single cell multiome atac + gene expression kit  (10X Genomics)

Journal: Scientific Reports

Article Title: Analysis of changes in intercellular communications in Alzheimer’s disease reveals conserved changes in glutamatergic transmission in mice and humans

doi: 10.1038/s41598-025-10795-4

Figure Lengend Snippet: Characterization of single cell sequencing data from mouse and human postmortem brain samples. ( A ) Diagram of the experimental workflow for snRNA-seq and snATAC-seq performed on the same nuclei. The ENT of mice aged 2 months and 8 months, both 5xFAD and control ( n = 2 per age and genotype), was dissected, nuclei were isolated, and sequencing performed using the Single Cell Multiome ATAC + Gene Expression kit from 10x Genomics. ( B ) All single-nucleus sequencing data for mice aged 2 months and 8 months, both 5xFAD and control, represented in 2D UMAP (WNN) with general cell type annotations. Cell type clusters are colored accordingly for ( B , G ): glutamatergic neurons in blue, GABAergic neurons in green, OPCs in pink, oligodendrocytes in purple, microglia in red, astrocytes in orange, and endothelial cells in yellow. ( C ) Dotplot showing expression of known marker genes based on previously published work in each detected cell type in the mouse snRNA-seq portion of the multiome data. The size of the dots corresponds to the proportion of cells in which a gene was expressed, and color represents average normalized expression within that cell type. ( D–F ) Coverage plots showing known marker gene accessibility as captured by the snATAC-seq portion of the multiome data. Coverage plots show density of reads within the genome, with a peak on the coverage plot indicating many reads in that portion of the genome, meaning chromatin was open in that region, while a flat line indicates no reads and potential chromatin inaccessibility. Chromatin accessibility was reflective of gene expression (i.e., the area near the transcription start site is more open in genes that are more highly expressed in defined cell types). Shown are coverage plots for Slc17a7 ( D ), a marker for glutamatergic neurons; Mog ( E ), a marker for oligodendrocytes; and C1qb ( F ), a marker for microglia. ( G ) UMAP of merged, re-processed, and annotated snRNA-seq data from postmortem tissue samples obtained from AD, MCI, and non-cognitively impaired human brains, with cell types annotated and colored in the same way as equivalent cell types detected in the corresponding mouse model. This is a combination of previously published datasets (AD and controls) , and newly sequenced tissue (from an individual with MCI). ( H ) Dotplot showing expression of known marker genes, homologous to those used in annotation of mouse data, in the annotated human snRNA-seq data.

Article Snippet: The ENT of mice aged 2 months and 8 months, both 5xFAD and control ( n = 2 per age and genotype), was dissected, nuclei were isolated, and sequencing performed using the Single Cell Multiome ATAC + Gene Expression kit from 10x Genomics. ( B ) All single-nucleus sequencing data for mice aged 2 months and 8 months, both 5xFAD and control, represented in 2D UMAP (WNN) with general cell type annotations.

Techniques: Sequencing, Control, Isolation, Gene Expression, Expressing, Marker

Journal: Scientific Reports

Article Title: Analysis of changes in intercellular communications in Alzheimer’s disease reveals conserved changes in glutamatergic transmission in mice and humans

doi: 10.1038/s41598-025-10795-4

Figure Lengend Snippet: Multiomics approach reveals links between glutamatergic signaling via Grm1 and trophic signaling via BMPs. ( A–C ) Coverage plots of mouse ATAC-seq data with peaks highlighted according to in which genotype linkages were detected using DIRECT-NET. Blue indicates linkage to the gene of interest in control mice only. Red indicates linkage to the gene of interest in 5xFAD mice only. Purple indicates linkage to the gene of interest in both genotypes. Only high confidence (HC) links are plotted. ( A ) Coverage plot of Gria4 and the surrounding genomic area with links to the Gria4 transcriptional start site (TSS). A violin plot of Gria4 RNA expression is shown to the right. Links detected are either in non-coding regions of the genome, or to other parts of the Gria4 gene. ( B ) Coverage plot of Grin2b and surrounding genomic area with links to the Grin2b TSS. Links are detected within non-coding regions of the genome, the Grin2b gene itself, and Gm8994. ( C ) Coverage plot of Grm1 and surrounding genomic area with links to the Grm1 TSS. Links are detected within non-coding regions of the genome, the Grm1 gene itself, and genes Shprh and Fbxo30 . ( D ) Gene regulatory network (GRN) resulting from DIRECT-NET analysis of genes upregulated in 5xFAD mice at 2 months of age. Only HC links were utilized to detect transcription factors interacting with genes. Transcription factors are plotted in light blue, and whether transcription factors are proximal or distal to genes on which they act is shown via color: proximal in purple, and distal in orange. ( E–G ) GO analysis of genes in the GRN obtained in Fig. 5D for biological processes (E), cellular component (F), and molecular function (G). Only significantly enriched terms are shown. ( H ) GRN resulting from DIRECT-NET analysis of genes upregulated in 5xFAD mice at 8 months of age. This is the equivalent to ( D ), but for mice at 8 months of age. Notably, due to larger differences in chromatin accessibility, there are many more genes detected in the network at 8 months of age in mice compared to 2 months of age. ( I–K ) GO analysis of genes in the GRN obtained in Fig. 5H for biological processes (I), cellular component (J), and molecular function (K). Only significantly enriched terms are shown.

Article Snippet: The ENT of mice aged 2 months and 8 months, both 5xFAD and control ( n = 2 per age and genotype), was dissected, nuclei were isolated, and sequencing performed using the Single Cell Multiome ATAC + Gene Expression kit from 10x Genomics. ( B ) All single-nucleus sequencing data for mice aged 2 months and 8 months, both 5xFAD and control, represented in 2D UMAP (WNN) with general cell type annotations.

Techniques: Control, RNA Expression

Journal: Frontiers in Immunology

Article Title: Integrated single-cell chromatin and transcriptomic analyses of peripheral immune cells in patients with alopecia areata

doi: 10.3389/fimmu.2025.1565241

Figure Lengend Snippet: Cytokine and chemokine Expression, cell functionality markers, transcription factor predictions, and comparative analysis in AA. (A, B) Heatmaps of cytokine and chemokine expression across cell types. (C) Heatmaps of functional signatures: senescence, exhaustion, activation, cytotoxicity. (D) Word cloud of top transcription factors (TFs) from ATAC-seq data. (E) Dot plots showing top predicted TFs per cell type (NK, CD8+, monocytes). (F) Bar plot of pathway overlap among DEGs. (G) Flow cytometry validation of immune subsets. Statistical analysis is denoted by asterisks: ***p < 0.001, **p < 0.01, *p < 0.05.

Article Snippet: Finally, single-cell chromatin accessibility and gene expression profiling was performed using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit (10x Genomics, USA), in accordance with the manufacturer’s protocol.

Techniques: Expressing, Functional Assay, Activation Assay, Flow Cytometry, Biomarker Discovery