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analysis ○ single cell transcriptomics  (Human Protein Atlas)

 
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    Human Protein Atlas analysis ○ single cell transcriptomics
    Analysis ○ Single Cell Transcriptomics, supplied by Human Protein Atlas, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/single+cell+transcriptomic+analysis/cell+database+proteomics+renal+single/pm41763199-281-111-116
    Average 86 stars, based on 1 article reviews
    analysis ○ single cell transcriptomics - by Bioz Stars, 2026-09
    86/100 stars

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    Related Articles

    Expressing:

    Article Title: Multi-ancestry genome-wide association study of serum creatine kinase implicates myopathy genes and muscle pathways
    Article Snippet: .. The y axis is capped at −log 10 (P) = 50; peaks exceeding this value are truncated and marked with arrows, with lead variants and mapped genes rs7305678 (CD163/APOBEC1), rs11559024 (CKM), rs12975366 (LILRB5) and rs7481951 (ANO5). (B & C) MAGMA tissue and cell-type enrichment analysis based on (B) GTEx expression data, (C) Human Protein Atlas single-cell expression profiles; the dashed line indicates the Bonferroni-corrected significance threshold, and significant tissues and cell types are shown in red. ..

    Article Title: Proteomic signatures of the APOE ε 4 and APOE ε 2 genetic variants and Alzheimer’s disease
    Article Snippet: Three single-cell RNA sequencing resources were used: the ROSMAP aged prefrontal cortex atlas , the BBB atlas , and the Human Protein Atlas . .. For the Human Protein Atlas 81-cell-type reference, enrichment was assessed using expression-weighted cell-type enrichment (EWCE ) R package (v1.18.0). ..

    Single Cell:

    Article Title: Multi-ancestry genome-wide association study of serum creatine kinase implicates myopathy genes and muscle pathways
    Article Snippet: .. The y axis is capped at −log 10 (P) = 50; peaks exceeding this value are truncated and marked with arrows, with lead variants and mapped genes rs7305678 (CD163/APOBEC1), rs11559024 (CKM), rs12975366 (LILRB5) and rs7481951 (ANO5). (B & C) MAGMA tissue and cell-type enrichment analysis based on (B) GTEx expression data, (C) Human Protein Atlas single-cell expression profiles; the dashed line indicates the Bonferroni-corrected significance threshold, and significant tissues and cell types are shown in red. ..

    Article Title: Renal tubular Nfe2l1 protect cisplatin-induced acute kidney injury via suppressing ACSL4-dependent ferroptosis.
    Article Snippet: .. This research utilized the KIT renal single- cell proteomics database (https://humphreyslab.com/SingleCell/) and the HUMAN PROTEIN ATLAS (https://www.proteinatlas.org/) to identify that Nfe2l1 is predominantly expressed in renal tubules (Fig. 1A–E), which was validated by murine immunofluorescence staining (Fig. 1F). ..

    Article Title: Analysing cell death patterns to predict outcomes and treatment options in patients with high-grade serous ovarian carcinoma.
    Article Snippet: .. Tumour immune single-cell hub (TISCH) and Human Protein Atlas (HPA) AR TIC LE IN PR ES S TISCH (http://tisch.comp Genomics.org) is a large online database that focuses on the TME for single-cell RNA sequencing. ..

    Article Title: Renal tubular Nfe2l1 protect cisplatin-induced acute kidney injury via suppressing ACSL4-dependent ferroptosis.
    Article Snippet: Protein levels were quantified using ImageJ software. .. The distribution of Nfe2l1 in the kidney was predicted using the KIT renal single-cell proteomics database (https://humphreyslab.com/SingleCell/) and the HUMAN PROTEIN ATLAS (https://www. proteinatlas.org/). ..

    Article Title: Integrative multi-omics and machine learning reveals the spatial niche distribution and role of CYP27A1 + TAMs in immunotherapy response in non-small cell lung cancer
    Article Snippet: .. In the Human Protein Atlas single-cell clustering, CYP27A1 is part of cluster 58 (Macrophages - Innate immune response) with a confidence score of 1 ( ). (Confidence is the fraction of times a gene was assigned to the cluster in repeated clustering, and therefore reflects how strongly associated it is to the cluster. ..

