nuclei rna sequencing snrna seq data  (Broad Clinical Labs)

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

Journal: bioRxiv

Article Title: Conserved Neuronal-like and Secretory Programs Define the Spatial Architecture of Gastroenteropancreatic Neuroendocrine Tumors

doi: 10.64898/2025.12.28.696762

Figure Lengend Snippet: (A) Multiome sample processing and sequencing workflow. Archival, flash-frozen NET samples were apportioned for nuclei isolation and subsequent joint single-nuclei RNA-sequencing and ATAC-sequencing using the 10x Genomics protocol. Formalin-fixed, paraffin-embedded (FFPE) slides were generated from each sample and used to generate spatial transcriptomics data using the 10x Genomics Visium protocol. (B) Clinical characteristics of the cohort, including tumor origin, stage, grade, treatment status, and availability of multi-omic data after quality control. (C) UMAP embeddings of snRNA-seq and snATAC-seq data colored by annotated cell types. Bar plots indicate the relative abundance of major cell populations across samples.

Article Snippet: Processed single-nuclei RNA-seq data will be deposited in the Broad Institute Single Cell Portal ( https://singlecell.broadinstitute.org/single_cell ).

Techniques: Sequencing, Isolation, RNA Sequencing, Formalin-fixed Paraffin-Embedded, Generated, Control

Journal: bioRxiv

Article Title: Conserved Neuronal-like and Secretory Programs Define the Spatial Architecture of Gastroenteropancreatic Neuroendocrine Tumors

doi: 10.64898/2025.12.28.696762

Figure Lengend Snippet: (A,B) Violin plots showing cNMF program scores stratified by tumor type and clinical stage for siNETs (A) and pNETs (B). Differences between primary and metastatic tumors were assessed using a two-sided Wilcoxon rank-sum test. (C) Validation in an independent bulk RNA-seq pNET cohort showing decreased neuronal p-cNMF1 scores and increased secretory p-cNMF2 scores in metastatic samples. Statistical significance was assessed using a two-sided Wilcoxon rank-sum test (* = p value < 0.05, ** = p value < 0.01).

Article Snippet: Processed single-nuclei RNA-seq data will be deposited in the Broad Institute Single Cell Portal ( https://singlecell.broadinstitute.org/single_cell ).

Techniques: Biomarker Discovery, RNA Sequencing