Journal: STAR Protocols

Article Title: Protocol for quantifying drug sensitivity in 3D patient-derived ovarian cancer models

doi: 10.1016/j.xpro.2024.103274

Figure Lengend Snippet:

Article Snippet: CD326 (EpCAM) antibody, anti-human, PE, REAfinity (flow cytometry 1:200) , Miltenyi Biotec , Cat# 130-110-999; RRID: AB_2657495.

Techniques: Immunofluorescence, Flow Cytometry, Control, Recombinant, Red Blood Cell Lysis, Saline, Software, Cell Culture, Plasmid Preparation, Microscopy

Journal: Frontiers in Immunology

Article Title: Impact of an Immune Modulator Mycobacterium-w on Adaptive Natural Killer Cells and Protection Against COVID-19

doi: 10.3389/fimmu.2022.887230

Figure Lengend Snippet: Relationship between NKG2C + ANK cells and COVID-19: Scatter dot with bar plot showing expression of NKG2C + ANK cells at baseline in the overall cohort (no infection, n=64 and infection, n=16), control group (no infection, n=20 and infection, n=10) and Mw group (no infection, n=44 and infection, n=6) with respect to SARS-CoV-2 infection. Black and red upside shaded triangles represent NKG2C + ANK for Control group and Mw group respectively and unshaded upside triangles represent NKG2C + ANK of both groups combined. ***p < 0.001, **p < 0.01 and *P < 0.05.

Article Snippet: For surface staining, 0.5 × 10 6 cells were washed with phosphate-buffered saline and stained with the following antibodies that were used for phenotypic analysis: CD3(APC-H7, SK-7) CD16 (PE-Cy7, B73.1), CD56 (APC R700, NCAM16.2), CD57 (BV605, NK-1), NKG2A (PE-Cy7, Z199), CD4 (APC-H7), CD8 (Per-CP Cy), CD45RA (FITC), and CD45RO (BV605), from BD Biosciences, (San Jose, CA, United States) and NKG2C (PE, REA205) from Miltenyi Biotec (Bergisch Gladbach, Germany).

Techniques: Expressing, Infection, Control

Journal: Frontiers in Immunology

Article Title: Impact of an Immune Modulator Mycobacterium-w on Adaptive Natural Killer Cells and Protection Against COVID-19

doi: 10.3389/fimmu.2022.887230

Figure Lengend Snippet: Impact of Mw on both ANK cells and iNK) cells: (A) Scatter dot with bar plot showing the expression of NKG2C + ANK cells (Mw group -n=30 and control group- n=15) and (B) NKG2A + iNK cells (Mw group-n=30 and control group- n=15) with and without of Mw vaccine at baseline and day 60. (C) Scatter dot with bar plot showing kinetics of NKG2C + ANK cells, and (D) NKG2A + iNK cells expression in Mw group (n=30) at baseline, day 30, day 60, and day 100. (E) log2FC expression of NKG2C + and NKG2A + in both Mw group (n=30) and vontrol group (n=15) at day 60 after normalization with baseline. Red upside and downside shaded triangles represent NKG2C + ANK and NKG2A + iNK, respectively, for Mw group. Black upside and downside shaded triangles represent NKG2C + ANK and NKG2A + iNK, respectively, for control group. ****p < 0.0001, **p <0.01, ***p <0.001, and ns, p-value not significant.

Article Snippet: For surface staining, 0.5 × 10 6 cells were washed with phosphate-buffered saline and stained with the following antibodies that were used for phenotypic analysis: CD3(APC-H7, SK-7) CD16 (PE-Cy7, B73.1), CD56 (APC R700, NCAM16.2), CD57 (BV605, NK-1), NKG2A (PE-Cy7, Z199), CD4 (APC-H7), CD8 (Per-CP Cy), CD45RA (FITC), and CD45RO (BV605), from BD Biosciences, (San Jose, CA, United States) and NKG2C (PE, REA205) from Miltenyi Biotec (Bergisch Gladbach, Germany).