    Immunofluorescence:

    Article Title: Renal tubular Nfe2l1 protect cisplatin-induced acute kidney injury via suppressing ACSL4-dependent ferroptosis.
    Article Snippet: .. This research utilized the KIT renal single- cell proteomics database (https://humphreyslab.com/SingleCell/) and the HUMAN PROTEIN ATLAS (https://www.proteinatlas.org/) to identify that Nfe2l1 is predominantly expressed in renal tubules (Fig. 1A–E), which was validated by murine immunofluorescence staining (Fig. 1F). ..

    Staining:

    Article Title: Renal tubular Nfe2l1 protect cisplatin-induced acute kidney injury via suppressing ACSL4-dependent ferroptosis.
    Article Snippet: .. This research utilized the KIT renal single- cell proteomics database (https://humphreyslab.com/SingleCell/) and the HUMAN PROTEIN ATLAS (https://www.proteinatlas.org/) to identify that Nfe2l1 is predominantly expressed in renal tubules (Fig. 1A–E), which was validated by murine immunofluorescence staining (Fig. 1F). ..

    RNA Sequencing:

    Article Title: Analysing cell death patterns to predict outcomes and treatment options in patients with high-grade serous ovarian carcinoma.
    Article Snippet: .. Tumour immune single-cell hub (TISCH) and Human Protein Atlas (HPA) AR TIC LE IN PR ES S TISCH (http://tisch.comp Genomics.org) is a large online database that focuses on the TME for single-cell RNA sequencing. ..

    other:

    Article Title: Integrated machine learning and multi-omics analysis identifies ALOX5 as a potential therapeutic target for tubulointerstitial inflammation in diabetic kidney disease.
    Article Snippet: Notably, CD163 staining did not show significant positivity, indicating a low proportion148 of CD163+ macrophages in the tissue, which correlates with the limited numbers of CD163+ macrophages observed in the149 single-cell analysis.For clearer visualization of colocalization, only representative protein combinations are shown in the main150 text, and the complete multichannel composite image has been moved to Supplementary Fig. 4.151 Given the ethical limitations on obtaining normal renal biopsy tissues, we confirmed the low expression levels in normal152 controls using single-cell transcriptomics and validated these findings with references from the Human Protein Atlas (HPA).153 Due to differences in staining methods, this comparison is qualitative rather than quantitative.

    Mouse Assay:

    Article Title: Citrate clearance is a major function of aconitase 2 in the canonical TCA cycle.
    Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS ○ Mice ○ Cell lines • METHOD DETAILS ○ DepMap data analysis ○ Generation of genetically edited lines ○ Western blotting ○ Viability assay ○ MitoTracker and TMRE assays ○ L-HPG nascent protein synthesis assay ○ OP-puro assay ○ EdU incorporation flow cytometry assay ○ Flow-based competition assay ○ Proliferation analyses ○ Oxygen consumption and extracellular acidification rates ○ Isotope tracing and steady-state metabolite measurement ○ Citrate uptake assays ○ GC-MS analysis ○ Pathology ○ Immunohistochemistry ○ RNA isolation and qPCR ○ RNA-sequencing and analysis ○ Single cell transcriptomics (Human Protein Atlas) ○ Statistics and reproducibility SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j.cell. ..

    Western Blot:

    Article Title: Citrate clearance is a major function of aconitase 2 in the canonical TCA cycle.
    Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS ○ Mice ○ Cell lines • METHOD DETAILS ○ DepMap data analysis ○ Generation of genetically edited lines ○ Western blotting ○ Viability assay ○ MitoTracker and TMRE assays ○ L-HPG nascent protein synthesis assay ○ OP-puro assay ○ EdU incorporation flow cytometry assay ○ Flow-based competition assay ○ Proliferation analyses ○ Oxygen consumption and extracellular acidification rates ○ Isotope tracing and steady-state metabolite measurement ○ Citrate uptake assays ○ GC-MS analysis ○ Pathology ○ Immunohistochemistry ○ RNA isolation and qPCR ○ RNA-sequencing and analysis ○ Single cell transcriptomics (Human Protein Atlas) ○ Statistics and reproducibility SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j.cell. ..

