Journal: STAR Protocols

Article Title: Protocol for large-scale, high-yield, high-purity extracellular vesicle purification from human plasma

doi: 10.1016/j.xpro.2026.104428

Figure Lengend Snippet: Fusion assay demonstrating the uptake of EVs from different fractions by cells EV populations were stained with DiI dye, then incubated with hTERT-HUVEC cells for 16 h. Cells were then fixed and DNA was stained with DAPI. Images taken at 20X and 100X magnification. Scale bar=10 μm

Article Snippet: hTERT-HUVEC (Human Telomerase Reverse Transcriptase (hTERT), Human umbilical vein endothelial cells (HUVEC)) , ATCC , CRL-4053 TM.

Techniques: Single Vesicle Fusion Assay, Staining, Incubation

Journal: Advanced materials technologies

Article Title: Perforated and Endothelialized Elastomeric Tubes for Vascular Modeling

doi: 10.1002/admt.201800741

Figure Lengend Snippet: Endothelialization of the perforated PDMS tubes. (A, B) Fluorescence micrographs showing the proliferation of HUVECs in the perforated PDMS tube during a 6-day culture period. (C) Quantification of numbers of HUVECs during the 14-day culture. Data are presented as mean ± standard deviation (STD); N = 6. (D) Cytoskeleton characterization of the endothelialized, perforated PDMS tubes at low and high magnifications. (E) Confocal orthogonal views showing the expressions of CD31 of the formed confluent endothelium.

Article Snippet: Cells HUVECs and HUVECs expressing GFP (Angio-Proteomie, Boston, MA, USA) were cultured in 75-cm 3 flasks in endothelial growth medium (EGM, Lonza, Basel, Switzerland) with 10 vol.% fetal bovine serum (FBS, Thermo Fisher, Waltham, MA, USA) and 1 vol.% penicillin-streptomycin (pen/strep, Thermo Fisher).

Techniques: Fluorescence, Standard Deviation

Journal: Advanced materials technologies

Article Title: Perforated and Endothelialized Elastomeric Tubes for Vascular Modeling

doi: 10.1002/admt.201800741

Figure Lengend Snippet: Tumor spheroid angiogenesis from perforated PDMS tubes. (A, B) Areas and circularities of the MCF-7 breast tumor spheroids at different time points of culture in the GelMA/collagen I matrix. Data are presented as mean ± standard deviation (STD); N = 16 (Day 3), 21 (Day 4), 21 (Day 5), 20 (Day 6), and 15 (Day 7). Spheroids were not formed until Day 3. (C, D) Area and circularity distributions of the MCF-7 breast tumor spheroids at Day 7. (E) Morphologies of the MCF-7 breast tumor spheroids and outward migration of the MCF-7 cells at Day 1 and Day 7. (F) VEGF secretions by the MCF-7 breast tumor spheroids at different time points of the culture, either in the absence or in the presence of the perforated, endothelialized PDMS tube. Data are presented as mean ± standard deviation (STD); N = 3. (G) Directional endothelial cell migration from the perforated PDMS tube towards the MCF-7 breast tumor spheroid at different time points of culture in the GelMA/collagen I matrix, under static conditions. HUVECs were GFP-labeled. The autofluorescence from the MCF-7 spheroid might be attributed to its high cell density.

Article Snippet: Cells HUVECs and HUVECs expressing GFP (Angio-Proteomie, Boston, MA, USA) were cultured in 75-cm 3 flasks in endothelial growth medium (EGM, Lonza, Basel, Switzerland) with 10 vol.% fetal bovine serum (FBS, Thermo Fisher, Waltham, MA, USA) and 1 vol.% penicillin-streptomycin (pen/strep, Thermo Fisher).

Techniques: Standard Deviation, Migration, Labeling

Journal: Nature communications

Article Title: Stress-induced RNA-chromatin interactions promote endothelial dysfunction.

doi: 10.1038/s41467-020-18957-w

Figure Lengend Snippet: Fig. 1 High glucose and TNFα induce a profound gene expression and phenotypic change. a HUVECs were treated in biological duplicates as Day 0: 25 mM mannitol as normal glucose and osmolarity control (NM); Day 3: combined treatment consisting 25 mM D-glucose and 5 ng/mL TNFα (H + T) for 3 days; and Day 7: H + T treatment for 7 days. Each group of treated cells was subjected to single-cell RNA-seq (scRNA-seq), Hi-C, and iMARGI assays. b t-SNE plot of scRNA-seq (4000–15,000 cells per sample) showed clear separation by treatment condition into three distinct clusters. c Principal component analysis of scRNA-seq data: single cells are plotted in the first two PC space and are labeled in red (Day 0, i.e., NM), green (Day 3, i.e., 3-day H + T treatment), and blue (Day 7, i.e., 7-day H + T treatment). d Expression heatmap (z-scaled) of top DE genes in single ECs grouped into functional pathways. Cells were ordered by increasing SERPINE1 expression (per each sample separately) and binned per 100 cells for the analysis. A total of 269 bins in Day 0, 177 bins in Day 3, and 148 bins in Day 7. e t-SNE plots of the expression level of selected genes in each single cell across the time course. The RNA levels are represented by log-normalized unique molecular identifier counts. f mRNA levels of eNOS and α-SMA in NM vs. H + T-treated HUVECs and cells untreated (NT) or treated with TGF-β (10 ng/mL) and IL-1β (5 ng/mL; T + I) for 3 or 7 days. The respective control was set as 1. Relative eNOS level: data represent mean ± SEM from five independent experiments; relative α-SMA level in H + T treatment: data represent mean ± SEM from seven independent experiments; relative α-SMA level in T + I treatment: data represent mean ± SEM from four independent experiments. *P = 0.0067, 0.0087, 0.0057, and 0.0017 from left to right based on ANOVA with Bonferroni as post hoc test. g Cell morphology under bright field (BF), immunofluorescent staining of α-SMA, and VE-cadherin (VE-cad), phalloidin staining of cytoskeleton, and DRAQ5 (DRAQ) staining of the nuclei. Representative images from five independent experiments are shown. Scale bar of BF = 100 µm; scale bars of (immuno)fluorescent staining = 50 µm. Source data are provided as a Source data file.

