Journal: Cell reports

Article Title: Heterogeneity and transcriptional drivers of triple-negative breast cancer

doi: 10.1016/j.celrep.2023.113564

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Mouse monoclonal anti-cPARP (164Dy) , BD Biosciences , Cat# 552596; RRID: AB_394437.

Techniques: Recombinant, Mass Spectrometry, shRNA, Plasmid Preparation

Journal: Cell Reports

Article Title: COX2 regulates senescence secretome composition and senescence surveillance through PGE 2

doi: 10.1016/j.celrep.2021.108860

Figure Lengend Snippet:

Article Snippet: Mouse anti-CX3CR1-164Dy , Fluidigm , # 3164023B, RRID: AB_2832247.

Techniques: Recombinant, Enzyme-linked Immunosorbent Assay, Plasmid Preparation, Software, Sequencing

Journal: Cell reports

Article Title: Mass Cytometry Reveals Global Immune Remodeling with Multi-lineage Hypersensitivity to Type I Interferon in Down Syndrome

doi: 10.1016/j.celrep.2019.10.038

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Mouse monoclonal anti-human CD45RO (clone UCHL1) , Fluidigm , Cat#3164007B; RRID:AB_2811092.

Techniques: Recombinant, Mass Cytometry, Software

Journal: Cell

Article Title: NKG2A blockade potentiates CD8 T-cell immunity induced by cancer vaccines

doi: 10.1016/j.cell.2018.10.028

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: CD’S’ – 164 Dy (HP-3G10) , Fluidigm , Prod#: 3164009B; RRID: AB_2687651.

Techniques: Blocking Assay, Purification, Recombinant, Staining, Transfection, Cell Stimulation, Mutagenesis, Transgenic Assay, Marker, Sequencing, Expressing, Plasmid Preparation, Software, CRISPR

Journal: STAR Protocols

Article Title: CyTOF protocol for immune monitoring of solid tumors from mouse models

doi: 10.1016/j.xpro.2022.101949

Figure Lengend Snippet:

Article Snippet: Anti-Mouse CD62L-164Dy dilution 1:100 , Standard BioTools , 3164003B.

Techniques: Blocking Assay, Purification, Recombinant, Staining, Sterility, Antibody Labeling, Software, Transferring, Microscopy

Journal: bioRxiv

Article Title: SCA-1 micro-heterogeneity in the fate decision of dystrophic fibro/adipogenic progenitors

doi: 10.1101/2020.05.14.096438

Figure Lengend Snippet: (A) Schematic representation of the workflow applied to study FAP heterogeneity. (B) Representative viSNE maps of total mononuclear cells isolated from young wild type and mdx mice. The four clusters produce by FlowSOM algorithm were mapped onto the viSNE maps and correspond to the following mononuclear cell populations: FAPs (blue), endothelial cells (orange), leukocytes (green) and muscle satellite cells (MuSCs, red). (C) Representative Self Organizing Maps (SOMs) of FAPs identified in (A). SOMs were obtained with the FlowSOM algorithm. Each node represents a cluster of cells, nodes with similar expression profile are linked by an edge. Colour of nodes indicate SCA-1 expression level. Node outlines indicate the four metaclusters (red, blue, black and green) obtained by the algorithm. Red and blue shadings highlight FAPs expressing high levels (red and blue metaclusters, called SCA1-High-FAPs) and low levels (black and green metaclusters, called SCA1-Low-FAPs) of SCA-1. (D) Stacked bar plot showing the fraction of SCA1-High-FAPs and SCA1-Low-FAPs in wild type and mdx mice. Data are presented as mean ± SEM. Statistical significance was estimated by a One-way ANOVA, * p ≤ 0.05, ** p ≤ 0.01. n = 4. (E) Representative SCA-1 histograms of FAPs from wild type and mdx mice identified in (B) and their standard deviations (SD) showing a typical micro-heterogeneity profile. (F) Sorting strategy to decompose SCA-1 micro-heterogeneity and to isolate SCA1-High-FAPs and SCA1-Low-FAPs from mdx mice. Complete strategy, Fluorescence minus one (FMO) controls and cell states purity in Supplementary Figure 3.

Article Snippet: The full list of antibodies purchased from Fluidigm is: anti-CD45 89Y (3089005B); anti-CD146 141Pr (3155006B); anti-cleaved CASP-3 142Nd (3142004A); anti-CD34 144Nd (3143009B); anti-phospho-EGFR 146Nd (3146007A); anti-CD140a 148Nd (3148018B); anti-pRB 150Nd (3150013A); anti-CD140b 151Eu (3151017B); anti-Vimentin 154Sm (3154014A); anti-CD90.2 156Gd (3156006B); anti-phospho-STAT3 158Gd (3158005A); anti-CXCR-4 159Tb (3159030B); anti-Integrin alpha-7 161Dy (67-0010-05); anti-SCA-1 164Dy (3164005B); anti-phospho-CREB-1 176Yb (3176005A); DNA1 191Ir and DNA2 193Ir (201192A); Cisplatin 195Pt (201194); anti-CD31 165Ho (3165013B); anti-Actin 175Lu (3175026A); anti-c-kit 166Er (3166004B).