    Viability Assay:

    Article Title: Citrate clearance is a major function of aconitase 2 in the canonical TCA cycle.
    Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS ○ Mice ○ Cell lines • METHOD DETAILS ○ DepMap data analysis ○ Generation of genetically edited lines ○ Western blotting ○ Viability assay ○ MitoTracker and TMRE assays ○ L-HPG nascent protein synthesis assay ○ OP-puro assay ○ EdU incorporation flow cytometry assay ○ Flow-based competition assay ○ Proliferation analyses ○ Oxygen consumption and extracellular acidification rates ○ Isotope tracing and steady-state metabolite measurement ○ Citrate uptake assays ○ GC-MS analysis ○ Pathology ○ Immunohistochemistry ○ RNA isolation and qPCR ○ RNA-sequencing and analysis ○ Single cell transcriptomics (Human Protein Atlas) ○ Statistics and reproducibility SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j.cell. ..

    Flow Cytometry:

    Article Title: Citrate clearance is a major function of aconitase 2 in the canonical TCA cycle.
    Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS ○ Mice ○ Cell lines • METHOD DETAILS ○ DepMap data analysis ○ Generation of genetically edited lines ○ Western blotting ○ Viability assay ○ MitoTracker and TMRE assays ○ L-HPG nascent protein synthesis assay ○ OP-puro assay ○ EdU incorporation flow cytometry assay ○ Flow-based competition assay ○ Proliferation analyses ○ Oxygen consumption and extracellular acidification rates ○ Isotope tracing and steady-state metabolite measurement ○ Citrate uptake assays ○ GC-MS analysis ○ Pathology ○ Immunohistochemistry ○ RNA isolation and qPCR ○ RNA-sequencing and analysis ○ Single cell transcriptomics (Human Protein Atlas) ○ Statistics and reproducibility SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j.cell. ..

    Competitive Binding Assay:

    Article Title: Citrate clearance is a major function of aconitase 2 in the canonical TCA cycle.
    Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS ○ Mice ○ Cell lines • METHOD DETAILS ○ DepMap data analysis ○ Generation of genetically edited lines ○ Western blotting ○ Viability assay ○ MitoTracker and TMRE assays ○ L-HPG nascent protein synthesis assay ○ OP-puro assay ○ EdU incorporation flow cytometry assay ○ Flow-based competition assay ○ Proliferation analyses ○ Oxygen consumption and extracellular acidification rates ○ Isotope tracing and steady-state metabolite measurement ○ Citrate uptake assays ○ GC-MS analysis ○ Pathology ○ Immunohistochemistry ○ RNA isolation and qPCR ○ RNA-sequencing and analysis ○ Single cell transcriptomics (Human Protein Atlas) ○ Statistics and reproducibility SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j.cell. ..

    Gas Chromatography-Mass Spectrometry:

    Article Title: Citrate clearance is a major function of aconitase 2 in the canonical TCA cycle.
    Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS ○ Mice ○ Cell lines • METHOD DETAILS ○ DepMap data analysis ○ Generation of genetically edited lines ○ Western blotting ○ Viability assay ○ MitoTracker and TMRE assays ○ L-HPG nascent protein synthesis assay ○ OP-puro assay ○ EdU incorporation flow cytometry assay ○ Flow-based competition assay ○ Proliferation analyses ○ Oxygen consumption and extracellular acidification rates ○ Isotope tracing and steady-state metabolite measurement ○ Citrate uptake assays ○ GC-MS analysis ○ Pathology ○ Immunohistochemistry ○ RNA isolation and qPCR ○ RNA-sequencing and analysis ○ Single cell transcriptomics (Human Protein Atlas) ○ Statistics and reproducibility SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j.cell. ..

