rnascope tm negative control probe dapb (of bacillus subtilis strain)  (Advanced Cell Diagnostics Inc)

Journal: Bio-protocol

Article Title: Single Molecule Fluorescence In Situ Hybridization Using RNAscope to Study Hematopoietic and Vascular Interactions in the Zebrafish Embryo and Larva

doi: 10.21769/BioProtoc.5269

Figure Lengend Snippet: . Top panel: schematic representation of a 48 hpf embryo (reproduced with modifications from [16]); red line = aorta (from which hematopoietic stem cell precursors emerge); blue line = vein (showing particularly the vein plexus, constituting the CHT). The embryo used expresses eGFP under the control of the vascular kdrl promotor [ Tg(kdrl: eGFP) fish line]. Bottom panels: spinning disk confocal images obtained either in the trunk region (left: AGM) or in the tail region (right: CHT). Images shown were obtained either from maximal z-projections of z-stacks or from single z-sections with 3× magnification of regions in white boxes. Green channel: vascular cells expressing soluble eGFP [aortic and vein endothelial cells, including cells of the hemogenic endothelium (HE; white arrows) in the trunk and tail regions] as well as newly born HSPCs (white asterisks). Magenta: RNAscope spots indicating expression of cmyb mRNAs in the HE and in HSPCs. Note the presence of RNAscope spots in the trunk (top left image) and in the gut region (magenta arrows) that indicate the potential expression of cmyb in more differentiated patrolling immune cells. AGM: aorta gonad mesonephros; CHT: caudal hematopoietic tissue; HSPCs: hematopoietic stem and progenitor cells. Scale bars = 20 μm.

Article Snippet: RNAscope TM negative control probe DapB (of Bacillus subtilis strain) (ACD BioTechne, catalog numbers: 310043, 310043-C2, 310043-C3 for the three channels C1, C2, and C3, respectively) 13.

Techniques: Control, Expressing, RNAscope

Journal: Bio-protocol

Article Title: Single Molecule Fluorescence In Situ Hybridization Using RNAscope to Study Hematopoietic and Vascular Interactions in the Zebrafish Embryo and Larva

doi: 10.21769/BioProtoc.5269

Figure Lengend Snippet: Spinning disk confocal images obtained with a 5 dpf larva [ Tg(kdrl:eGFP ) fish line] expressing eGFP in endothelial cells under the control of the vascular kdrl promotor. Images show the pronephros region with a maximal z-projection (left) of a z-stack encompassing a total of 240 sections, each interspaced by 0.5 μm, and z-sections (right: images of sections 52/240, 86/240, 186/240, and 222/240 from top to bottom, respectively). The cmyb RNAscope signals (magenta) correspond to hematopoietic stem and progenitor cells (HSPCs) accumulated in the peri-glomerular region (white arrow), surrounded by vessels. Note the more distant localization of cmyb signals (magenta arrows, hypothetically in HSPCs) along vessels (green arrows). This unveils the potential complexity of the pronephros niche. ISV = intersegmental vessel. This z-stack is also visualized in and reconstituted in 3D using Imaris in . Note also the nonspecific capture of the dye in the notochord, which facilitated the localization of the glomerulus. Scale bars = 20 μm.

Article Snippet: RNAscope TM negative control probe DapB (of Bacillus subtilis strain) (ACD BioTechne, catalog numbers: 310043, 310043-C2, 310043-C3 for the three channels C1, C2, and C3, respectively) 13.

Techniques: Expressing, Control, RNAscope

Journal: Bio-protocol

Article Title: Single Molecule Fluorescence In Situ Hybridization Using RNAscope to Study Hematopoietic and Vascular Interactions in the Zebrafish Embryo and Larva

doi: 10.21769/BioProtoc.5269

Figure Lengend Snippet: Spinning disk confocal images obtained with a 5 dpf larva [ Tg(runx1+23:eGFP ) fish line] expressing eGFP in HSPCs under the control of the runx1+23 enhancer. Panels are constituted from images obtained either in the trunk region (left: AGM) or in the tail (right: CHT), either from maximum z-projections of z-stacks or from single z-sections with 2× magnification of regions in white boxes, highlighting hematopoietic clusters (dashed lines). RNAscope signals (magenta) colocalize in the majority with HSPCs (see also Figure 7 and for 3D reconstitution). AGM: aorta gonad mesonephros; CHT: caudal hematopoietic tissue; HSPCs: hematopoietic stem and progenitor cells. Scale bars = 20 μm.

