Journal: Nature Communications

Article Title: IKKε and TBK1 prevent RIPK1 dependent and independent inflammation

doi: 10.1038/s41467-023-44372-y

Figure Lengend Snippet: a , b Graphs showing spleen to body weight ratio a and peripheral blood analysis assayed by differential hematology analyzer b of 8-13 week-old mice with the indicated genotypes. c , d Graphs showing flow cytometry analysis of CD11b + CD115+ (monocytes) and CD11b + Ly6G+ (neutrophils) in bone marrow c and spleen d of 8–13 week-old mice with the indicated genotypes. e Graphs showing ratio of CD69+ (activated) to CD62L+ (naive) T cells amongst live CD45 + CD3+ splenocytes of 8–13 weeks old mice week-old mice with the indicated genotypes. Each dot represents one mouse. ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.005, ∗∗∗∗ p < 0.0001 (one-way ANOVA t-test with post-hoc multiple test). Violin plots show the median of biological replicates and interquartile range of data. Source data for a – e are provided as a source data file.

Article Snippet: 2×10 6 cells were stained with different set of fluorochrome conjugated antibodies: (i) anti-CD4 (eBioscience, cat no. 25-0041-81, 1:200), anti-CD8 (eBioscience, cat no. 11-0081-82, 1:100), anti-CD3e (eBioscience, cat no. 45-0031-82, 1:200), anti-CD45 (eBioscience, cat no. 67-0451-82, 1:200), anti-CD62L (eBioscience, cat no. 17-0621-82, 1:200), anti-CD69 (eBioscience, cat no. 12-0691-82, 1:200); (ii) anti-CD45 (eBioscience, cat no. 67-0451-82, 1:200), anti-Ly6G (eBioscience, cat no. 46-9668-82, 1:100), anti-CD19 (eBioscience, cat no. 78-0193-82, 1:200), anti-CD11b (BD Horizon, cat no. 562317, 1:100); (iii) anti-CD19 (eBioscience, cat no. 63-5941-82, 1:100), anti-CD3e (eBioscience, cat no. 63-0031-82, 1:100), anti-B220 (eBioscience, cat no. 63-0452-82, 1:100), anti-NK1.1(eBioscience, cat no. 63-5941-82, 1:100), anti-CD115 (BioLegend, cat no. 53-1152-82, 1:50), anti-Ly6G cat no. 46-9668-82, 1:100), anti-CD11b (BD Horizon, cat no. 562317, 1:100), (iv) anti-CD3 (Invitrogen, cat no. HM3428, 1:100), anti-Foxp3 (Thermoscientific, cat no. 12-5773-82, 1:20), anti-CD25 (BioLegend, cat no. 25-0251-82, 1:100), anti-CD4 (BioLegend, cat no. 17-0042-82, 1:100); (v) anti-CD4 (eBioscience, cat no. 25-0041-81, 1:100), anti-CD8 (eBioscience, cat no. 11-0081-82, 1:200), anti-CD3e (eBioscience, cat no. 45-0031-82, 1:200), anti-CD45 (eBioscience, cat no. 67-0451-82, 1:200); and (vi) anti-CD45 (eBioscience, cat no. 67-0451-82, 1:200) with anti-IL18Ra (Thermoscientific, cat no. 157903, 1:100) or anti-IL-33R (Biolegend, cat no. 145303, 1:100) in the presence of Live/Dead fixable yellow dead cell stain (Invitrogen, cat no. L34959) and CD16/32 (BD, cat no. 553142).

Techniques: Flow Cytometry

Journal: Nature Communications

Article Title: IKKε and TBK1 prevent RIPK1 dependent and independent inflammation