    Immunohistochemistry:

    Article Title: Citrate clearance is a major function of aconitase 2 in the canonical TCA cycle.
    Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS ○ Mice ○ Cell lines • METHOD DETAILS ○ DepMap data analysis ○ Generation of genetically edited lines ○ Western blotting ○ Viability assay ○ MitoTracker and TMRE assays ○ L-HPG nascent protein synthesis assay ○ OP-puro assay ○ EdU incorporation flow cytometry assay ○ Flow-based competition assay ○ Proliferation analyses ○ Oxygen consumption and extracellular acidification rates ○ Isotope tracing and steady-state metabolite measurement ○ Citrate uptake assays ○ GC-MS analysis ○ Pathology ○ Immunohistochemistry ○ RNA isolation and qPCR ○ RNA-sequencing and analysis ○ Single cell transcriptomics (Human Protein Atlas) ○ Statistics and reproducibility SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j.cell. ..

    Isolation:

    Article Title: Citrate clearance is a major function of aconitase 2 in the canonical TCA cycle.
    Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS ○ Mice ○ Cell lines • METHOD DETAILS ○ DepMap data analysis ○ Generation of genetically edited lines ○ Western blotting ○ Viability assay ○ MitoTracker and TMRE assays ○ L-HPG nascent protein synthesis assay ○ OP-puro assay ○ EdU incorporation flow cytometry assay ○ Flow-based competition assay ○ Proliferation analyses ○ Oxygen consumption and extracellular acidification rates ○ Isotope tracing and steady-state metabolite measurement ○ Citrate uptake assays ○ GC-MS analysis ○ Pathology ○ Immunohistochemistry ○ RNA isolation and qPCR ○ RNA-sequencing and analysis ○ Single cell transcriptomics (Human Protein Atlas) ○ Statistics and reproducibility SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j.cell. ..

    Real-time Polymerase Chain Reaction:

    Article Title: Citrate clearance is a major function of aconitase 2 in the canonical TCA cycle.
    Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS ○ Mice ○ Cell lines • METHOD DETAILS ○ DepMap data analysis ○ Generation of genetically edited lines ○ Western blotting ○ Viability assay ○ MitoTracker and TMRE assays ○ L-HPG nascent protein synthesis assay ○ OP-puro assay ○ EdU incorporation flow cytometry assay ○ Flow-based competition assay ○ Proliferation analyses ○ Oxygen consumption and extracellular acidification rates ○ Isotope tracing and steady-state metabolite measurement ○ Citrate uptake assays ○ GC-MS analysis ○ Pathology ○ Immunohistochemistry ○ RNA isolation and qPCR ○ RNA-sequencing and analysis ○ Single cell transcriptomics (Human Protein Atlas) ○ Statistics and reproducibility SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j.cell. ..

    RNA sequencing:

    Article Title: Citrate clearance is a major function of aconitase 2 in the canonical TCA cycle.
    Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS ○ Mice ○ Cell lines • METHOD DETAILS ○ DepMap data analysis ○ Generation of genetically edited lines ○ Western blotting ○ Viability assay ○ MitoTracker and TMRE assays ○ L-HPG nascent protein synthesis assay ○ OP-puro assay ○ EdU incorporation flow cytometry assay ○ Flow-based competition assay ○ Proliferation analyses ○ Oxygen consumption and extracellular acidification rates ○ Isotope tracing and steady-state metabolite measurement ○ Citrate uptake assays ○ GC-MS analysis ○ Pathology ○ Immunohistochemistry ○ RNA isolation and qPCR ○ RNA-sequencing and analysis ○ Single cell transcriptomics (Human Protein Atlas) ○ Statistics and reproducibility SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j.cell. ..

    Single-cell Transcriptomics:

    Article Title: Citrate clearance is a major function of aconitase 2 in the canonical TCA cycle.
    Article Snippet: .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS ○ Mice ○ Cell lines • METHOD DETAILS ○ DepMap data analysis ○ Generation of genetically edited lines ○ Western blotting ○ Viability assay ○ MitoTracker and TMRE assays ○ L-HPG nascent protein synthesis assay ○ OP-puro assay ○ EdU incorporation flow cytometry assay ○ Flow-based competition assay ○ Proliferation analyses ○ Oxygen consumption and extracellular acidification rates ○ Isotope tracing and steady-state metabolite measurement ○ Citrate uptake assays ○ GC-MS analysis ○ Pathology ○ Immunohistochemistry ○ RNA isolation and qPCR ○ RNA-sequencing and analysis ○ Single cell transcriptomics (Human Protein Atlas) ○ Statistics and reproducibility SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j.cell. ..



