Journal: bioRxiv

Article Title: Cholesterol remodels the endoplasmic reticulum to control myofibroblastic CAF function

doi: 10.64898/2026.02.16.706237

Figure Lengend Snippet: (A) Measurement of the relative incorporation of [U- 14 C]glucose into protein, non-polar, RNA, DNA and polar fractions following 24 hours of labelling, n=3. (B) Relative incorporation of [1- 14 C]acetate into the lipid fraction of NFs and CAFs, n=3. (C) Gene Set Enrichment Analysis (GSEA) plot derived from RNA-Seq analysis of CAFs versus NFs, showing enrichment of a “lipid metabolic process” signature (GO:0006629). (D) Heatmap of cholesterol biosynthesis gene expression in NFs and CAFs, as determined by RNA-Seq analysis, n=3. (E) Quantification of relative total cholesterol levels in NFs and CAFs, n=3. (F) UMAP visualisation of 19,601 patient-derived breast tumour stromal cells analysed by single cell RNA-Seq (scRNA-Seq) from the Human Breast Cancer Atlas . Stromal clusters corresponding to immunomodulatory CAFs (iCAFs), myCAFs, perivascular (PVL) and endothelial cell subsets are indicated by colour (top). Feature plots illustrating expression of SQLE (bottom left) and SC5D (bottom right) in breast tumour stromal cell clusters. Gene expression is represented by log-normalised expression values. The myCAF cluster is delineated by a dashed line. (G) Representative filipin staining (green) of free cholesterol in NFs and CAFs. Nuclei are stained with Draq5 (blue). Dashed boxes indicate magnified regions shown to the right. White scale bar represents 10 µm, yellow scale bar represents 5 µm. (H) Quantification of relative cholesterol levels in the ER-enriched fraction isolated from NFs and CAFs, n=3.

Article Snippet: Filipin was removed, and cells were washed and imaged in PBS containing 5 μM Draq5 staining solution (Miltenyi Biotec) using a Zeiss Elyra PS.1 confocal microscope (Zeiss) equipped with a 63X/1.4 oil DIC objective.

Techniques: Derivative Assay, RNA Sequencing, Gene Expression, Single Cell, Expressing, Staining, Isolation

Journal: Development (Cambridge, England)

Article Title: Single-cell transcriptomic profiling of the whole colony of Botrylloides diegensis : insights into tissue specialization and blastogenesis

doi: 10.1242/dev.204265

Figure Lengend Snippet: Overview of the experimental pipeline and clustering results. (A) Single cells were prepared using the acetic methanol (ACME) maceration method . Cells were stained with DRAQ5 and sorted by FACS. Cells were captured in droplets using a 10x Chromium system. Single-cell libraries were prepared and sequenced. After mapping the transcripts to the genome, clustering analysis was performed to identify the cell types. (B) UMAP clustering analysis revealed 29 single-cell clusters. Each cluster was color-coded. (C) Heatmap of the top five marker genes in each cluster.

Article Snippet: ACME-fixed cells were stained with the DNA dye DRAQ5 to sort intact single cells from cellular debris and aggregates (eBioscience 0.66 μl/ml of 5 mM stock).

Techniques: Staining, Marker