Journal: eLife

Article Title: DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci

doi: 10.7554/eLife.102489

Figure Lengend Snippet: ( A ) Workflow of DNA O-MAP integrated with sample multiplexing quantitative proteomics. ( B ) Schematic of the three DNA loci examined in the TMT16plex experiment: pericentromeric alpha satellites, telomeres, and mitochondrial genomes. ( C ) Co-localization of DNA fluorescent in situ hybridization (FISH) and the streptavidin staining of the proteins biotinylated by DNA O-MAP targeting the pericentromeric alpha satellites, telomeres, and mitochondrial genomes. Scale bar: 5 µm. ( D ) Principal component analysis of scaled intensities of proteins enriched by the pan-alpha probe, telomere probe, mitochondrial genome oligo pool, and no-primary-probe control. ( E ) Unsupervised hierarchical clustering of scaled intensities of proteins enriched by the pan-alpha probe, telomere probe, mitochondrial genome oligo pool, and no-primary-probe control. ( F ) Log 2 fold change of proteins compared to no-primary-probe control, grouped by HPA subcellular location. Significance calculated based on Welch’s t -test for pairwise comparisons (****p-value <0.0001). Log 2 fold change of proteins compared to mitochondrial probe enriched proteins for the RNA Polymerases ( G ), mtDNA nucleoid packaging proteins ( H ), Shelterin ( I ), and CENP-A nucleosomal complexes ( J ). Significance calculated based on Welch’s t -test for pairwise comparisons (p-value: *<0.05, **<0.01, ***<0.001, ****<0.0001).

Article Snippet: Final ssDNA probe was purified using a Zymo DNA Clean and Concentrator-100 (DCC-100) kit according to the manufacturer’s protocol for oligo purification.

Techniques: Multiplexing, Quantitative Proteomics, In Situ Hybridization, Staining, Control

Journal: Stem Cells Translational Medicine

Article Title: Extracellular vesicles conjugated with c(RGDyk) peptide targeting integrin αVβ3 repair optic nerve injury through YAP/TAZ and Smad2/3 signaling

doi: 10.1093/stcltm/szag006

Figure Lengend Snippet: Conjugation and characterization of EVs. (A) Schematic diagram of conjugating c(RGDyK), RKK12 peptides, and Cyanine-5.5 dye to EVs by a two-step. (B) Expression of exosomal marker, CD63, CD9, CD81, and TSG101 from MSCs and Naïve or conjugated EVs. (C) Size distributions of Naïve and conjugated EVs based on Nano particle Tracking Analysis (NTA). (D) Transmission electron micrograph (TEM) images of Naïve and conjugated EVs. Scale bar, 100 nm. (E) Verification of the expression of integrin family proteins in R28 and CCD-986SK cells. (F) Uptake analysis of Cy5.5-labeld EVs in R28 cells. Cells were incubated with 100 μg/mL of Cy5.5-labeled EVs. Confocal microscopy demonstrated the presence of Cy5.5-labeled EVs in cells after 1 or 24 h of incubation. Magnification × 400. (G) Flow cytometric analyses of R28 cells (control) or Cy5.5_Naïve EVs, or c(RGDyK)_EVs. Cy5.5-c(RGDyK)-EVs were added with free c(RGDyK) peptide. (H) Zeta potential measurements were performed after peptide conjugation. (* P < .05, ** P < .01). All figures are original and were created by the authors.

Article Snippet: Cyanine 5.5 azide (Cy5.5 azide; Lumiprobe Co., Hallandale Beach, FL, USA) was also introduced onto peptide-conjugated EVs according to the manufacturer’s protocol.

Techniques: Conjugation Assay, Expressing, Marker, Transmission Assay, Incubation, Labeling, Confocal Microscopy, Control, Zeta Potential Analyzer