Article Snippet: RNAscope TM negative control probe DapB (of Bacillus subtilis strain) (ACD BioTechne, catalog numbers: 310043, 310043-C2, 310043-C3 for the three channels C1, C2, and C3, respectively) 13.

Techniques: Expressing, Control, RNAscope

Journal: Bio-protocol

Article Title: Single Molecule Fluorescence In Situ Hybridization Using RNAscope to Study Hematopoietic and Vascular Interactions in the Zebrafish Embryo and Larva

doi: 10.21769/BioProtoc.5269

Figure Lengend Snippet: All data shown are extracted from a single caudal hematopoietic tissue (CHT) z-stack showing the expression of cmyb (RNAscope, spots in magenta) in hematopoietic cells expressing eGFP under the control of the runx1+23 enhancer (the same 5 dpf larva and images as in Figure 6). (A) File conversion with Imaris File Converter. (B) Imaris 3D visualization in surpass mode. (C) Step-by-step workflow of cell segmentation, as detailed in Data Analysis, Section B. 3D cells and RNAscope signal segmentation with Imaris – Cell Biologist package .

Article Snippet: RNAscope TM negative control probe DapB (of Bacillus subtilis strain) (ACD BioTechne, catalog numbers: 310043, 310043-C2, 310043-C3 for the three channels C1, C2, and C3, respectively) 13.

Techniques: Expressing, RNAscope, Control

Journal: Bio-protocol

Article Title: Single Molecule Fluorescence In Situ Hybridization Using RNAscope to Study Hematopoietic and Vascular Interactions in the Zebrafish Embryo and Larva

doi: 10.21769/BioProtoc.5269

Figure Lengend Snippet: . Top panel: schematic representation of a 5 dpf larva (reproduced with modifications from [16]); red line = aorta; blue line = vein. The larva used expresses eGFP under the control of the vascular kdrl promotor [ Tg(kdrl: eGFP) fish line]. Bottom panels: spinning disk confocal images obtained either in the trunk region (left: AGM) or in the tail region (right: CHT). Images shown were obtained either from maximal z-projections of z-stacks or from single z-sections with 1.5× magnification of regions in white boxes. Green channel: vascular cells expressing soluble eGFP (aortic and veinous endothelial cells in the trunk and tail regions). Magenta: RNAscope spots indicating expression of cmyb mRNAs in HSPCs. Note that RNAscope signals cannot be superposed to individual cells because HSPCs are no longer expressing eGFP driven by the vascular kdrl promoter, as is the case in 48 hpf embryos (owing to distant timing from their emergence, half-life of eGFP, and division cycles diluting the fluorescent protein). Note the structural evolution of the vein niche, notably in the CHT, in comparison with the 48 hpf embryo shown in Figure 3, and the relatively regular positioning of hematopoietic clusters (delimited by dashed lines in the bottom right image). AGM: aorta gonad mesonephros; CHT: caudal hematopoietic tissue; HSPCs: hematopoietic stem and progenitor cells. Scale bars = 20 μm.

Article Snippet: RNAscope TM negative control probe DapB (of Bacillus subtilis strain) (ACD BioTechne, catalog numbers: 310043, 310043-C2, 310043-C3 for the three channels C1, C2, and C3, respectively) 13.

Techniques: Control, Expressing, RNAscope, Comparison

Journal: Bio-protocol

Article Title: Single Molecule Fluorescence In Situ Hybridization Using RNAscope to Study Hematopoietic and Vascular Interactions in the Zebrafish Embryo and Larva

doi: 10.21769/BioProtoc.5269

Figure Lengend Snippet: Top images show Ibidi dishes, with the recommended dissection area on the top and the agarose mounting area at the bottom (white rectangles). 48 hpf embryos (a, b) and 5 dpf larvae (a’, b’) were either (a, a’) or not (b, b’) treated with proteinase K and all of them with RNAscope reagents. Images show that the whole procedure leads to virtually total transparency of the specimen, which reaches a maximum for embryos [becoming barely visible as in (a)]. This transparency requires controlling all steps of reagent/buffer removal under the binoculars. Yolks were dissected, as well as the eyes facing the glass bottom of the dish to ensure flatness.

