeping gene Tbp . Data were analyzed using a 2-way analysis of variance followed by a Tukey’s post hoc test, and heatmaps are represented as expression values ( z scores) for differentially expressed genes. (A–C) p < .05 ( ∗ ), p < .01 ( ∗∗ ), p < .0001 ( ∗∗∗∗ ). (D–F, J) a ST-CON vs. ST-LPS; b ST-LPS vs. LT-LPS; c LT-CON vs. LT-LPS. p < .05 (a, b, c), p < .01 (aa, bb, cc), p < .001 (aaa, bbb, ccc), p < .0001 (aaaa, bbbb, cccc). Cbm, cerebellum; CON, control; Ctx, cortex; Hip, hippocampus; Hyp, hypothalamus; IFN-γ, interferon gamma; IL, interleukin; i.p., intraperitoneally; LPS, lipopolysaccharide; LT, long-term; Mdb, midbrain; mRNA, messenger RNA; Pfc, prefrontal cortex; ST, short-term; Str, striatum; TNF-α, tumor necrosis factor α.

Article Snippet: Heatmaps of gene expression z scores (see for additional information) for ST- and LT-CON and LPS-groups were generated in GraphPad Prism version 10 (GraphPad Software).

Techniques: Expressing, Real-time Polymerase Chain Reaction, Saline, Control

Journal: Biological Psychiatry Global Open Science

Article Title: Regional Molecular Changes in Chronic Lipopolysaccharide-Induced Neuroinflammation

doi: 10.1016/j.bpsgos.2025.100515

Figure Lengend Snippet: Brain tissue expression of apoptotic markers and H&E stained sections of rat sagittal hippocampus. (A) Heatmap of real-time polymerase chain reaction results showing the effect of ST- and LT-LPS treatment on the mRNA expression of apoptotic markers in the Hyp, Pfc, Str, Hip, Mdb, Ctx, and Cbm. (B) Heatmaps of the sagittal plane of the rat brain showing upregulated or downregulated mRNA expression in the different brain regions as a result of LPS. LPS (1 mg/kg, i.p.; ST, n = 8; LT, n = 9) and saline (0.1 mL, i.p.; ST, n = 10; LT, n = 10) were administered once off (ST; n = 18) and once a week for 4 weeks (LT; n = 19). Data are presented as mean ± SD relative to the housekeeping gene Tbp . Data were analyzed using a 2-way analysis of variance followed by a Tukey’s post hoc test, and heatmaps are represented as expression values ( z scores) for differentially expressed genes. (A) a ST-CON vs. ST-LPS; b ST-LPS vs. LT-LPS; c LT-CON vs. LT-LPS. p < .05 (a, b, c), p < .01 (aa, bb, cc), p < .001 (aaa, bbb, ccc), p < .0001 (aaaa, bbbb, cccc). (C, D) H&E staining of rat sagittal hippocampus (scale bars = 50 μm) after treatment with (C) saline (0.1 mL, i.p.) CON showing the normal structure, (D) LPS (1 mg/kg, i.p.) showing vacuolated cells (black arrows) and immune cell infiltration (blue arrows). Bax, Bcl-2-associated X protein; Bcl2, B-cell leukemia/lymphoma 2 protein; Cbm, cerebellum; CON, control; Ctx, cortex; H&E, hematoxylin and eosin; Hip, hippocampus; Hyp, hypothalamus; i.p., intraperitoneally; LPS, lipopolysaccharide; LT, long-term; Mdb, midbrain; mRNA, messenger RNA; Pfc, prefrontal cortex; ST, short-term; Str, striatum.

Article Snippet: Heatmaps of gene expression z scores (see for additional information) for ST- and LT-CON and LPS-groups were generated in GraphPad Prism version 10 (GraphPad Software).

Techniques: Expressing, Staining, Real-time Polymerase Chain Reaction, Saline, Control

Journal: Biological Psychiatry Global Open Science

Article Title: Regional Molecular Changes in Chronic Lipopolysaccharide-Induced Neuroinflammation

doi: 10.1016/j.bpsgos.2025.100515

Figure Lengend Snippet: Brain tissue mRNA expression of neurotrophic factors and associations of molecular and behavioral outcomes in LPS treatment. Heatmaps of real-time polymerase chain reaction results showing the effect of ST- and LT-LPS treatment on the mRNA expression of Creb (B, F) and neurotrophic markers (A, C, D, E, G, H) in the Hyp, Pfc, Str, Hip, Mdb, Ctx, and Cbm. (E–H) Heatmaps of the sagittal plane of the rat brain showing the upregulated or downregulated mRNA expression in the different brain regions as a result of LPS. LPS (1 mg/kg, i.p.; ST, n = 8; LT, n = 9) and saline (0.1 mL, i.p.; ST, n = 10; LT, n = 10) were administered once off (ST; n = 18) and once a week for 4 weeks (LT; n = 19). Data are presented as mean ± SD relative to the housekeeping gene Tbp . Data were analyzed using a 2-way analysis of variance followed by a Tukey’s post hoc test, and heatmaps are presented as expression values ( z scores) for differentially expressed genes. ( A – D ) a ST-CON vs. ST-LPS; b ST-LPS vs. LT-LPS; c LT-CON vs. LT-LPS. p < .05 (a, b, c), p < .01 (aa, bb, cc), p < .001 (aaa, bbb, ccc), p < .0001 (aaaa, bbbb, cccc). (I) Volcano plot of all behavioral and molecular data with filtering criteria of |log 2 FC| > 1.3 and p < .05, and (J) Pearson’s correlation coefficient matrix heatmap of all molecular and behavioral analysis; p < .05. B dnf , brain-derived neurotrophic factor; Cbm, cerebellum; CON, control; C reb , cyclic-AMP response-element binding protein; Ctx, cortex; FC, fold change; Hip, hippocampus; Hyp, hypothalamus; I fn -γ, interferon gamma; I l , interleukin; i.p., intraperitoneally; LPS, lipopolysaccharide; LT, long-term; Mdb, midbrain; mRNA, messenger RNA; N gf , nerve growth factor; Pfc, prefrontal cortex; ST, short-term; Str, striatum.

Article Snippet: Heatmaps of gene expression z scores (see for additional information) for ST- and LT-CON and LPS-groups were generated in GraphPad Prism version 10 (GraphPad Software).

Techniques: Expressing, Real-time Polymerase Chain Reaction, Saline, Derivative Assay, Control, Binding Assay