dynamicarray 96 96 chips  (fluidigm)

Journal: Cancer metastasis reviews

Article Title: The genomic regulation of metastatic dormancy

doi: 10.1007/s10555-022-10076-w

Figure Lengend Snippet: Studies identifying dormancy-associated/regulating genomic signatures

Article Snippet: Breast , Human PDXs: HCI-001, HCI-002, HCI-010 , NOD/SCID , Orthotopic , Early-stage (low burden) vs. late-stage (high burden) metastases in lung, LN, BM, liver, brain , Fluidigm 96.96 qPCR DynamicArray chips , Upregulated: TGFR2, BCL2L1, EPHA4, AR, LGR5, IGFBP6, TGFB2, SOX2, BMI1, CXCL12, TWIST1, BCL2, NOTCH4, KRT5, POU4F1, TGFB1, THY1, CDKN1B, WNT2, SKP2, DAND5, PGR, CHEK1, CDJ3, MTOR, TP73, TGFBR3, ESR2, ESR1, MAX, NTRK2, NOTCH3, FIGF, MME, TP63, TP53, MYCN, SNAI2, ITGA6, JAG1, ACTA2 Downregulated: PTEN, TGFBR1, ERBB3, CDH1, CDK2, MUC1, VEGFA, CAV2, MYC, ITGB1, PARP2, EMP1, CD24, VIM , [ 85 ].

Techniques: In Vivo, Isolation, Microarray, Infection, Retroviral, cDNA Library Assay, shRNA, Luciferase, Selection, In Vitro

Journal: bioRxiv

Article Title: Hematopoietic stem cell requirement for macrophage regeneration is tissue-specific

doi: 10.1101/2021.04.08.439077

Figure Lengend Snippet: A. Microscopy image of the peritoneal cells after loading them into the Fluidigm C1 fluidics chip. Bright field and fluorescence microscopy images obtained after cell loading reveals the size (small vs. large) and source (RFP + LT-HSC or RFP − host) of the SPM and LPM. B. Histograms depicting the size distribution of the two main cell clusters identified by hierarchical clustering of transcription factor expression profiles, shown in D. C. t-SNE visualization of the similarity of single isolated peritoneal macrophages derived from transplanted LT-HSC (RFP + ) or host (RFP − ), based on transcription factor expression profiles. The lack of defined clusters in t-SNE map indicate that LT-HSC-derived macrophages are similar to their host-derived counterpart. D. Hierarchical clustering of transcription factor expression profiles, determined by Fluidigm Biomark single-cell multiplexed qPCR, of single-sorted peritoneal macrophages derived from transplanted LT-HSC (indicated with red bars) or host cells. Analysis yielded two main cell clusters that were identified as LPM (Cluster 1) and SPM (Cluster 2), based on their size distributions shown in B. E. Analysis of in vivo phagocytosis of pHrodo-labeled E. coli particles by LPM (I-A/I-E) and SPM (I-A/I-E + ) derived from transplanted LT-HSC (RFP + ) or host cells (RFP), 2 hr after i.p. injection. F. Quantification of in vivo phagocytosis of E. coli particles by LPM and SPM derived from transplanted LT-HSC (RFP + , red) or host cells (RFP, gray), as percentage of cells that contained phagocytosed E. coli among the specific cell type. G. Example of morphology, F4/80 expression and E. coli uptake by LPM and SPM. Data shown (E,F) are representative of 2 independent experiments and are mean + SD of 5 total mice (2 control and 3 chimeric animals).

Article Snippet: Single-cell multiplexed qPCR experiments were performed using Fluidigm’s (San Francisco, CA, USA) 96.96 qPCR DynamicArray microfluidic chips as previously described ( ).

Techniques: Microscopy, Fluorescence, Expressing, Isolation, Derivative Assay, In Vivo, Labeling, Injection, Control

Journal: Cellular and Molecular Gastroenterology and Hepatology

Article Title: Transcriptomic Dissection of Hepatocyte Heterogeneity: Linking Ploidy, Zonation, and Stem/Progenitor Cell Characteristics

doi: 10.1016/j.jcmgh.2019.08.011

Figure Lengend Snippet: Nuclearity-based dissection of 4c hepatocytes. ( A ) Microscopic identification of the nuclearity of 4c hepatocytes using the C1 microfluidics platform. A total of 106 mononucleated and 69 binucleated hepatocytes were included in this analysis. Images were taken using the BZX-710 microscope (Keyence). ( B ) PCA for mononucleated and binucleated 4c hepatocytes using 40 genes. ( C ) Violin plots of nonmonotonically expressed hepatic genes ( top ), zone 3–enriched genes ( middle ), zone 1–enriched genes ( bottom left ), and LPC marker genes ( bottom right ). P values were calculated using the Welch t test.

Article Snippet: Single-cell gene-expression experiments were performed using Fluidigm’s 96.96 or 48.48 quantitative PCR DynamicArray microfluidic chips (Fluidigm) according to the manufacturer’s instructions.

Techniques: Dissection, Microscopy, Marker