Techniques: Isolation, Expressing, Fluorescence

Journal: bioRxiv

Article Title: SCA-1 micro-heterogeneity in the fate decision of dystrophic fibro/adipogenic progenitors

doi: 10.1101/2020.05.14.096438

Figure Lengend Snippet: (A) SCA-1 histograms of the whole FAP compartment (left), freshly isolated cell states (middle) and cell states expanded 9 days in Cytogrow (right). FAP compartment was analysed as followed: CD45 - CD31 - cells isolated by MACS were stained with antibodies against Integrin alpha-7 and SCA-1; next a gating strategy (Supplemetary Figure 4B; unstained cells in Supplementary Figure 4A) was applied to obtain Integrin alpha-7 - SCA-1 + cells. Cell states were isolated as described and then analysed by flow cytometry (gating strategy in Supplementary Figure 4D and 4E for SCA1-High-FAPs and SCA1-Low-FAPs respectively; controls in Supplementary Figure 4C). n =3. (B) Representative crop of micrographs of SCA1-High-FAPs (left) and SCA1-Low-FAPs (right) cultured ex vivo . Cytoplasms were stained with CFSE (yellow) and nuclei were counterstained with Hoechst 33342 (blue). Scale bar 50 μm. (C), (D) and (E) Box plots representing CFSE positive area, aspect ratio (AR) and roundness of SCA1-High-FAPs (n = 96) and SCA1-Low-FAPs (n = 94) from three different biological replicates. Whiskers are minimum and maximum values of the distribution. Statistical significance was estimated by a two tailed Mann-Whitney test after a normality test.

Article Snippet: The full list of antibodies purchased from Fluidigm is: anti-CD45 89Y (3089005B); anti-CD146 141Pr (3155006B); anti-cleaved CASP-3 142Nd (3142004A); anti-CD34 144Nd (3143009B); anti-phospho-EGFR 146Nd (3146007A); anti-CD140a 148Nd (3148018B); anti-pRB 150Nd (3150013A); anti-CD140b 151Eu (3151017B); anti-Vimentin 154Sm (3154014A); anti-CD90.2 156Gd (3156006B); anti-phospho-STAT3 158Gd (3158005A); anti-CXCR-4 159Tb (3159030B); anti-Integrin alpha-7 161Dy (67-0010-05); anti-SCA-1 164Dy (3164005B); anti-phospho-CREB-1 176Yb (3176005A); DNA1 191Ir and DNA2 193Ir (201192A); Cisplatin 195Pt (201194); anti-CD31 165Ho (3165013B); anti-Actin 175Lu (3175026A); anti-c-kit 166Er (3166004B).

Techniques: Isolation, Staining, Flow Cytometry, Cell Culture, Ex Vivo, Two Tailed Test, MANN-WHITNEY

Journal: bioRxiv

Article Title: SCA-1 micro-heterogeneity in the fate decision of dystrophic fibro/adipogenic progenitors

doi: 10.1101/2020.05.14.096438

Figure Lengend Snippet: (A) Experimental design to induce adipogenic differentiation of mdx FAP cell states. GM = growth medium; AIM = adipogenic induction medium; MM = maintenance medium. (B) and (C) Bar plots showing the percentage of ORO positive cells and PPAR-gamma positive cells per field. AM = adipogenic medium (AM = AIM + MM). n = 4. Statistical analysis was performed by a Two-way ANOVA. (D) Representative micrographs of (B) and (C). Cells were immunolabelled for PPAR-gamma (yellow) and nuclei were counterstained with Hoechst 33342 (blue). Lipid droplets were stained with ORO (red). (E) Experimental design applied to obtain fully differentiated adipocytes. (F) Bar plot indicating the percentage of ORO positive cells. n = 3. Statistical significance was calculated through a Student t-test. (G) Representative micrographs of (F). Lipid droplets in red (ORO staining) and nuclei in blue (Hoechst 33342). (H) Representative viSNE maps showing the expression of SCA-1 and phospho-CREB-1 assessed by mass cytometry in FAPs isolated from mdx mouse by MACS and cultured 72 hours either in GM or AIM. (I) Cluster 1 (in blue) and cluster 2 (in orange) obtained applying the FlowSOM algorithm and then mapped onto viSNE maps. (J) Plot representing the expression in arbitrary units of SCA-1 and phospho-CREB-1 identified in (J). (H) Representative viSNE maps of FAPs isolated by MACS from mdx mice and then incubated either to GM or to AIM. The upper maps show expression level of SCA-1, while the lower maps show the level of phospho-CREB-1. n = 3. (I) Representative viSNE maps showing the two clusters produced by the clustering approach. (J) Dot plot showing the expression level of SCA-1 and the level of phospho-CREB-1 (both in arbitrary units) in the metaclusters from (I). Data are presented as mean ± SEM. ** p ≤ 0.01, *** p ≤ 0.001. Scale bars 100 μm.

