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Mechanism-specific prediction of TBI treatment by EG-gel. (A) Principal component analysis (PCA) of Sham, TBI, and EG-gel groups in transcriptomic space. (B) Volcano plots of differentially expressed genes for Sham vs TBI and TBI vs EG-gel comparisons. Red and blue points indicate significantly up and downregulated genes. (C) Venn diagrams of mRNA expression among the three groups. (D) Heat map of differentially expressed genes among the three groups. (E) KEGG pathway analysis for differentially expressed genes. (F) The top 20 of KEGG terms enrichment of RNA sequences. (G) Bar chart of the top 20 enriched GO terms of RNA <t>sequences.</t> <t>RNA-seq</t> was performed on peri-injury cortical tissue (n = 6 per group), differential expression was called using fold change ≥1.5, p-value <0.05, q-value <0.05, and group mean FPKM ≥0.5.
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nebnext ultra ii directional rna library prep kit  (New England Biolabs)
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Mechanism-specific prediction of TBI treatment by EG-gel. (A) Principal component analysis (PCA) of Sham, TBI, and EG-gel groups in transcriptomic space. (B) Volcano plots of differentially expressed genes for Sham vs TBI and TBI vs EG-gel comparisons. Red and blue points indicate significantly up and downregulated genes. (C) Venn diagrams of mRNA expression among the three groups. (D) Heat map of differentially expressed genes among the three groups. (E) KEGG pathway analysis for differentially expressed genes. (F) The top 20 of KEGG terms enrichment of RNA sequences. (G) Bar chart of the top 20 enriched GO terms of RNA <t>sequences.</t> <t>RNA-seq</t> was performed on peri-injury cortical tissue (n = 6 per group), differential expression was called using fold change ≥1.5, p-value <0.05, q-value <0.05, and group mean FPKM ≥0.5.
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Mechanism-specific prediction of TBI treatment by EG-gel. (A) Principal component analysis (PCA) of Sham, TBI, and EG-gel groups in transcriptomic space. (B) Volcano plots of differentially expressed genes for Sham vs TBI and TBI vs EG-gel comparisons. Red and blue points indicate significantly up and downregulated genes. (C) Venn diagrams of mRNA expression among the three groups. (D) Heat map of differentially expressed genes among the three groups. (E) KEGG pathway analysis for differentially expressed genes. (F) The top 20 of KEGG terms enrichment of RNA sequences. (G) Bar chart of the top 20 enriched GO terms of RNA <t>sequences.</t> <t>RNA-seq</t> was performed on peri-injury cortical tissue (n = 6 per group), differential expression was called using fold change ≥1.5, p-value <0.05, q-value <0.05, and group mean FPKM ≥0.5.
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nebnext ultra ii fs dna library  (New England Biolabs)
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Mechanism-specific prediction of TBI treatment by EG-gel. (A) Principal component analysis (PCA) of Sham, TBI, and EG-gel groups in transcriptomic space. (B) Volcano plots of differentially expressed genes for Sham vs TBI and TBI vs EG-gel comparisons. Red and blue points indicate significantly up and downregulated genes. (C) Venn diagrams of mRNA expression among the three groups. (D) Heat map of differentially expressed genes among the three groups. (E) KEGG pathway analysis for differentially expressed genes. (F) The top 20 of KEGG terms enrichment of RNA sequences. (G) Bar chart of the top 20 enriched GO terms of RNA <t>sequences.</t> <t>RNA-seq</t> was performed on peri-injury cortical tissue (n = 6 per group), differential expression was called using fold change ≥1.5, p-value <0.05, q-value <0.05, and group mean FPKM ≥0.5.
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truseq stranded total rna library prep gold kit  (Illumina Inc)
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Mechanism-specific prediction of TBI treatment by EG-gel. (A) Principal component analysis (PCA) of Sham, TBI, and EG-gel groups in transcriptomic space. (B) Volcano plots of differentially expressed genes for Sham vs TBI and TBI vs EG-gel comparisons. Red and blue points indicate significantly up and downregulated genes. (C) Venn diagrams of mRNA expression among the three groups. (D) Heat map of differentially expressed genes among the three groups. (E) KEGG pathway analysis for differentially expressed genes. (F) The top 20 of KEGG terms enrichment of RNA sequences. (G) Bar chart of the top 20 enriched GO terms of RNA <t>sequences.</t> <t>RNA-seq</t> was performed on peri-injury cortical tissue (n = 6 per group), differential expression was called using fold change ≥1.5, p-value <0.05, q-value <0.05, and group mean FPKM ≥0.5.
Truseq Stranded Total Rna Library Prep Gold Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 98/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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nebnext ultratm rna library prep kit  (New England Biolabs)