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    Single-Cell RNA Sequencing Revealed That DP MΦs Had High Expression of Retnla Cardiac CD45 + immune cells were sorted from the sham group, 1 week post-TAC group (acute stress phase), and 9 weeks post-TAC group (chronic heart failure phase), and single-cell <t>transcriptomic</t> analysis was performed using the 10X Genomics platform. (A) Uniform manifold approximation and projection dimensionality reduction analysis identified that mononuclear MΦs consisted of Lyve1 hi MΦs, Lyve1 hi MHCⅡ hi MΦs, MHCⅡ hi MΦs, and monocytes after reclustering under “Lyve1score” and “MHCⅡscore” dimensions. (B) Nineteen representative differentially expressed genes are plotted as a heatmap. (C) The percentage of MΦ subsets among the total MΦs across conditions. (D) Volcano plots of differentially expressed genes across conditions including both up-regulated and down-regulated genes (minimum percentage: 0.1; logFC threshold: 0.1; adjusted P value < 0.05). Genes of interest are highlighted in red. (E) The percentage of Retlna-positive cells among the MΦ subsets detected with flow cytometry. (F) The relative expression levels of Retnla and Mgl2 in heart tissues were measured by quantitative polymerase chain reaction 3 days after diphtheria toxin injection between the sham and TAC groups (4 weeks post-TAC) using a DP MΦ–reduced model (TAC reduced). Values were analyzed by using analysis of variance with Tukey post hoc analysis. (G) Pathway enrichment analysis (gProfiler, Gene Ontology biological processes) using differentially expressed genes across conditions. ∗∗ P < 0.01; ∗∗∗ P < 0.001. avg = average; FC = fold change; mRNA = messenger RNA; other abbreviations as in <xref ref-type=Figure 1 , Figure 2 , Figure 3 . " width="250" height="auto" />
    Single Cell Transcriptomic Analysis, supplied by 10X Genomics, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Single-cell transcriptome analysis of the microglia (A) UMAP shows the distribution of each subtype of microglia. (B) The sector graph shows the composition of cells in subclusters by groups. (C) Violin plot depicts the expression levels of known core signature genes for each microglia subcluster. (D) Representative immunofluorescence double staining images of NFKBIA (red), IBA1 (green), and nuclei were labeled with DAPI located in hippocampus in the NC and LPS groups. Scale bar = 75 μm or 25 μm. Quantitative analysis of the proportion of NFKBIA + cells in microglia (IBA1+) in hippocampal DG subregion. Data are shown as mean ± SEM, independent samples t-test, n = 4, ∗∗ p < 0.01. (E) Marker genes enriched KEGG pathway analyses in various microglia subpopulations. (F) GO analysis shows the top five signaling pathways across the four subpopulations, MG0, MG4, MG5 and MG7.

    Journal: iScience

    Article Title: Single-cell transcriptomics of neuroinflammation and cerebrovascular endothelial cells in the aged rat hippocampus

    doi: 10.1016/j.isci.2025.113332

    Figure Lengend Snippet: Single-cell transcriptome analysis of the microglia (A) UMAP shows the distribution of each subtype of microglia. (B) The sector graph shows the composition of cells in subclusters by groups. (C) Violin plot depicts the expression levels of known core signature genes for each microglia subcluster. (D) Representative immunofluorescence double staining images of NFKBIA (red), IBA1 (green), and nuclei were labeled with DAPI located in hippocampus in the NC and LPS groups. Scale bar = 75 μm or 25 μm. Quantitative analysis of the proportion of NFKBIA + cells in microglia (IBA1+) in hippocampal DG subregion. Data are shown as mean ± SEM, independent samples t-test, n = 4, ∗∗ p < 0.01. (E) Marker genes enriched KEGG pathway analyses in various microglia subpopulations. (F) GO analysis shows the top five signaling pathways across the four subpopulations, MG0, MG4, MG5 and MG7.

    Article Snippet: Based on these results, we conducted single-cell transcriptome analysis (scRNA-seq) on aging rat hippocampus on day 3 after LPS or vehicle injection using the 10X Genomics platform to examine changes in the neuroinflammatory microenvironment ( H).