Techniques: Expressing, Control

Journal: Frontiers in Immunology

Article Title: Impact of an Immune Modulator Mycobacterium-w on Adaptive Natural Killer Cells and Protection Against COVID-19

doi: 10.3389/fimmu.2022.887230

Figure Lengend Snippet: Impact of Mw on upregulation of NKG2C + ANK cells with respect to NKG2C expression at baseline: Scatter dot with bar plot showing the kinetics of (A) NKG2C + ANK cells (n=15) and (C) NKG2A + iNK (n=15) cells expression in Mw group at baseline, days 30 and 60 in respect to <15% NKG2C at baseline. (B) NKG2C + ANK (n=15) cells and (D) NKG2A + iNK (n=15) cell expression in Mw group at baseline, days 30 and 60 in respect to >15% NKG2C at baseline. Log2FC expression of (E) NKG2C + ANK and (F) NKG2A + iNK cells at day 60 after normalization with baseline value in Mw group (>/<15%, n=15) and control group. Red upside and downside shaded triangles represent NKG2C + ANK and NKG2A + iNK respectively for Mw group. Black upside and downside shaded triangles represent NKG2C + ANK and NKG2A + iNK, respectively, for control group. ****p < 0.0001, **p < 0.01, *p < 0.05, and ns, p-value not significant.

Article Snippet: For surface staining, 0.5 × 10 6 cells were washed with phosphate-buffered saline and stained with the following antibodies that were used for phenotypic analysis: CD3(APC-H7, SK-7) CD16 (PE-Cy7, B73.1), CD56 (APC R700, NCAM16.2), CD57 (BV605, NK-1), NKG2A (PE-Cy7, Z199), CD4 (APC-H7), CD8 (Per-CP Cy), CD45RA (FITC), and CD45RO (BV605), from BD Biosciences, (San Jose, CA, United States) and NKG2C (PE, REA205) from Miltenyi Biotec (Bergisch Gladbach, Germany).

Techniques: Expressing, Control

Journal: Frontiers in Immunology

Article Title: Impact of an Immune Modulator Mycobacterium-w on Adaptive Natural Killer Cells and Protection Against COVID-19

doi: 10.3389/fimmu.2022.887230

Figure Lengend Snippet: Mw showed sustained effect on NKG2C/NKG2A ratios until 100 days and Impact of Mw intracellular cytokine (IFN-γ) release: Scatter dot with bar plot showing (A) NKG2C/NKG2A ratio of control group (n=15) and Mw group (n=30) at baseline and day 60. (B) Kinetics of NKG2C/NKG2A ratio at baseline, days 30, 60, and 100 in Mw group. (C, D) Kinetics of NKG2C/NKG2A ratio at baseline and day 60 on the basis of >/< 15% NKG2C at baseline in Mw group and control group, respectively. (E) intracellular IFN-γ release in both control (n=5) and Mw (n=5) groups at baseline and day 60. Red and black shaded circles represent Mw group and control group, respectively. ****p < 0.0001, *p < 0.05 and ns, p-value not significant.

Article Snippet: For surface staining, 0.5 × 10 6 cells were washed with phosphate-buffered saline and stained with the following antibodies that were used for phenotypic analysis: CD3(APC-H7, SK-7) CD16 (PE-Cy7, B73.1), CD56 (APC R700, NCAM16.2), CD57 (BV605, NK-1), NKG2A (PE-Cy7, Z199), CD4 (APC-H7), CD8 (Per-CP Cy), CD45RA (FITC), and CD45RO (BV605), from BD Biosciences, (San Jose, CA, United States) and NKG2C (PE, REA205) from Miltenyi Biotec (Bergisch Gladbach, Germany).

Techniques: Control

Journal: Frontiers in Immunology

Article Title: Impact of an Immune Modulator Mycobacterium-w on Adaptive Natural Killer Cells and Protection Against COVID-19

doi: 10.3389/fimmu.2022.887230

Figure Lengend Snippet: Impact of the second dose of Mw on ANK and INK cells: Scatter dot with bar plot showing expression of (A) NKG2C + ANK (day 60, single dose; n=17, double dose; n=12 and day 100, single dose; n=17, double dose; n=12), (B) NKG2A + iNK cells (day 60, single dose; n=12, double dose; n=12 and day 100, single dose; n=17, double dose; n=12) and (C) NKG2C/NKG2A (day 60, single dose; n=17, double dose; n=12 and day 100, single dose; n=17, double dose; n=12) ratio with respect to single and double dose of Mw vaccine at day 60 and 100. Red upside and downside shaded triangles represent NKG2C + ANK and NKG2A + iNK, respectively, for Mw group. Red-shaded circle represents Mw group. ***p < 0.001, *p < 0.05 and ns, p value not significant.