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Mechanism-specific prediction of TBI treatment by EG-gel. (A) Principal component analysis (PCA) of Sham, TBI, and EG-gel groups in transcriptomic space. (B) Volcano plots of differentially expressed genes for Sham vs TBI and TBI vs EG-gel comparisons. Red and blue points indicate significantly up and downregulated genes. (C) Venn diagrams of mRNA expression among the three groups. (D) Heat map of differentially expressed genes among the three groups. (E) KEGG pathway analysis for differentially expressed genes. (F) The top 20 of KEGG terms enrichment of RNA sequences. (G) Bar chart of the top 20 enriched GO terms of RNA <t>sequences.</t> <t>RNA-seq</t> was performed on peri-injury cortical tissue (n = 6 per group), differential expression was called using fold change ≥1.5, p-value <0.05, q-value <0.05, and group mean FPKM ≥0.5.
Nebnext Ultratm Rna Library Prep Kit, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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nebnext ultra rna library prep kit  (New England Biolabs)
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Mechanism-specific prediction of TBI treatment by EG-gel. (A) Principal component analysis (PCA) of Sham, TBI, and EG-gel groups in transcriptomic space. (B) Volcano plots of differentially expressed genes for Sham vs TBI and TBI vs EG-gel comparisons. Red and blue points indicate significantly up and downregulated genes. (C) Venn diagrams of mRNA expression among the three groups. (D) Heat map of differentially expressed genes among the three groups. (E) KEGG pathway analysis for differentially expressed genes. (F) The top 20 of KEGG terms enrichment of RNA sequences. (G) Bar chart of the top 20 enriched GO terms of RNA <t>sequences.</t> <t>RNA-seq</t> was performed on peri-injury cortical tissue (n = 6 per group), differential expression was called using fold change ≥1.5, p-value <0.05, q-value <0.05, and group mean FPKM ≥0.5.
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quick 16stm ngs library prep kit  (Zymo Research)
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Mechanism-specific prediction of TBI treatment by EG-gel. (A) Principal component analysis (PCA) of Sham, TBI, and EG-gel groups in transcriptomic space. (B) Volcano plots of differentially expressed genes for Sham vs TBI and TBI vs EG-gel comparisons. Red and blue points indicate significantly up and downregulated genes. (C) Venn diagrams of mRNA expression among the three groups. (D) Heat map of differentially expressed genes among the three groups. (E) KEGG pathway analysis for differentially expressed genes. (F) The top 20 of KEGG terms enrichment of RNA sequences. (G) Bar chart of the top 20 enriched GO terms of RNA <t>sequences.</t> <t>RNA-seq</t> was performed on peri-injury cortical tissue (n = 6 per group), differential expression was called using fold change ≥1.5, p-value <0.05, q-value <0.05, and group mean FPKM ≥0.5.
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quick 16s ngs library prep kit  (Zymo Research)
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Mechanism-specific prediction of TBI treatment by EG-gel. (A) Principal component analysis (PCA) of Sham, TBI, and EG-gel groups in transcriptomic space. (B) Volcano plots of differentially expressed genes for Sham vs TBI and TBI vs EG-gel comparisons. Red and blue points indicate significantly up and downregulated genes. (C) Venn diagrams of mRNA expression among the three groups. (D) Heat map of differentially expressed genes among the three groups. (E) KEGG pathway analysis for differentially expressed genes. (F) The top 20 of KEGG terms enrichment of RNA sequences. (G) Bar chart of the top 20 enriched GO terms of RNA <t>sequences.</t> <t>RNA-seq</t> was performed on peri-injury cortical tissue (n = 6 per group), differential expression was called using fold change ≥1.5, p-value <0.05, q-value <0.05, and group mean FPKM ≥0.5.
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a nebnext ultra ii dna library prep kit for illumina  (New England Biolabs)
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Mechanism-specific prediction of TBI treatment by EG-gel. (A) Principal component analysis (PCA) of Sham, TBI, and EG-gel groups in transcriptomic space. (B) Volcano plots of differentially expressed genes for Sham vs TBI and TBI vs EG-gel comparisons. Red and blue points indicate significantly up and downregulated genes. (C) Venn diagrams of mRNA expression among the three groups. (D) Heat map of differentially expressed genes among the three groups. (E) KEGG pathway analysis for differentially expressed genes. (F) The top 20 of KEGG terms enrichment of RNA sequences. (G) Bar chart of the top 20 enriched GO terms of RNA <t>sequences.</t> <t>RNA-seq</t> was performed on peri-injury cortical tissue (n = 6 per group), differential expression was called using fold change ≥1.5, p-value <0.05, q-value <0.05, and group mean FPKM ≥0.5.
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Mechanism-specific prediction of TBI treatment by EG-gel. (A) Principal component analysis (PCA) of Sham, TBI, and EG-gel groups in transcriptomic space. (B) Volcano plots of differentially expressed genes for Sham vs TBI and TBI vs EG-gel comparisons. Red and blue points indicate significantly up and downregulated genes. (C) Venn diagrams of mRNA expression among the three groups. (D) Heat map of differentially expressed genes among the three groups. (E) KEGG pathway analysis for differentially expressed genes. (F) The top 20 of KEGG terms enrichment of RNA sequences. (G) Bar chart of the top 20 enriched GO terms of RNA sequences. RNA-seq was performed on peri-injury cortical tissue (n = 6 per group), differential expression was called using fold change ≥1.5, p-value <0.05, q-value <0.05, and group mean FPKM ≥0.5.