Article Snippet: The full list of antibodies purchased from Fluidigm is: anti-CD45 89Y (3089005B); anti-CD146 141Pr (3155006B); anti-cleaved CASP-3 142Nd (3142004A); anti-CD34 144Nd (3143009B); anti-phospho-EGFR 146Nd (3146007A); anti-CD140a 148Nd (3148018B); anti-pRB 150Nd (3150013A); anti-CD140b 151Eu (3151017B); anti-Vimentin 154Sm (3154014A); anti-CD90.2 156Gd (3156006B); anti-phospho-STAT3 158Gd (3158005A); anti-CXCR-4 159Tb (3159030B); anti-Integrin alpha-7 161Dy (67-0010-05); anti-SCA-1 164Dy (3164005B); anti-phospho-CREB-1 176Yb (3176005A); DNA1 191Ir and DNA2 193Ir (201192A); Cisplatin 195Pt (201194); anti-CD31 165Ho (3165013B); anti-Actin 175Lu (3175026A); anti-c-kit 166Er (3166004B).

Techniques: Staining, Expressing, Mass Cytometry, Isolation, Cell Culture, Incubation, Produced

Journal: bioRxiv

Article Title: SCA-1 micro-heterogeneity in the fate decision of dystrophic fibro/adipogenic progenitors

doi: 10.1101/2020.05.14.096438

Figure Lengend Snippet: (A) viSNE map representing the different clusters identified as distinct cell populations according to the expression of specific biomarkers. Identified populations are: Myocytes, B-cells, FAPs, Smooth Muscle cells, MuSCs, Endothelial Cells, Macrophages, T-cells, Tenocytes and Neurons. (B) The FAPs population subset has been re-clustered, leading to 4 distinct clusters according to their gene expression profile. The four clusters (0, 1, 2, 3) were mapped onto the viSNE map of FAPs. (C) The expression of SCA-1 antigen has been mapped to each cell of the dataset. (D) viSNE map of FAPs in which clusters 0, 2, 3 are collapsed together to obtain two clusters expressing high level (SCA-1 High) and low level (SCA-1 Low) of SCA-1. (E) Stacked bar plot showing the percentage of the two population on the basis of SCA-1 expression levels across different ages.

Article Snippet: The full list of antibodies purchased from Fluidigm is: anti-CD45 89Y (3089005B); anti-CD146 141Pr (3155006B); anti-cleaved CASP-3 142Nd (3142004A); anti-CD34 144Nd (3143009B); anti-phospho-EGFR 146Nd (3146007A); anti-CD140a 148Nd (3148018B); anti-pRB 150Nd (3150013A); anti-CD140b 151Eu (3151017B); anti-Vimentin 154Sm (3154014A); anti-CD90.2 156Gd (3156006B); anti-phospho-STAT3 158Gd (3158005A); anti-CXCR-4 159Tb (3159030B); anti-Integrin alpha-7 161Dy (67-0010-05); anti-SCA-1 164Dy (3164005B); anti-phospho-CREB-1 176Yb (3176005A); DNA1 191Ir and DNA2 193Ir (201192A); Cisplatin 195Pt (201194); anti-CD31 165Ho (3165013B); anti-Actin 175Lu (3175026A); anti-c-kit 166Er (3166004B).

Techniques: Expressing

Journal: bioRxiv

Article Title: SCA-1 micro-heterogeneity in the fate decision of dystrophic fibro/adipogenic progenitors

doi: 10.1101/2020.05.14.096438

Figure Lengend Snippet: Two FAP cell states expressing high and low levels of SCA-1 respectively were isolated from the hind limb muscles of mdx mice. The two cell states were tested for their differentiation and proliferation properties in vitro . SCA1-High-FAPs are more proliferating and more adipogenic cells in comparison with SCA1-Low-FAPs. Leukocytes from old dystrophic mice strongly inhibit adipogenesis in SCA1-Low-FAPs while are less effective on SCA1-High-FAPs.

Article Snippet: The full list of antibodies purchased from Fluidigm is: anti-CD45 89Y (3089005B); anti-CD146 141Pr (3155006B); anti-cleaved CASP-3 142Nd (3142004A); anti-CD34 144Nd (3143009B); anti-phospho-EGFR 146Nd (3146007A); anti-CD140a 148Nd (3148018B); anti-pRB 150Nd (3150013A); anti-CD140b 151Eu (3151017B); anti-Vimentin 154Sm (3154014A); anti-CD90.2 156Gd (3156006B); anti-phospho-STAT3 158Gd (3158005A); anti-CXCR-4 159Tb (3159030B); anti-Integrin alpha-7 161Dy (67-0010-05); anti-SCA-1 164Dy (3164005B); anti-phospho-CREB-1 176Yb (3176005A); DNA1 191Ir and DNA2 193Ir (201192A); Cisplatin 195Pt (201194); anti-CD31 165Ho (3165013B); anti-Actin 175Lu (3175026A); anti-c-kit 166Er (3166004B).

Techniques: Expressing, Isolation, In Vitro