Journal: Cell Reports

Article Title: Stromal Cell-Contact Dependent PI3K and APRIL Induced NF-κB Signaling Prevent Mitochondrial- and ER Stress Induced Death of Memory Plasma Cells

doi: 10.1016/j.celrep.2020.107982

Figure Lengend Snippet:

Article Snippet: Anti-mouse CD19, APC, REA749 , Miltenyi Biotec , Catalog # 130-112-036; RRID: AB_2655824.

Techniques: Recombinant, Electron Microscopy, Staining, Software

Journal: Cell Reports Medicine

Article Title: Ablation of ERO1A induces lethal endoplasmic reticulum stress responses and immunogenic cell death to activate anti-tumor immunity

doi: 10.1016/j.xcrm.2023.101206

Figure Lengend Snippet:

Article Snippet: Anti-mouse CD19 APC , Tonbo , Cat# 20-0193; RRID: AB_2621562.

Techniques: Control, Purification, Virus, Recombinant, CCK-8 Assay, Transfection, Protease Inhibitor, SYBR Green Assay, Saline, Lysis, Multiplex Assay, Cytotoxicity Assay, Cell Isolation, Enzyme-linked Immunosorbent Assay, Bicinchoninic Acid Protein Assay, Software

Journal: Nature Communications

Article Title: SARS-CoV-2 in severe COVID-19 induces a TGF-β-dominated chronic immune response that does not target itself

doi: 10.1038/s41467-021-22210-3

Figure Lengend Snippet: Peripheral blood activated/differentiated B cells (CD27 high CD38 high ) were isolated and sorted by FACS for single cell sequencing (gating strategy in Supplementary Fig. ). a Percentage of CD27 high CD38 high cells among live B cells. Each sample is represented by a circle. The line indicates the median. Unpaired two-sided Mann–Whitney U test. b UMAP representation of 72,277 CD27 high CD38 high sorted B cells from 9 COVID-19 ICU patients and three healthy controls. Between 2416 and 11,229 cells were recovered per sample. Transcriptionally similar clusters were identified using shared nearest neighbor (SNN) modularity optimization (left). The combination of CD19 , MS4A1 , CD27 , CD38 , IFIT1 , MIKI67 , IRF4 , and PRDM1 expression were used for annotation of the different activation/differentiation stages (right). c Heatmap of genes that resemble markers for the six different clusters. Depicted are genes with a p -value < 0.01 (two-sided Wilcoxon rank sum test) after Bonferroni correction, and an average absolute fold-change > log2(1.3). Shown are z -scores of the average expression. d UMAP representation of the expression levels of selected signature genes for activated/differentiated B cells. e UMAP representation of analyzed cells from one healthy control and two ICU patients, representing early (first week, patient #1) and late (>7days, patient #5) phase after ICU admission. f Percentage of cells belonging to a defined cluster among all sequenced B cells per donor. Each dot represents one time point from one single donor. Donors were grouped as “HC” for healthy controls (3 donors), “1st week” for patients within 7 days after ICU admission (six donors) and “Late” for patients who have been admitted to the ICU for more than a week at the time of analysis (eight donors). The line indicates the median. Significance was determined by using a two-sided analysis of varience (ANOVA) folowed by Tukey’s multiple comparison test with corrected p values as indicated in the figure.

Article Snippet: To that end, PBMCs were stained as described but with the following anti-human antibodies: CD19 (LT19, Miltenyi Biotec, Cat. No. 130-113-728, 1:400), CD3 (BW264/56, VioBlue, Miltenyi Biotec, Cat. No. 130-113-133, 1:400), CD14 (TÜK4, VioBlue, Miltenyi Biotec, Cat. No. 130-113-152, 1:200), CD27 (MT271, PE, Miltenyi Biotec, Cat. No. 130-097-926, 1:100), and CD38 (IB6, PE-Vio770, Miltenyi Biotec, Cat. No. 130-113-990, 1:200).