Article Snippet: Plasmid transfection was performed using the CytofectTM HUVEC Transfection kit (Cell Applications) following the manufacturer’s protocol in 6-well or 12-well plates.

Techniques: Gene Expression, Control, RNA Sequencing, Hi-C, Labeling, Expressing, Functional Assay, Staining

Journal: Nature communications

Article Title: Stress-induced RNA-chromatin interactions promote endothelial dysfunction.

doi: 10.1038/s41467-020-18957-w

Figure Lengend Snippet: Fig. 2 Overview of time-course Hi-C and iMARGI data. a, b Proportions of intrachromosomal (yellow) and interchromosomal read pairs (blue) in Hi-C (a) and iMARGI data (b) at the three time points (columns). c An example of interchromosomal iMARGI read pairs mapped to chromosome 2 near LINC00607 (left) and chromosome 7 near SERPINE1 (right). The RNA end (pink) and the DNA end (green) of each read pair is linked by a horizontal line. d Examples of overlapping iMARGI read pairs on a contact matrix from the RNA end (rows) to the DNA end (columns) with SEs (marked in light blue and in SE tracks) in control (Day 0) ECs. Genome region: chr1:75,000,0000–chr1:125,000,000. Resolution = 200 kb. e Proportions of iMARGI read pairs with the RNA ends (pink) or the DNA ends (green) in Day 0 (Ctrl) and Days 3 and 7 (H + T) ECs mapped to HUVEC SEs. Dotted line: the relative size of HUVEC SEs compared to the size of the genome. Source data are provided as a Source data file.

Article Snippet: Plasmid transfection was performed using the CytofectTM HUVEC Transfection kit (Cell Applications) following the manufacturer’s protocol in 6-well or 12-well plates.

Techniques: Hi-C, Control

Journal: Nature communications

Article Title: Stress-induced RNA-chromatin interactions promote endothelial dysfunction.

doi: 10.1038/s41467-020-18957-w

Figure Lengend Snippet: Fig. 4 Inhibition of LINC00607 attenuates SERPINE1 induction and EC dysfunction. a Illustration of LINC00607 genomic locus and gene structure and LNA GapmeRs targeting of LINC00607 RNA. b HUVECs were transfected with scramble (scr) or two LNAs targeting LINC00607. LINC00607 RNA and SERPINE1 mRNA levels were quantified. Data represent mean ± SEM from seven independent experiments. c qPCR of LINC00607 in subcellular fractionations of HUVECs transfected with scr, LNA1, or LNA2. Data represent mean ± SEM from four independent experiments. d RNA-seq was performed with cells transfected as in b in biological replicates. Heatmap is plotted based on z-scaled log-transformed gene expression levels. e, f ECs transfected with scr or LNA1 and then treated by H + T were used in e monocyte adhesion assay and in f SA-β-gal assay. In e, the number of attached monocytes to ECs were quantified. Data represent mean ± SEM from eight independent experiments performed with peripheral blood-derived monocytes from four individual donors. Representative images show the attachment of fluorescently labeled peripheral blood-derived monocytes to ECs for experiments performed with monocytes from three different donors. In f, ECs with positive β-gal staining were quantified. The positively stained cell number in scr control was set to 100 (%). f Data represent mean ± SEM from four independent experiments respectively. Scale bar = 200 μm. * denotes p = 0.0289, 0.0013, 0.001, 0.0001, 0.0025, and 0.024 from left to right (in b) and p = 0.0023, 0.0079, and 0.0249 from left to right (in c) between indicated groups based on ANOVA followed by Bonferroni post hoc test (in b and c); p = 0.0039 (in e) and 0.0014 (in f), as compared to scr group based on two-tailed paired t test (in e and f). Source data are provided as a Source data file.

Article Snippet: Plasmid transfection was performed using the CytofectTM HUVEC Transfection kit (Cell Applications) following the manufacturer’s protocol in 6-well or 12-well plates.

Techniques: Inhibition, Transfection, RNA Sequencing, Transformation Assay, Gene Expression, Cell Adhesion Assay, Derivative Assay, Labeling, Staining, Control, Two Tailed Test