    Techniques: Expressing, Immunofluorescence, Double Staining, Labeling, Marker, Protein-Protein interactions

    Single-cell transcriptome analysis of the cerebral vascular endothelial cells (A–C) UMAP plot and bar plot showing the distribution of 6 subpopulations of cerebral vascular endothelial cells in the LPS and NC groups. (D) Violin plot shows the gene expression related to vascular origin (arterial, venous, and capillary), including arterial endothelial cell marker genes Fbln5, Bmx, Efnb2 , Vegfc . The venous endothelial cells highly expressed gene Nr2f and capillary endothelial cells highly expressed gene Rgcc and Slc16a1 . (E) Expression profiles of EC0 Marker genes including Mfge8, Lrg1, Lgals9, Cldn5, Ocln, Tjp1, Ddit4/Redd1, Mfsd2a are shown using the UMAP visualization approach. (F) Marker genes in the EC0 subpopulation are enriched with GO functional analysis. (G) Volcano plot depicts the DEGs at overall level of cerebral vascular endothelial cells between LPS and NC groups. DEGs (|log2(fold change)| > 1, p Value FDR <0.05, Difference = |pct.1- pct.2 | > 0.2) were colored (red for upregulated DEGs and blue for downregulated DEGs. (H and I) GO analysis shows the upregulated signaling pathway at overall level of cerebral vascular endothelial cells and EC0 subpopulation respectively.

    Journal: iScience

    Article Title: Single-cell transcriptomics of neuroinflammation and cerebrovascular endothelial cells in the aged rat hippocampus

    doi: 10.1016/j.isci.2025.113332

    Figure Lengend Snippet: Single-cell transcriptome analysis of the cerebral vascular endothelial cells (A–C) UMAP plot and bar plot showing the distribution of 6 subpopulations of cerebral vascular endothelial cells in the LPS and NC groups. (D) Violin plot shows the gene expression related to vascular origin (arterial, venous, and capillary), including arterial endothelial cell marker genes Fbln5, Bmx, Efnb2 , Vegfc . The venous endothelial cells highly expressed gene Nr2f and capillary endothelial cells highly expressed gene Rgcc and Slc16a1 . (E) Expression profiles of EC0 Marker genes including Mfge8, Lrg1, Lgals9, Cldn5, Ocln, Tjp1, Ddit4/Redd1, Mfsd2a are shown using the UMAP visualization approach. (F) Marker genes in the EC0 subpopulation are enriched with GO functional analysis. (G) Volcano plot depicts the DEGs at overall level of cerebral vascular endothelial cells between LPS and NC groups. DEGs (|log2(fold change)| > 1, p Value FDR <0.05, Difference = |pct.1- pct.2 | > 0.2) were colored (red for upregulated DEGs and blue for downregulated DEGs. (H and I) GO analysis shows the upregulated signaling pathway at overall level of cerebral vascular endothelial cells and EC0 subpopulation respectively.

    Article Snippet: Based on these results, we conducted single-cell transcriptome analysis (scRNA-seq) on aging rat hippocampus on day 3 after LPS or vehicle injection using the 10X Genomics platform to examine changes in the neuroinflammatory microenvironment ( H).