doi: 10.1038/s41467-023-44372-y

Figure Lengend Snippet: a Schematic depicting the breeding strategy used to generate mice with combined inhibition of TBK1 and IKKε kinase activities in myeloid cells. Created with BioRender.com. b , c Graph showing spleen to body weight ratio b and representative pictures of spleens c of 8–13 week-old mice with the indicated genotypes. d Graphs depicting peripheral blood analysis of mice with the indicated genotypes, assayed by differential hematology analyzer. e , f Graphs showing cell counts and percentage of CD11b + Ly6G+ (neutrophils) e , as well as CD3 + CD4+ and CD3 + CD8+ cells f among live and CD45+ splenocytes of 8–13 week-old mice with the indicated genotypes. g Graphs showing the ratio of CD69+ (activated) to CD62L+ (naive) T cells amongst live CD45 + CD3+ splenocytes of 8-13 week-old mice with indicated genotypes. Each dot represents one mouse. ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.005, ∗∗∗∗ p < 0.0001 (one-way ANOVA t-test with post-hoc multiple test). Violin plots show the median of biological replicates and interquartile range of data. Source data for b and d – g are provided as a source data file.

Article Snippet: 2×10 6 cells were stained with different set of fluorochrome conjugated antibodies: (i) anti-CD4 (eBioscience, cat no. 25-0041-81, 1:200), anti-CD8 (eBioscience, cat no. 11-0081-82, 1:100), anti-CD3e (eBioscience, cat no. 45-0031-82, 1:200), anti-CD45 (eBioscience, cat no. 67-0451-82, 1:200), anti-CD62L (eBioscience, cat no. 17-0621-82, 1:200), anti-CD69 (eBioscience, cat no. 12-0691-82, 1:200); (ii) anti-CD45 (eBioscience, cat no. 67-0451-82, 1:200), anti-Ly6G (eBioscience, cat no. 46-9668-82, 1:100), anti-CD19 (eBioscience, cat no. 78-0193-82, 1:200), anti-CD11b (BD Horizon, cat no. 562317, 1:100); (iii) anti-CD19 (eBioscience, cat no. 63-5941-82, 1:100), anti-CD3e (eBioscience, cat no. 63-0031-82, 1:100), anti-B220 (eBioscience, cat no. 63-0452-82, 1:100), anti-NK1.1(eBioscience, cat no. 63-5941-82, 1:100), anti-CD115 (BioLegend, cat no. 53-1152-82, 1:50), anti-Ly6G cat no. 46-9668-82, 1:100), anti-CD11b (BD Horizon, cat no. 562317, 1:100), (iv) anti-CD3 (Invitrogen, cat no. HM3428, 1:100), anti-Foxp3 (Thermoscientific, cat no. 12-5773-82, 1:20), anti-CD25 (BioLegend, cat no. 25-0251-82, 1:100), anti-CD4 (BioLegend, cat no. 17-0042-82, 1:100); (v) anti-CD4 (eBioscience, cat no. 25-0041-81, 1:100), anti-CD8 (eBioscience, cat no. 11-0081-82, 1:200), anti-CD3e (eBioscience, cat no. 45-0031-82, 1:200), anti-CD45 (eBioscience, cat no. 67-0451-82, 1:200); and (vi) anti-CD45 (eBioscience, cat no. 67-0451-82, 1:200) with anti-IL18Ra (Thermoscientific, cat no. 157903, 1:100) or anti-IL-33R (Biolegend, cat no. 145303, 1:100) in the presence of Live/Dead fixable yellow dead cell stain (Invitrogen, cat no. L34959) and CD16/32 (BD, cat no. 553142).

Techniques: Inhibition

Journal: Nature Communications

Article Title: IKKε and TBK1 prevent RIPK1 dependent and independent inflammation

doi: 10.1038/s41467-023-44372-y

Figure Lengend Snippet: a Representative images of liver sections from 8-13 week-old mice with the indicated genotypes immunostained for CD45 and cleaved caspase 8 or stained with hematoxylin and eosin (H&E). Scale bars, 1 mm (black) and 100 μm (green). b , c Serum ALT, ALP and AST levels of 8-13-week-old mice with the indicated genotypes. Each dot represents one mouse. ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.005, ∗∗∗∗ p < 0.0001. (one-way ANOVA t-test with post-hoc multiple test). Violin plots show the median of biological replicates and interquartile range of data. Source data for b , c are provided as a source data file.

