scrna seq data processing cellranger  (10X Genomics)

Journal: iScience

Article Title: Chondrolectin regulates the sublaminar localization and regenerative function of muscle satellite cells in mice

doi: 10.1016/j.isci.2026.115703

Figure Lengend Snippet: Chodl mRNA is highly expressed in quiescent SCs (A) Chodl gene expression in various cell types in the mouse. Data were explored through the Tabula Muris data portal. (B) Relative expression of the Chodl gene in SCs, bladder cells, and a non-annotated cell population in (A). (C) UMAP-embedding of the scRNA-seq data on SCs isolated from non-injured muscles and injured muscles at 5 dpi in 2-month-old mice. (D) Violin plots show subcluster-specific gene expression ( Pax7 , Myog , Mki67 ) and enrichment of Chodl in the QSCs and ASCs. Colored by cluster identity. Abbreviations: QSC, quiescent SCs; SSC, self-renewal SCs; ASC, activated SCs; PSC, proliferating SCs; CSC, committed SCs; DSC, differentiating SCs. (E) qRT-PCR analysis of Chodl expression level in mouse QSC, ASC, and myoblast. n = 3 mice. (F) Immunoblot analysis showing CHODL expression in mouse myoblasts during myogenic differentiation. Relative band densitometry was calculated using ImageJ. (G) qRT-PCR analysis of Chodl in TA muscles post CTX injury in the mouse. n = 4 mice. Data are represented as mean ± SEM. The p values in E and G were analyzed using one-way ANOVA and Tukey post hoc test; ∗ p < 0.05, ∗∗ p < 0.01, and ∗∗∗ p < 0.001.

Article Snippet: To gain insight into the expression pattern of Chodl across various tissues, we conducted a comprehensive analysis using the scRNA-seq data publicly available from Tabula Muris , Our analysis revealed that Chodl mRNA was mainly enriched in SCs, bladder cells, and a non-annotated cell population, while not detected in other cell types, including fibro-adipogenic progenitors (FAPs) ( A and 1B).

Techniques: Gene Expression, Expressing, Isolation, Muscles, Quantitative RT-PCR, Western Blot, Cell Characterization

Journal: Journal of Translational Medicine

Article Title: mTOR inhibition promotes ATRA-induced cancer cell differentiation by overcoming a metabolic hyperactive state

doi: 10.1186/s12967-026-08218-7

Figure Lengend Snippet: Single-cell multiomic characterization of a differentiation-stalled state in ATRA-treated HL-60 cells. A . UMAP visualization of scATAC-seq data from HL-60 cells treated with ATRA for 0, 1, 3, or 6 days, colored by three identified clusters. C1 represents naïve cells; C2 and C3 represent ATRA-induced cell clusters. B . Heatmap showing the relative proportion of cells from each treatment time point within clusters C1–C3. C . Bar plot showing predicted lineage identity of each cluster, as determined by projection onto a reference atlas of normal human hematopoiesis. Each color represents a distinct hematopoietic lineage. D . Heatmap of scores of peak-to-gene (P2G) linkages derived from the integrated scATAC-seq and scRNA-seq data across the three clusters. E . GO enrichment analysis of featured P2G-linked genes. F . Feature plots from integrated scATAC-seq and scRNA-seq data. Top panels show gene activity from scATAC-seq; bottom panels show matched gene expression from scRNA-seq

Article Snippet: HL-60 scRNA-seq data were downloaded from National Omics Data Encyclopedia (NODE) with project ID OEP00001921, treated by ATRA for 0, 1, 3, 6 days.

Techniques: Single Cell, Derivative Assay, Activity Assay, Gene Expression