    Techniques: Gene Expression, Marker, Expressing, Functional Assay

    Single-Cell RNA Sequencing Revealed That DP MΦs Had High Expression of Retnla Cardiac CD45 + immune cells were sorted from the sham group, 1 week post-TAC group (acute stress phase), and 9 weeks post-TAC group (chronic heart failure phase), and single-cell transcriptomic analysis was performed using the 10X Genomics platform. (A) Uniform manifold approximation and projection dimensionality reduction analysis identified that mononuclear MΦs consisted of Lyve1 hi MΦs, Lyve1 hi MHCⅡ hi MΦs, MHCⅡ hi MΦs, and monocytes after reclustering under “Lyve1score” and “MHCⅡscore” dimensions. (B) Nineteen representative differentially expressed genes are plotted as a heatmap. (C) The percentage of MΦ subsets among the total MΦs across conditions. (D) Volcano plots of differentially expressed genes across conditions including both up-regulated and down-regulated genes (minimum percentage: 0.1; logFC threshold: 0.1; adjusted P value < 0.05). Genes of interest are highlighted in red. (E) The percentage of Retlna-positive cells among the MΦ subsets detected with flow cytometry. (F) The relative expression levels of Retnla and Mgl2 in heart tissues were measured by quantitative polymerase chain reaction 3 days after diphtheria toxin injection between the sham and TAC groups (4 weeks post-TAC) using a DP MΦ–reduced model (TAC reduced). Values were analyzed by using analysis of variance with Tukey post hoc analysis. (G) Pathway enrichment analysis (gProfiler, Gene Ontology biological processes) using differentially expressed genes across conditions. ∗∗ P < 0.01; ∗∗∗ P < 0.001. avg = average; FC = fold change; mRNA = messenger RNA; other abbreviations as in <xref ref-type=Figure 1 , Figure 2 , Figure 3 . " width="100%" height="100%">

    Journal: JACC: Basic to Translational Science

    Article Title: TIMD4 hi MHCⅡ hi Macrophages Preserve Heart Function Through Retnla

    doi: 10.1016/j.jacbts.2024.08.009

    Figure Lengend Snippet: Single-Cell RNA Sequencing Revealed That DP MΦs Had High Expression of Retnla Cardiac CD45 + immune cells were sorted from the sham group, 1 week post-TAC group (acute stress phase), and 9 weeks post-TAC group (chronic heart failure phase), and single-cell transcriptomic analysis was performed using the 10X Genomics platform. (A) Uniform manifold approximation and projection dimensionality reduction analysis identified that mononuclear MΦs consisted of Lyve1 hi MΦs, Lyve1 hi MHCⅡ hi MΦs, MHCⅡ hi MΦs, and monocytes after reclustering under “Lyve1score” and “MHCⅡscore” dimensions. (B) Nineteen representative differentially expressed genes are plotted as a heatmap. (C) The percentage of MΦ subsets among the total MΦs across conditions. (D) Volcano plots of differentially expressed genes across conditions including both up-regulated and down-regulated genes (minimum percentage: 0.1; logFC threshold: 0.1; adjusted P value < 0.05). Genes of interest are highlighted in red. (E) The percentage of Retlna-positive cells among the MΦ subsets detected with flow cytometry. (F) The relative expression levels of Retnla and Mgl2 in heart tissues were measured by quantitative polymerase chain reaction 3 days after diphtheria toxin injection between the sham and TAC groups (4 weeks post-TAC) using a DP MΦ–reduced model (TAC reduced). Values were analyzed by using analysis of variance with Tukey post hoc analysis. (G) Pathway enrichment analysis (gProfiler, Gene Ontology biological processes) using differentially expressed genes across conditions. ∗∗ P < 0.01; ∗∗∗ P < 0.001. avg = average; FC = fold change; mRNA = messenger RNA; other abbreviations as in Figure 1 , Figure 2 , Figure 3 .

    Article Snippet: Figure 5 Single-Cell RNA Sequencing Revealed That DP MΦs Had High Expression of Retnla Cardiac CD45 + immune cells were sorted from the sham group, 1 week post-TAC group (acute stress phase), and 9 weeks post-TAC group (chronic heart failure phase), and single-cell transcriptomic analysis was performed using the 10X Genomics platform. (A) Uniform manifold approximation and projection dimensionality reduction analysis identified that mononuclear MΦs consisted of Lyve1 hi MΦs, Lyve1 hi MHCII hi MΦs, MHCII hi MΦs, and monocytes after reclustering under “Lyve1score” and “MHCIIscore” dimensions. (B) Nineteen representative differentially expressed genes are plotted as a heatmap. (C) The percentage of MΦ subsets among the total MΦs across conditions. (D) Volcano plots of differentially expressed genes across conditions including both up-regulated and down-regulated genes (minimum percentage: 0.1; logFC threshold: 0.1; adjusted P value < 0.05).

    Techniques: RNA Sequencing, Expressing, Flow Cytometry, Real-time Polymerase Chain Reaction, Injection