Article Snippet: 2×10 6 cells were stained with different set of fluorochrome conjugated antibodies: (i) anti-CD4 (eBioscience, cat no. 25-0041-81, 1:200), anti-CD8 (eBioscience, cat no. 11-0081-82, 1:100), anti-CD3e (eBioscience, cat no. 45-0031-82, 1:200), anti-CD45 (eBioscience, cat no. 67-0451-82, 1:200), anti-CD62L (eBioscience, cat no. 17-0621-82, 1:200), anti-CD69 (eBioscience, cat no. 12-0691-82, 1:200); (ii) anti-CD45 (eBioscience, cat no. 67-0451-82, 1:200), anti-Ly6G (eBioscience, cat no. 46-9668-82, 1:100), anti-CD19 (eBioscience, cat no. 78-0193-82, 1:200), anti-CD11b (BD Horizon, cat no. 562317, 1:100); (iii) anti-CD19 (eBioscience, cat no. 63-5941-82, 1:100), anti-CD3e (eBioscience, cat no. 63-0031-82, 1:100), anti-B220 (eBioscience, cat no. 63-0452-82, 1:100), anti-NK1.1(eBioscience, cat no. 63-5941-82, 1:100), anti-CD115 (BioLegend, cat no. 53-1152-82, 1:50), anti-Ly6G cat no. 46-9668-82, 1:100), anti-CD11b (BD Horizon, cat no. 562317, 1:100), (iv) anti-CD3 (Invitrogen, cat no. HM3428, 1:100), anti-Foxp3 (Thermoscientific, cat no. 12-5773-82, 1:20), anti-CD25 (BioLegend, cat no. 25-0251-82, 1:100), anti-CD4 (BioLegend, cat no. 17-0042-82, 1:100); (v) anti-CD4 (eBioscience, cat no. 25-0041-81, 1:100), anti-CD8 (eBioscience, cat no. 11-0081-82, 1:200), anti-CD3e (eBioscience, cat no. 45-0031-82, 1:200), anti-CD45 (eBioscience, cat no. 67-0451-82, 1:200); and (vi) anti-CD45 (eBioscience, cat no. 67-0451-82, 1:200) with anti-IL18Ra (Thermoscientific, cat no. 157903, 1:100) or anti-IL-33R (Biolegend, cat no. 145303, 1:100) in the presence of Live/Dead fixable yellow dead cell stain (Invitrogen, cat no. L34959) and CD16/32 (BD, cat no. 553142).

Techniques: Staining

Journal: Nature Communications

Article Title: IKKε and TBK1 prevent RIPK1 dependent and independent inflammation

doi: 10.1038/s41467-023-44372-y

Figure Lengend Snippet: a Representative images of liver sections from 8 to 13 week-old mice with the indicated genotypes immunostained for CD45 and cleaved caspase 8 or stained with hematoxylin and eosin (H&E). Scale bars, 1 mm (black) and 100 μm (green). b , c Serum ALT, ALP, and AST levels of 8-13-week-old mice with the indicated genotypes. Each dot represents one mouse. ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.005, ∗∗∗∗ p < 0.0001. (one-way ANOVA t-test with post-hoc multiple test). Violin plots show the median of biological replicates and interquartile range of data. Source data for b and c are provided as a source data file.