Journal: Bioactive Materials

Article Title: Small extracellular vesicle-integrated by herbal hydrogels for spatiotemporal immunomodulation and neurovascular repair following traumatic brain injury

doi: 10.1016/j.bioactmat.2026.02.056

Figure Lengend Snippet: Mechanism-specific prediction of TBI treatment by EG-gel. (A) Principal component analysis (PCA) of Sham, TBI, and EG-gel groups in transcriptomic space. (B) Volcano plots of differentially expressed genes for Sham vs TBI and TBI vs EG-gel comparisons. Red and blue points indicate significantly up and downregulated genes. (C) Venn diagrams of mRNA expression among the three groups. (D) Heat map of differentially expressed genes among the three groups. (E) KEGG pathway analysis for differentially expressed genes. (F) The top 20 of KEGG terms enrichment of RNA sequences. (G) Bar chart of the top 20 enriched GO terms of RNA sequences. RNA-seq was performed on peri-injury cortical tissue (n = 6 per group), differential expression was called using fold change ≥1.5, p-value <0.05, q-value <0.05, and group mean FPKM ≥0.5.

Article Snippet: For library construction, 1–2 μg of total RNA per sample was used. mRNA was enriched using oligo (dT) selection, and libraries were prepared using the KAPA Stranded RNA-Seq Library Prep Kit (Roche).

Techniques: Expressing, RNA Sequencing, Quantitative Proteomics