Journal: Genome Biology

Article Title: txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility

doi: 10.1186/s13059-023-03150-1

Figure Lengend Snippet: txci-ATAC-seq generates high-quality single-cell ATAC libraries at high throughput. a Schematic of molecular details of txci-ATAC-seq library generation. b Experimental workflow for txci-ATAC-seq barnyard library generation. After 96-plex tagmentation, nuclei are overloaded on a 10X Chromium microfluidics device. Following nucleus encapsulation in the formed droplets, 10% of the GEMs can be used for quality control and the remaining 90% for data analysis. c-e) txci-ATAC-seq QC metrics for human (GM12878) and mouse (CH12) cell lines supplemented with SBS primer during in-droplet PCR. c “Knee” plot showing the unique reads (log 10 scale) against the rank of each barcode (log 10 scale) ordered from most unique reads (left) to least (right). The dashed line indicates the threshold (1000 reads) used to identify cell barcodes (orange points). d Scatter plots showing the number of unique reads mapped to either the human or mouse genome for both true and pseudo-barnyard experiments. Values were log 10 -transformed after adding a pseudo-count of 1 to all values. The percentage shown in the true barnyard panel (6.6%) represents the estimated collision rate. e Scatter plots showing the FRiDHS against the estimated complexity for each cell barcode detected as either mouse (blue) or human (red) cell. The estimated complexity is shown on a log 10 scale

Article Snippet: After quenching enzyme activity, the nuclei were pooled into a 12-tube strip and then transferred to a 15-ml conical tube preloaded with 400 μl tagmentation washing buffer (TMG, which contains 10 mM Tris acetate pH 7.8 (Boston BioProducts, Cat. BB-2412), 5 mM magnesium acetate (Sigma, Cat. 63,052-100ML), and 10% (v/v) glycerol (VWR, Cat. RC3290-32) diluted in nuclease-free water.

Techniques: High Throughput Screening Assay, Encapsulation, Control, Transformation Assay

Journal: Molecules

Article Title: The Proteolytic Activity of Neutrophil-Derived Serine Proteases Bound to the Cell Surface Arming Lung Epithelial Cells for Viral Defense

doi: 10.3390/molecules29184449

Figure Lengend Snippet: Summary of the proteolytic cleavage sites of proteases at the S2′ site. ( A ) Amino acid alignment of the S2′ region of the SARS-CoV-2 S protein. ( B ) S2′-peptides were incubated with TMPRSS2, furin, NE, CatG, and PR3 for 2 h at 37 °C. The hydrolysis of the peptide bonds is summarized in a digestion map (blue bars denote the fragments, and red arrows indicate the cleavage sites). Three independent experiments, n = 3. ( C ) Peptides were incubated with furin in the presence or absence of additional Ca 2+ ions, with a CaCl 2 final concentration of 1.2 mM (left panel). Quantification (right panel). n = 3.

Article Snippet: Human NE (4 μg/mL, neutrophil-derived human NE, PN: 16-14-051200, Lot No. EH 2020-03, Athens Research and Technology, Athens, GA, USA), human CatG (4 μg/mL, neutrophil-derived CatG, PN: 16-14-030107, Lot No. CG 2017-01, Athens Research and Technology, Athens, GA, USA), 4 μg/mL recombinant human furin (4 μL furin, containing 5 mM CaCl 2 based on the company’s production, was added to 94 μL PBS pH 7.4, with a final concentration of 0.2 mM; furin Cat. No. 450-47, Lot No. 1011516, Peprotech, Cranbury, NJ, USA) with or without the addition of CaCl 2 to a final concentration of 1.2 mM, or recombinant human TMPRSS2 (4 μg/mL, Cat. No. CSB-YP023924HU, Batch No. DA0471a3g001, BIOZOL, CUSABIO Technology, LLC, TX, USA) was incubated with 200 μg/mL peptide in PBS pH 7.4 (or in the case of TMPRSS2, Tris pH 7.8, 7.7 mM Tris/HCl and 150 mM NaCl) for 2 h at 37 °C.

Techniques: Incubation, Concentration Assay