Techniques: Isolation, Sequencing, MANN-WHITNEY, Expressing, Activation Assay, Control, Comparison

Journal: Nature Communications

Article Title: SARS-CoV-2 in severe COVID-19 induces a TGF-β-dominated chronic immune response that does not target itself

doi: 10.1038/s41467-021-22210-3

Figure Lengend Snippet: a Titration of SARS-Cov-2-S protein-specific IgG, IgA, and IgM antibodies in the serum of three COVID-19 ICU patients. ΔMFI calculation as described in Fig. . Dotted line indicates a ΔMFI of 1500. b Workflow for the isolation and analysis of SARS-CoV-2-and measles-reactive CD4 + T lymphocytes. c Cells for single cell sequencing were sorted using FACS as PI - CD19 - CD14 - CD3 + CD4 + CD154 + or CD137 + (gating strategy as used for the analysis shown in Supplementary Fig. ). UMAP representation of 3727 CD4 + T cells from three COVID-19 ICU patients and two healthy controls (SARS-CoV-2-stimulated cells from one control and measles-stimulated cells from another control). Four clusters were identified based on transcriptional similarity using shared nearest-neighbor (SNN) modularity optimization (left). An additional CD14 + cluster (124 cells) and six outlying T cells with considerably less UMI-counts than the average were also identified but excluded from further analysis. Heatmap of signature genes of the four clusters. Depicted are genes with an absolute log2 fold change > log2(2) and a p -value < 0.01 after Bonferroni correction (two-sided Wilcoxon rank sum test). Colors corresponds to z -scores of the average expression. d Expression levels of selected signature genes and cytokines.

Article Snippet: To that end, PBMCs were stained as described but with the following anti-human antibodies: CD19 (LT19, Miltenyi Biotec, Cat. No. 130-113-728, 1:400), CD3 (BW264/56, VioBlue, Miltenyi Biotec, Cat. No. 130-113-133, 1:400), CD14 (TÜK4, VioBlue, Miltenyi Biotec, Cat. No. 130-113-152, 1:200), CD27 (MT271, PE, Miltenyi Biotec, Cat. No. 130-097-926, 1:100), and CD38 (IB6, PE-Vio770, Miltenyi Biotec, Cat. No. 130-113-990, 1:200).

Techniques: Titration, Isolation, Sequencing, Control, Expressing

Journal: Nature Communications

Article Title: SARS-CoV-2 in severe COVID-19 induces a TGF-β-dominated chronic immune response that does not target itself

doi: 10.1038/s41467-021-22210-3

Figure Lengend Snippet: Bronchoalveolar lavage (BAL) cells for single cell sequencing were enriched for CD45 + cells via MACS and live cells were further sorted using FACS (gating strategy in Supplementary Fig. ). a UMAP of 5459 cells representing clusters containing T cells, B cells, and CD14 -expressing cells from patient #1 on day 59 following ICU admission. B and T cell cluster identification based on BCR/TCR, CD19 , CD3E , CD4 , and CD8A expression (see Supplementary Fig. ). UMAP representation of expression of TGFB1 , IL21 , CD40LG , and IFNG . b UMAP coordinates and clustering was computed for 433 and 2723 cells from patient #9 on days 31 and 46 following ICU admission, respectively. UMAP representation of expression of TGFB1 , IL21 , CD40LG , and IFNG at the two different time points is shown side by side.

Article Snippet: To that end, PBMCs were stained as described but with the following anti-human antibodies: CD19 (LT19, Miltenyi Biotec, Cat. No. 130-113-728, 1:400), CD3 (BW264/56, VioBlue, Miltenyi Biotec, Cat. No. 130-113-133, 1:400), CD14 (TÜK4, VioBlue, Miltenyi Biotec, Cat. No. 130-113-152, 1:200), CD27 (MT271, PE, Miltenyi Biotec, Cat. No. 130-097-926, 1:100), and CD38 (IB6, PE-Vio770, Miltenyi Biotec, Cat. No. 130-113-990, 1:200).

Techniques: Sequencing, Expressing