Article Snippet: 2×10 6 cells were stained with different set of fluorochrome conjugated antibodies: (i) anti-CD4 (eBioscience, cat no. 25-0041-81, 1:200), anti-CD8 (eBioscience, cat no. 11-0081-82, 1:100), anti-CD3e (eBioscience, cat no. 45-0031-82, 1:200), anti-CD45 (eBioscience, cat no. 67-0451-82, 1:200), anti-CD62L (eBioscience, cat no. 17-0621-82, 1:200), anti-CD69 (eBioscience, cat no. 12-0691-82, 1:200); (ii) anti-CD45 (eBioscience, cat no. 67-0451-82, 1:200), anti-Ly6G (eBioscience, cat no. 46-9668-82, 1:100), anti-CD19 (eBioscience, cat no. 78-0193-82, 1:200), anti-CD11b (BD Horizon, cat no. 562317, 1:100); (iii) anti-CD19 (eBioscience, cat no. 63-5941-82, 1:100), anti-CD3e (eBioscience, cat no. 63-0031-82, 1:100), anti-B220 (eBioscience, cat no. 63-0452-82, 1:100), anti-NK1.1(eBioscience, cat no. 63-5941-82, 1:100), anti-CD115 (BioLegend, cat no. 53-1152-82, 1:50), anti-Ly6G cat no. 46-9668-82, 1:100), anti-CD11b (BD Horizon, cat no. 562317, 1:100), (iv) anti-CD3 (Invitrogen, cat no. HM3428, 1:100), anti-Foxp3 (Thermoscientific, cat no. 12-5773-82, 1:20), anti-CD25 (BioLegend, cat no. 25-0251-82, 1:100), anti-CD4 (BioLegend, cat no. 17-0042-82, 1:100); (v) anti-CD4 (eBioscience, cat no. 25-0041-81, 1:100), anti-CD8 (eBioscience, cat no. 11-0081-82, 1:200), anti-CD3e (eBioscience, cat no. 45-0031-82, 1:200), anti-CD45 (eBioscience, cat no. 67-0451-82, 1:200); and (vi) anti-CD45 (eBioscience, cat no. 67-0451-82, 1:200) with anti-IL18Ra (Thermoscientific, cat no. 157903, 1:100) or anti-IL-33R (Biolegend, cat no. 145303, 1:100) in the presence of Live/Dead fixable yellow dead cell stain (Invitrogen, cat no. L34959) and CD16/32 (BD, cat no. 553142).

Techniques: Staining

Journal: Nature Communications

Article Title: IKKε and TBK1 prevent RIPK1 dependent and independent inflammation

doi: 10.1038/s41467-023-44372-y

Figure Lengend Snippet: a Representative images of liver sections from 8 to 13 week-old mice with the indicated genotypes immunostained for CD45 and cleaved caspase 3 or stained with hematoxylin and eosin (H&E). Scale bars, 1 mm (black) and 100μm (green). b , c Graphs showing histological colitis and ileitis scores b and cleaved caspase-3 containing crypt percentage among 100 randomly counted crypts in 8-13 weeks-old mice of the indicated genotypes. Each dot represents one mouse. ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.005, ∗∗∗∗ p < 0.0001. (one-way ANOVA t-test with post-hoc multiple test). Violin plots show the median of biological replicates and interquartile range of data. Source data for b, c are provided as a source data file.

Article Snippet: 2×10 6 cells were stained with different set of fluorochrome conjugated antibodies: (i) anti-CD4 (eBioscience, cat no. 25-0041-81, 1:200), anti-CD8 (eBioscience, cat no. 11-0081-82, 1:100), anti-CD3e (eBioscience, cat no. 45-0031-82, 1:200), anti-CD45 (eBioscience, cat no. 67-0451-82, 1:200), anti-CD62L (eBioscience, cat no. 17-0621-82, 1:200), anti-CD69 (eBioscience, cat no. 12-0691-82, 1:200); (ii) anti-CD45 (eBioscience, cat no. 67-0451-82, 1:200), anti-Ly6G (eBioscience, cat no. 46-9668-82, 1:100), anti-CD19 (eBioscience, cat no. 78-0193-82, 1:200), anti-CD11b (BD Horizon, cat no. 562317, 1:100); (iii) anti-CD19 (eBioscience, cat no. 63-5941-82, 1:100), anti-CD3e (eBioscience, cat no. 63-0031-82, 1:100), anti-B220 (eBioscience, cat no. 63-0452-82, 1:100), anti-NK1.1(eBioscience, cat no. 63-5941-82, 1:100), anti-CD115 (BioLegend, cat no. 53-1152-82, 1:50), anti-Ly6G cat no. 46-9668-82, 1:100), anti-CD11b (BD Horizon, cat no. 562317, 1:100), (iv) anti-CD3 (Invitrogen, cat no. HM3428, 1:100), anti-Foxp3 (Thermoscientific, cat no. 12-5773-82, 1:20), anti-CD25 (BioLegend, cat no. 25-0251-82, 1:100), anti-CD4 (BioLegend, cat no. 17-0042-82, 1:100); (v) anti-CD4 (eBioscience, cat no. 25-0041-81, 1:100), anti-CD8 (eBioscience, cat no. 11-0081-82, 1:200), anti-CD3e (eBioscience, cat no. 45-0031-82, 1:200), anti-CD45 (eBioscience, cat no. 67-0451-82, 1:200); and (vi) anti-CD45 (eBioscience, cat no. 67-0451-82, 1:200) with anti-IL18Ra (Thermoscientific, cat no. 157903, 1:100) or anti-IL-33R (Biolegend, cat no. 145303, 1:100) in the presence of Live/Dead fixable yellow dead cell stain (Invitrogen, cat no. L34959) and CD16/32 (BD, cat no. 553142).