Article Snippet: For surface staining, 0.5 × 10 6 cells were washed with phosphate-buffered saline and stained with the following antibodies that were used for phenotypic analysis: CD3(APC-H7, SK-7) CD16 (PE-Cy7, B73.1), CD56 (APC R700, NCAM16.2), CD57 (BV605, NK-1), NKG2A (PE-Cy7, Z199), CD4 (APC-H7), CD8 (Per-CP Cy), CD45RA (FITC), and CD45RO (BV605), from BD Biosciences, (San Jose, CA, United States) and NKG2C (PE, REA205) from Miltenyi Biotec (Bergisch Gladbach, Germany).

Techniques: Expressing

Journal: eLife

Article Title: The transcription factor RUNX2 drives the generation of human NK cells and promotes tissue residency

doi: 10.7554/eLife.80320

Figure Lengend Snippet: ( A ) Expression of tissue-resident (CD69, CD49a, CXCR4) and circulation-specific factors (CD49e, CX3CR1, CCR7, CD62L, S1PR1) in NK cells of RUNX2(-I) knockdown and overexpression cultures, was checked with flow cytometry (mean ± SEM; n=4). Histograms display expression of markers in representative donors. ( B ) Percentage of NK cells with a circulatory (EOMES low T-BET high ) or tissue-resident (EOMES high T-BET low ) phenotype, determined by flow cytometry (mean ± SEM; n=4). Dot plots represent typical samples. ( C ) The expression of NK cell receptors NKp44, NKp46, NKG2C, NKG2A, CD94, KIR2DL1, KIR2DS1, KIR2DL2, KIR2DL3, KIR3DL1, KIR3DS1, and KIR2DS4 in gated NK cells from RUNX2(-I) knockdown and overexpression cultures was measured with flow cytometry (mean ± SEM; n=3–9). Statistical significance was determined using the paired Student's t-test. *, **, and *** represent statistical significance compared to control-transduced cultures with p<0.05, p<0.01, and p<0.001, respectively.

Article Snippet: NKG2A , CD159a , Allophycocyanin (APC) , REA110 , Miltenyi Biotec, Leiden, The Netherlands.

Techniques: Expressing, Knockdown, Over Expression, Flow Cytometry, Control

Journal: eLife

Article Title: The transcription factor RUNX2 drives the generation of human NK cells and promotes tissue residency

doi: 10.7554/eLife.80320

Figure Lengend Snippet: ( A ) Tracks of gene loci of RUNX2 ChIP-seq, histone (H3K27ac and H3K4me3) ChIP-seq, and ATAC-seq of PB NK cells are presented for gene loci of tissue-resident (top panel) markers and circulatory associated markers (bottom panel). ( B ) Tracks of gene loci of NK cell receptors NCR2/NKp44, NCR1/NKp46, KLRC2/NKG2C, KIR2DS4, KLRC1/NKG2A, KLRD1/CD94, KIR2DL3, KIR3DL1, and KIR2DL4 are depicted. ( A–B ) Significant RUNX2 ChIP peaks are marked in green and those that also contain a RUNX2 motif are highlighted in pink.

Article Snippet: NKG2A , CD159a , Allophycocyanin (APC) , REA110 , Miltenyi Biotec, Leiden, The Netherlands.

Techniques: ChIP-sequencing

Journal: eLife

Article Title: The transcription factor RUNX2 drives the generation of human NK cells and promotes tissue residency

doi: 10.7554/eLife.80320

Figure Lengend Snippet: Antibodies and kits used in flow cytometric analysis.

Article Snippet: NKG2A , CD159a , Allophycocyanin (APC) , REA110 , Miltenyi Biotec, Leiden, The Netherlands.

Techniques: Marker, Blocking Assay, Staining