snrna seq data  (Broad Clinical Labs)

Journal: Journal of Neurochemistry

Article Title: A High‐Resolution Transcriptomic Atlas of Cell Types in the Ventral Visual Thalamus

doi: 10.1111/jnc.70406

Figure Lengend Snippet: snRNA‐Seq identifies distinct neuronal and glial cell types in vLGN. (A) Schematic of viral infection following AAV1‐Cre injection. (B) Trans‐synaptic labeling of retinorecipient cells in ventral lateral geniculate nucleus (vLGN) of H2B‐transgenic mice following intraocular delivery of AAV1‐Cre. White dashed line outlines vLGN. mCherry(H2B)‐labeled cells are present in vLGN (arrowheads). (C) Identification and isolation of H2b‐mCherry+ nuclei by FACS sorting. (D) UMAP (uniform manifold approximation and projection) plot of 10 266 cell nuclei from the ventral lateral geniculate nucleus (vLGN), clustered by expression of high‐variance genes and colored according to cluster identity. (E) Violin plots showing expression of pan‐neuronal marker genes ( Syn1, Rbfox3 ); oligodendrocyte marker gene ( Olig1 ); macrophage marker gene ( Cx3cr1 ); endothelial cell marker gene ( Cldn5 ); pericyte marker gene ( Vtn ); astrocyte marker genes ( Aldoc ); microglia marker gene ( Mrc1 ); excitatory neuron marker gene ( Slc17a6, Slc17a7 ); and inhibitory neuron marker genes ( Gad1, Gad2 ). (F) UMAP recolored to illustrate expression levels of marker genes. (G) UMAP clustered by expression of high‐variance genes and colored according to predicted cell type.

Article Snippet: Resource availability : A user‐friendly interface for visualizing and exploring the snRNA‐Seq data is available at the Broad Institute Single Cell Portal at https://singlecell.broadinstitute.org/single_cell/study/SCP3575 .

Techniques: Infection, Injection, Labeling, Transgenic Assay, Isolation, Expressing, Marker

Journal: Journal of Neurochemistry

Article Title: A High‐Resolution Transcriptomic Atlas of Cell Types in the Ventral Visual Thalamus

doi: 10.1111/jnc.70406

Figure Lengend Snippet: snRNA‐Seq elucidates 13 retinorecipient neuronal types in vLGN. (A) UMAP (uniform manifold approximation and projection) of 4489 neuron cell nuclei from the ventral lateral geniculate nucleus, clustered by expression of high‐variance genes and colored according to cluster identity. (B) Neuronal UMAP recolored to illustrate expression of 89 mCherry+ vLGN nuclei following AAV injection in neurons. (C) Dot plot of neuronal clusters showing the expression of inhibitory marker genes ( Gad1 and Gad2 ) and excitatory marker genes ( Slc17a6 and Slc17a7 ) separated by original identity. (D) Dot plot of neuronal clusters showing the expression of Nxph1 (vLGNe) separated by original identity. (E) Neuron UMAP recolored to illustrate expression levels of Nxph1 .

Article Snippet: Resource availability : A user‐friendly interface for visualizing and exploring the snRNA‐Seq data is available at the Broad Institute Single Cell Portal at https://singlecell.broadinstitute.org/single_cell/study/SCP3575 .

Techniques: Expressing, Injection, Marker

Journal: Briefings in Bioinformatics

Article Title: Decoding causal m 6 A: a bioinformatics roadmap for psychiatric disorders

doi: 10.1093/bib/bbag251

Figure Lengend Snippet: An end-to-end bioinformatics pipeline identifying causal m 6 A targets in depression. (A) The integrated workflow illustrating two distinct analytical phases: transitioning from descriptive functional convergence (using MeRIP-seq datasets: Study 2, 3, and 5) to causal SMR inference (using MDD GWAS summary statistics from the PGC and brain m 6 A-QTL datasets). (B) Number of enriched GO terms in the mouse studies. (C) Venn diagram showing the convergence of functional themes on “cognition”. (D) The seven specifically screened cognition-associated genes with differential m 6 A peaks. (E) Example IGV plot for the Cacna1e gene (see – for the full set of identified genes), showing differential m 6 A peaks from two of the analyzed studies. Where the regions with visible logFC value corresponds to the significantly DMPs. The log2 fold-change (logFC) values represent the ratio of m 6 A enrichment levels between depression models and their corresponding controls. (F) SMR locus plot, illustrating the causal mediation of MDD genetic risk through brain-specific m 6 A-QTLs at the ADARB1 locus. (G) snRNA-seq validation from the HPA, demonstrating that the prioritized causal target ( ADARB1 ) is highly specific to excitatory and inhibitory neuronal lineages, supporting a “Brain-First” functional etiology.

Article Snippet: To demonstrate Phase 3 of our roadmap and adhere to a cell-type specific annotation strategy, we validated our top causal target, ADARB1 , using single-nucleus RNA-seq (snRNA-seq) data from the Human Protein Atlas (HPA) (database access links are provided in Supplementary Methods).

Techniques: Functional Assay, Biomarker Discovery

Journal: Scientific Reports

Article Title: Cardiomyocyte-derived TGFB3 attenuates cardiac fibrosis and preserves cardiac function in heart failure

doi: 10.1038/s41598-026-42367-5

Figure Lengend Snippet: TGFB3 upregulation predominantly occurs in cardiomyocytes under pathological conditions. (A) UMAP visualization of single-nucleus RNA sequencing (snRNA-seq) data from mouse hearts (dataset SCP1303, Single Cell Portal). Left: expression pattern of Tgfb3 across all cardiac cell populations, with color intensity representing normalized expression levels. Right: cells colored according to cluster identity. (B) Bar graph showing Tgfb3 expression levels in cardiomyocytes (CM), fibroblasts (FB), and endothelial cells (EC) from sham and TAC groups, derived from a publicly available transcriptomic dataset (GEO accession: GSE180720 ). (C) qPCR analysis of Tgfb3 expression in isolated cardiomyocyte (CM) and non-cardiomyocyte (non-CM) fractions ( n = 4 per group). (D) Immunoblot analysis of TGFB3 protein levels in CM and non-CM fractions. cTnT and αSMA were used as markers of CM and non-CM, respectively; HSP90 served as a loading control. (E) qPCR analysis of Tgfb3 expression in primary cardiomyocytes treated with AngII (5 µM) or vehicle for 24 h ( n = 3 per group). (F) qPCR analysis of Tgfb3 expression in HL-1 cells treated with AngII (5 µM) or vehicle for 24 h ( n = 3 per group). (G) Immunoblot analysis of TGFB3 protein levels in HL-1 cells treated with AngII (5 µM) or vehicle for 48 h; HSP90 served as a loading control. Data are presented as mean ± SEM from three independent experiments. Statistical significance was tested by two-tailed unpaired Student’s t test in ( B, C, E, F ). p-values are indicated above each comparison.

Article Snippet: Publicly available single-nuclei RNA-sequencing (snRNA-seq) data from human hearts with dilated and hypertrophic cardiomyopathy were obtained from the study “Single-nuclei profiling of human dilated and hypertrophic cardiomyopathy” (SCP1303) hosted on the Single Cell Portal ( https://singlecell.broadinstitute.org/single_cell ) 30 .

Techniques: RNA Sequencing, Single Cell, Expressing, Derivative Assay, Isolation, Western Blot, Control, Two Tailed Test, Comparison