Techniques: Staining

Journal: Nature Communications

Article Title: IKKε and TBK1 prevent RIPK1 dependent and independent inflammation

doi: 10.1038/s41467-023-44372-y

Figure Lengend Snippet: a Representative images of liver sections from 8-13 week-old mice with the indicated genotypes immunostained for CD45 and cleaved caspase 3 or stained with hematoxylin and eosin (H&E). Scale bars, 1 mm (black) and 100 μm (green). b , c Graphs showing histological colitis and ileitis scores b and cleaved caspase-3 containing crypt percentage among 100 randomly counted crypts in 8–13 weeks-old mice of the indicated genotypes. Each dot represents one mouse. ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.005, ∗∗∗∗ p < 0.0001. (one-way ANOVA t-test with post-hoc multiple test). Violin plots show the median of biological replicates and interquartile range of data. Source data for b , c are provided as a source data file.

Article Snippet: 2×10 6 cells were stained with different set of fluorochrome conjugated antibodies: (i) anti-CD4 (eBioscience, cat no. 25-0041-81, 1:200), anti-CD8 (eBioscience, cat no. 11-0081-82, 1:100), anti-CD3e (eBioscience, cat no. 45-0031-82, 1:200), anti-CD45 (eBioscience, cat no. 67-0451-82, 1:200), anti-CD62L (eBioscience, cat no. 17-0621-82, 1:200), anti-CD69 (eBioscience, cat no. 12-0691-82, 1:200); (ii) anti-CD45 (eBioscience, cat no. 67-0451-82, 1:200), anti-Ly6G (eBioscience, cat no. 46-9668-82, 1:100), anti-CD19 (eBioscience, cat no. 78-0193-82, 1:200), anti-CD11b (BD Horizon, cat no. 562317, 1:100); (iii) anti-CD19 (eBioscience, cat no. 63-5941-82, 1:100), anti-CD3e (eBioscience, cat no. 63-0031-82, 1:100), anti-B220 (eBioscience, cat no. 63-0452-82, 1:100), anti-NK1.1(eBioscience, cat no. 63-5941-82, 1:100), anti-CD115 (BioLegend, cat no. 53-1152-82, 1:50), anti-Ly6G cat no. 46-9668-82, 1:100), anti-CD11b (BD Horizon, cat no. 562317, 1:100), (iv) anti-CD3 (Invitrogen, cat no. HM3428, 1:100), anti-Foxp3 (Thermoscientific, cat no. 12-5773-82, 1:20), anti-CD25 (BioLegend, cat no. 25-0251-82, 1:100), anti-CD4 (BioLegend, cat no. 17-0042-82, 1:100); (v) anti-CD4 (eBioscience, cat no. 25-0041-81, 1:100), anti-CD8 (eBioscience, cat no. 11-0081-82, 1:200), anti-CD3e (eBioscience, cat no. 45-0031-82, 1:200), anti-CD45 (eBioscience, cat no. 67-0451-82, 1:200); and (vi) anti-CD45 (eBioscience, cat no. 67-0451-82, 1:200) with anti-IL18Ra (Thermoscientific, cat no. 157903, 1:100) or anti-IL-33R (Biolegend, cat no. 145303, 1:100) in the presence of Live/Dead fixable yellow dead cell stain (Invitrogen, cat no. L34959) and CD16/32 (BD, cat no. 553142).

