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Lab products found in correlation

Lsm 510 meta, by Zeiss (2 mentions) Zen software, by Zeiss (2 mentions) Lsm 700, by Zeiss (2 mentions) Alexa fluor 488, by Thermo Fisher Scientific (2 mentions) Lsm 510, by Zeiss (2 mentions) Lsm 880, by Zeiss (2 mentions) Immersol 518f, by Zeiss (1 mentions) Histovt one, by Nacalai Tesque (1 mentions) Vectashield, by Vector Laboratories (1 mentions) Meta501, by Zeiss (1 mentions) Lsm 800, by Zeiss (1 mentions) Prism software, by GraphPad (1 mentions) Lysotracker red dnd 99, by Thermo Fisher Scientific (1 mentions) Uorescence microscopy, by Zeiss (1 mentions) 5 live, by Zeiss (1 mentions) Slowfade gold antifade with dapi, by Thermo Fisher Scientific (1 mentions) Anti rabbit igg secondary antibody, by Thermo Fisher Scientific (1 mentions) Bx51 microscope, by Olympus (1 mentions) Lsm 510 confocal microscope, by Zeiss (1 mentions) Zen 3, by Zeiss (1 mentions)

8 protocols using image browser

1

Visualizing N-cadherin Dynamics in Neural Crest Cells

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At the eight-cell stage, HaloTag N-cadherin mRNA (500 pg/embryo) and membrane-mCherry mRNA (300 pg/embryo) were injected, and the embryos were cultured until stage 19. HaloTag-N-cadherin–expressing NC explants were dissected and preincubated for 30 min at room temperature with Alexa Fluor 488–nonpermeable HaloTag ligand solution in 1× Marc’s modified Ringer (MMR; 1:1,000, Promega; Los and Wood, 2007 (link)), and the excess ligands were washed. Then labeled NC cells were cultured on fibronectin-coated coverslips (Tissue Tek II; Nalgene), and time-lapse imagining was performed (LSM 510 Meta; Carl Zeiss) immediately after cell attachment. The lens used for this imaging was a Plan-Apochromat 63×/1.4 oil objective. The temperature was ∼23°C. The imaging medium was Immersol 518F (Carl Zeiss). Images were obtained and analyzed with LSM 510 version 3.2 microscope operation software and Zeiss Image Browser (both from Carl Zeiss).
Kuriyama S., Theveneau E., Benedetto A., Parsons M., Tanaka M., Charras G., Kabla A, & Mayor R. (2014). In vivo collective cell migration requires an LPAR2-dependent increase in tissue fluidity. The Journal of Cell Biology, 206(1), 113-127.
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2

Immunohistochemistry of Hippocampal Cryosections

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Cryosections were processed for immunohistochemistry as described previously (Ohyama et al., 2005 (link); Seki et al., 2014 (link)). Briefly, cryosection of the hippocampus were incubated with primary antibodies overnight at 4°C. For some antibody labeling experiments (Ki67, phospho-vimentin), antigen retrieval with Histo VT One (Nacalai, Japan) was carried out following manufacturer’s instructions. After wash with PBS three times, the sections were incubated with secondary antibodies for 45 min at room temperature. After wash with PBS three times, the sections were mounted with Vectashield (Vector lab). Images were taken with a Zeiss confocal microscope LSM700. In some cases, fluorescence images were digitally zoomed at 0.5x to 2x. Stacks of optical sections (1.8 μm in thickness/optical section) were obtained at 0.9 μm increments on the z-axis using x20 objective. The images were corrected for brightness and contrast and composed using Zeiss Image Browser, ZEN software (Zeiss, Thomwood, NY) and Adobe Photoshop CS6 (San Jose, CA). Mice (n = 3–6) were examined for individual experiments, and, for quantification of some experiments, 9 sections at least were analyzed for each using Fiji of image J. Mean ± SE was indicated in the results.
Ohyama K., Shinohara H.M., Omura S., Kawachi T., Sato T, & Toda K. (2023). PSmad3+/Olig2− expression defines a subpopulation of gfap-GFP+/Sox9+ neural progenitors and radial glia-like cells in mouse dentate gyrus through embryonic and postnatal development. Frontiers in Neuroscience, 17, 1204012.
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3

Immunohistochemistry and Confocal Imaging Protocols

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Immunohistochemistry followed the methods described in17 (link). See Supplementary data for antisera used. For comparison of TH, CART and EYFP immunoreactivity, confocal images were taken on a Zeiss Meta 501 scanning confocal microscope. For comparing TH, Ki67 and PNMT immunoreactivity in Nrk mutant mice, confocal images were taken on a Zeiss LSM 800 confocal microscope. All images were processed by Zeiss Image Browser (v4.0.0241, Carl Zeiss Microimaging). Graphs were prepared by using Numbers software (version 3.6.2, Apple Inc.) or Prism software (version 7.0a, GraphPad). Statistically analysis was performed with Prism 7 software using two-way ANOVA for gene expression pattern, linear regression for correlation analysis, and chi-squared test for Nrk loss-of function analysis.
Chan W.H., Komada M., Fukushima T., Southard-Smith E.M., Anderson C.R, & Wakefield M.J. (2019). RNA-seq of Isolated Chromaffin Cells Highlights the Role of Sex-Linked and Imprinted Genes in Adrenal Medulla Development. Scientific Reports, 9, 3929.
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4