Article Snippet: RNAscope TM negative control probe DapB (of Bacillus subtilis strain) (ACD BioTechne, catalog numbers: 310043, 310043-C2, 310043-C3 for the three channels C1, C2, and C3, respectively) 13.

Techniques: Dissection, RNAscope

Journal: Bio-protocol

Article Title: Single Molecule Fluorescence In Situ Hybridization Using RNAscope to Study Hematopoietic and Vascular Interactions in the Zebrafish Embryo and Larva

doi: 10.21769/BioProtoc.5269

Figure Lengend Snippet: All data plotted are extracted from a single caudal hematopoietic tissue (CHT) z-stack showing the expression of cmyb (RNAscope spots) in hematopoietic cells expressing eGFP under the control of the runx1+23 enhancer. (A) Imaris Vantage 2D plotting, cell number of RNAscope spots relative to the cell area (µm). (B) Imaris vantage cumulative distribution function (CDF) plotting, cumulative number of spots percentage relative to the shortest distance to cell surface (µm). Solid pink line: our data; dashed pink line and light pink interval: confidence interval’s random distribution; red vertical line: calculated attraction distance. (C) Data extraction from Imaris and plotting in R studio using the ggstatsplot package. Top plot shows the correlation between cell size (µm) and number of spots per cell. Bottom plot shows the number of spots per cell depending on cell size [large cell > 11,490 voxels (corresponding to the median cell size), small cells < 11,490 voxels]. The code to generate the plots is given in Data analysis, section C.

Article Snippet: RNAscope TM negative control probe DapB (of Bacillus subtilis strain) (ACD BioTechne, catalog numbers: 310043, 310043-C2, 310043-C3 for the three channels C1, C2, and C3, respectively) 13.

Techniques: Expressing, RNAscope, Control, Extraction

Journal: Cell reports

Article Title: Glial progenitor heterogeneity and key regulators revealed by single-cell RNA sequencing provide insight to regeneration in spinal cord injury

doi: 10.1016/j.celrep.2023.112486

Figure Lengend Snippet: (A) Intermediate cells (arrows) assessed by the colocalization of tdT, GFAP (blue), and PDGFRα (green) in all the groups. Images were captured (A1) in the ventral column at 600–800 μm from epicenter in sham, 7 dpi, and SCI1M, and (A2) in ventral horn (GM) and lateral column (WM). (B) Intermediate cells with proliferation markers (arrows) identified by the colocalization of tdT (red), GFAP (blue), PDGFRα (green), and proliferative marker Ki67 (white) in ventral horn or ventral column at 600 μm (7 dpi) and 1,000 μm (SCI1M) caudal from epicenter. (C) Combined RNAscope and immunofluorescence of Ifit3 (red), S100b (blue), and PDGFRα (green) expression in intermediate cells with inflammation markers (arrows) in ventral horn at the segment adjacent to the injury site. (D and E) Cells with myeloid marker assessed by CD68 (green, D) or IBA1 (green, E) expression in tdT+ GFAP-expressing cells (red) at lateral horn or lateral column at 7 dpi (D1, at 200 μm rostral from the epicenter; D2, at the epicenter; E1, at 800 μm caudal from the epicenter; E2, at 400 μm caudal from the epicenter). (F and G) The expression pattern of phagocytosis gene Mertk at acute (F) and sub-chronic (G) stages. Scale bar, 10 μm (A, B, D, and E); scale bar (orthogonal views in A, and C), 5 μm.

Article Snippet: RNAscope negative control probe DapB , Advanced Cell Diagnostics , 310043.

Techniques: Marker, RNAscope, Immunofluorescence, Expressing

Journal: Cell reports

Article Title: Glial progenitor heterogeneity and key regulators revealed by single-cell RNA sequencing provide insight to regeneration in spinal cord injury

doi: 10.1016/j.celrep.2023.112486

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: RNAscope negative control probe DapB , Advanced Cell Diagnostics , 310043.

Techniques: Purification, Recombinant, RNAscope, Multiplex Assay, Negative Control, Sequencing, Software, Flow Cytometry, Microscopy