Techniques: Staining

Journal: Nature Communications

Article Title: IKKε and TBK1 prevent RIPK1 dependent and independent inflammation

doi: 10.1038/s41467-023-44372-y

Figure Lengend Snippet: a Graphs showing spleen to body weight ratio (left panel), peripheral blood analysis assayed by differential hematology analyzer (middle panel), and ratio of CD69+ (activated) to CD62L+ (naïve) T cells amongst live CD45 + CD3+ cells, as well as the percentage of CD11b + Ly6G+ (neutrophils) amongst live CD45+ cells (right panel) in spleens of 8-13 week-old mice with the indicated genotypes. b Representative images of ileum and colon sections from 8 to 13 week-old mice with indicated genotypes immunostained for CD45 and cleaved caspase-3. Scale bars, 100 μm. c Graphs showing histological colitis and ileitis scores from 8 to 13 week-old mice with indicated genotypes. d Graphs displaying the percentage of crypts that have cleaved caspase 3 signal among 100 randomly counted crypts. Each dot represents one mouse. ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.005, ∗∗∗∗ p < 0.0001 (one-way ANOVA t-test with post-hoc multiple test). Violin plots show the median of biological replicates and interquartile range of data. Source data for a and c , d are provided as a source data file.

Article Snippet: 2×10 6 cells were stained with different set of fluorochrome conjugated antibodies: (i) anti-CD4 (eBioscience, cat no. 25-0041-81, 1:200), anti-CD8 (eBioscience, cat no. 11-0081-82, 1:100), anti-CD3e (eBioscience, cat no. 45-0031-82, 1:200), anti-CD45 (eBioscience, cat no. 67-0451-82, 1:200), anti-CD62L (eBioscience, cat no. 17-0621-82, 1:200), anti-CD69 (eBioscience, cat no. 12-0691-82, 1:200); (ii) anti-CD45 (eBioscience, cat no. 67-0451-82, 1:200), anti-Ly6G (eBioscience, cat no. 46-9668-82, 1:100), anti-CD19 (eBioscience, cat no. 78-0193-82, 1:200), anti-CD11b (BD Horizon, cat no. 562317, 1:100); (iii) anti-CD19 (eBioscience, cat no. 63-5941-82, 1:100), anti-CD3e (eBioscience, cat no. 63-0031-82, 1:100), anti-B220 (eBioscience, cat no. 63-0452-82, 1:100), anti-NK1.1(eBioscience, cat no. 63-5941-82, 1:100), anti-CD115 (BioLegend, cat no. 53-1152-82, 1:50), anti-Ly6G cat no. 46-9668-82, 1:100), anti-CD11b (BD Horizon, cat no. 562317, 1:100), (iv) anti-CD3 (Invitrogen, cat no. HM3428, 1:100), anti-Foxp3 (Thermoscientific, cat no. 12-5773-82, 1:20), anti-CD25 (BioLegend, cat no. 25-0251-82, 1:100), anti-CD4 (BioLegend, cat no. 17-0042-82, 1:100); (v) anti-CD4 (eBioscience, cat no. 25-0041-81, 1:100), anti-CD8 (eBioscience, cat no. 11-0081-82, 1:200), anti-CD3e (eBioscience, cat no. 45-0031-82, 1:200), anti-CD45 (eBioscience, cat no. 67-0451-82, 1:200); and (vi) anti-CD45 (eBioscience, cat no. 67-0451-82, 1:200) with anti-IL18Ra (Thermoscientific, cat no. 157903, 1:100) or anti-IL-33R (Biolegend, cat no. 145303, 1:100) in the presence of Live/Dead fixable yellow dead cell stain (Invitrogen, cat no. L34959) and CD16/32 (BD, cat no. 553142).

Techniques:

Journal: Cell reports

Article Title: Wnt5 controls splenic myelopoiesis and neutrophil functional ambivalency during DSS-induced colitis

doi: 10.1016/j.celrep.2024.113934

Figure Lengend Snippet:

Article Snippet: Cit-Histone3 antibody , Abcam , Cat#Ab5103; RRID:AB_304752.

Techniques: Purification, Recombinant, Lysis, Cell Isolation, Flow Cytometry, Staining, Blocking Assay, SYBR Green Assay, RNA Sequencing Assay, Software