Lysosome Tracking in Recombinant Strains

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Recombinant and mock strains were cultured in SD and SG medium. The cells were washed with PBS buffer and stained with 100 nM Lyso-Tracker Red DND-99 (Molecular Probes, Leiden, The Netherlands) in PBS for 30 °C for 10 min. All strains were washed by PBS twice, and the intensity of protein expression observed by uorescence microscopy (Zeiss, Germany). Fluorescent images were analyzed using the Zeiss image Browser.
Park D.J., Nguyen N., Kim J.H., Nguyen N., Kim S.C., Cho B., Kim Y., & Min J. (2020). Quick Delivery of Aldehyde Dehydrogenase into Yeast Vacuoles by QRPL Peptide Sequence on Carboxypeptidase Y.
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5

Immunofluorescence Assay for PLCδ4 in Stem Cells

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Stem cells were plated at a concentration of 2 × 105 cells per plate, in 6-well plates containing coverslips. After a 24 hour cultivation, cells were fixed, incubated with rabbit polyclonal primary antibody anti-PLCδ4 antibody (1:200, Santa Cruz Biotechnology, Dallas, TX, USA), and anti-rabbit IgG secondary antibody conjugated to Alexa Fluor® 488 (1:500, Thermo-Fisher Scientific). Coverslips were assembled using SlowFade Gold Antifade with DAPI (Thermo-Fisher Scientific). Fluorescence images were obtained using confocal microscope Zeiss 5 LIVE (Carl Zeiss, Jena, Germany), at “Centro de Aquisição e Processamento de Imagens do ICB/UFMG” (CAPI), using 405 and 488 nm lasers for DAPI and Alexa Fluor® 488 excitations, respectively. The 63× immersion objective lenses, 1.4 numerical aperture was used, and the pinhole was kept near 1 Airy unit. Images were analyzed by Image Browser or ZEN software (Carl Zeiss). At least three assays were performed.
Kunrath-Lima M., de Miranda M.C., da Fonseca Ferreira A., Faraco C.C., de Melo M.I., Goes A.M., Rodrigues M.A., Faria J.A, & Gomes D.A. (2018). Phospholipase C delta 4 (PLCδ4) is a nuclear protein involved in cell proliferation and senescence in mesenchymal stromal stem cells. Cellular signalling, 49, 59-67.
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6

Immunohistochemical Analysis of IL-1β and IL-6

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The brain stem sections (5 μm) were blocked in 5% bovine serum albumin and 0.3% Triton X-100 for 30 min at room temperature, incubated in primary antibody anti-IL-1β (Proteintech, 16806-1-AP) and anti-IL-6 (Proteintech, 21865-1-AP) in primary antibody diluent (ScyTek laboratories, Logan, UT, USA) for 16 h at 4 °C. After PBS wash, the sections were incubated in Novolink Polymer solution (Leica Biosystems, Nussloch, GmbH) for 10 min under room temperature. The tissues were stained in DAB chromogen at room temperature, analyzed by Olympus BX51 microscope (Olympus Tokyo, Japan) and Image Browser (Carl Zeiss, MicroImaging, Jena, GmbH).
Ho C.Y., Lin Y.T., Chen H.H., Ho W.Y., Sun G.C., Hsiao M., Lu P.J., Cheng P.W, & Tseng C.J. (2020). CX3CR1-microglia mediates neuroinflammation and blood pressure regulation in the nucleus tractus solitarii of fructose-induced hypertensive rats. Journal of Neuroinflammation, 17, 185.
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7

Confocal Microscopy of BTV-1 Infection

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Confocal microscopy was performed by a method similar to that of Du et al. (38 (link)). Briefly 5 × 104 HeLa cells were synchronously infected with BTV-1 at an MOI of 10. Unbound virus was subsequently washed off, and coverslips were fixed at a time point either 0, 15, 20, or 45 min after infection. Coverslips were then processed for imaging. Slides were imaged using a Zeiss LSM510 confocal microscope using oil immersion with a ×63 objective at room temperature. Images were processed using a Zeiss image browser.
Patel A., Mohl B.P, & Roy P. (2016). Entry of Bluetongue Virus Capsid Requires the Late Endosome-specific Lipid Lysobisphosphatidic Acid. The Journal of Biological Chemistry, 291(23), 12408-12419.
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8

Analyzing Live Parasite Samples

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Live parasite samples were assessed, and images captured, using a Zeiss LSM510 or LSM880 laser scanning confocal microscope using 100× oil objectives and Zeiss Image Browser or ZEN 3.0 software.
Tremp A.Z., Saeed S., Sharma V., Lasonder E, & Dessens J.T. (2020). Plasmodium berghei LAPs form an extended protein complex that facilitates crystalloid targeting and biogenesis. Journal of Proteomics, 227, 103925.
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