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82 protocols using sp5 2

1

Confocal Microscopy of Fluorescent Proteins

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Barley leaves with transformed epidermal cells were vacuum infiltrated with 0.01% Tween20 and subsequently mounted in the same buffer under a coverslip for confocal microscopy. Leica SP5-X, SP5-II and SP8 confocal laser scanning microscopes mounted with ×63 water immersion lenses with a numerical aperture of 1.2 were used. For detection and localization of the fluorophores, green fluorescent protein (GFP) was excited at 488 nm and detected between 500 and 540 nm, monomeric yellow fluorescent protein (mYFP) was excited at 514 nm and detected between 528 nm and 560 nm, while mCherry was excited at 543 nm (Leica SP5-II) or 587 nm using the super continuum white laser (Leica SP5-X) and detected between 600 and 640 nm. To limit signal bleed-through between channels, the measurements of each fluorophore were performed in independent tracks exciting only one fluorophore at a time.
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2

Time-lapse Confocal Microscopy Protocol

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Time-lapse video microscopy measurements were performed using a laser scanning confocal microscope (Leica SP5 II) equipped with an environmental control chamber (Life Imaging Services) maintained at 37°C. Fluorescence and brightfield images were collected with 10X air objective (Leica 506505, HC PL Fluotar 10X/0.03) and 1.25 X air objective (Leica 506215, HCX PL Fluotar 1.25X/0.04). Time-lapse measurements were also collected using a stereomicroscope (Leica, M205 FA) equipped with color CMOS video camera (Leica, DFC3000 G). After collection, images were processed and analyzed using IMARIS, MetaMorph and ImageJ image analysis software.
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3

Visualization of Intracellular and Surface PLSCR1 Expression

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Non-treated THP-1 cells and primary monocytes were washed and resuspended in PBS and laid on coverslips pretreated with poly-L-lysine (0.1 mg/mL) (Sigma) for 20 min at room temperature. PMA-treated THP-1 and monocyte-derived macrophages (MDMs) were grown on non-treated coverslips, washed in PBS, and then fixed with 4% paraformaldehyde in PBS. Intracellular PLSCR1 was detected with the 1E9 mAb in 1% BSA-PBS, supplemented with 0.1% Triton X-100 for permeabilization, and then stained using Alexa488-coupled secondary antibody. Cell surface PLSCR1 was detected either with the 1E9 mAb or with the rabbit pAb. Samples were examined under an epifluorescence microscope (Leica DMB) with a cooled charge-coupled device camera (Micromax 1300Y/HS; Roper Princeton Instruments), using a Plan APO 100X objective. Images acquisition was perfomed with MetaMorph 7.6 (Molecular Devices). After culturing BMDMs for at least 10 days in 10 ng/ml mCSF (Miltenyi Biotec), cells were plated on non-treated coverslips, subsequently fixed and permeabilized as described above, and then labeled with TRITC-phalloidin (Sigma) and rabbit anti-Iba1 (Wako Chemicals GmbH) and an Alexa 647 coupled-goat anti-rabbit-IgG (Molecular Probes). Images were acquired using a confocal microscope (Leica SP5II) equipped with a Plan APO 63x objective (N.A. 1.40, pinhole 1.0).
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4

Immunofluorescent Staining of LKB1 in MCF-7 Cells

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MCF-7 cells were cultured on chamber slides in DMEM (Hyclone) supplemented with 10% FBS, fixed with 4% paraformaldehyde solution for 10 min at RT, washed three time with PBST and then permeabilized with 0.1% Trition X-100 for 10 min. The slides were blocked with 5% BSA and 10% horse serum in PBST for 1 h at RT and incubated with antibodies against LKB1 (1:200) (CST#3050) at 4°C overnight. After being rinsed with PBST three times, cells were incubated with secondary antibody Alexa Fluor 633 (Invitrogen #A21063) (1:200) for 1 h at RT. After being washed twice, cells were stained with 5 ?g/ml DAPI, followed by imaging with con-focal microscopy (Leica SP5II).
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5

Quantifying Neurite Mobility Using FRAP and 2P

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Transgenic animals were immobilized on agarose pads, as described53 (link) and placed on the stage of confocal microscope. UNC-70(TSMod) was analyzed with a Leica SP5 II and a 63x/1.3 oil immersion lens. Under the control of FRAP Wizard software, a short segment (2–4 μm long) of a TSMod-expressing neurite was illuminated at full power for 1.5s at 458nm and 514nm. The same region of interest (ROI) was subsequently imaged for 10 frames at 0.6 fps and 20 frames at 0.1 fps, exciting the Venus fluorophore. This system lacked the temporal resolution needed to analyze rapid recovery of cytosplasmic cytoTSMod. Therefore, a Prairie Technologies dual 2-photon microscope was used to image and bleach the neurite of cytoTSMod simultaneously using 920nm excitation with a 60x/0.9 water immersion lens. A line scan of ~10–20μm in length was imaged at 1000 fps for 1s to image the recovery process. Image stacks were analyzed to plot intensity vs. time and fitted with to
D=ln(2)ω2τ 59 (link).
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6

Quantifying Neurite Mobility Using FRAP and 2P

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Transgenic animals were immobilized on agarose pads, as described53 (link) and placed on the stage of confocal microscope. UNC-70(TSMod) was analyzed with a Leica SP5 II and a 63x/1.3 oil immersion lens. Under the control of FRAP Wizard software, a short segment (2–4 μm long) of a TSMod-expressing neurite was illuminated at full power for 1.5s at 458nm and 514nm. The same region of interest (ROI) was subsequently imaged for 10 frames at 0.6 fps and 20 frames at 0.1 fps, exciting the Venus fluorophore. This system lacked the temporal resolution needed to analyze rapid recovery of cytosplasmic cytoTSMod. Therefore, a Prairie Technologies dual 2-photon microscope was used to image and bleach the neurite of cytoTSMod simultaneously using 920nm excitation with a 60x/0.9 water immersion lens. A line scan of ~10–20μm in length was imaged at 1000 fps for 1s to image the recovery process. Image stacks were analyzed to plot intensity vs. time and fitted with to
D=ln(2)ω2τ 59 (link).
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7

In vivo NJP Ganglion Calcium Imaging

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In vivo NJP ganglion imaging was performed as described previously (Williams et al., 2016 (link)). Briefly, Piezo2-GCaMP* and P2ry1-GCaMP* mice were anesthetized by isoflurane inhalation and the left ganglion was surgically exposed after severing central connections and immobilized on a stable platform for confocal imaging (Leica SP5 II) of calcium transients. Stretch of the lower airways was achieved by gas infusion of (1 liter/min, 15 sec) through a tracheal cannula (PE10 tubing, Braintree Scientific) inserted below the thyroid cartilage and advanced to the level of the carina. The baseline activity for each neuron was defined as the average GCaMP3 fluorescence intensity over a three-minute period preceding stimulus delivery, and cells were excluded if they failed to display maximal responses to electrical stimulation greater than seven standard deviations above their baseline means at the conclusion of the experiment. Cells were identified as responsive if (1) maximum GCaMP3 fluorescence exceeded seven standard deviations above the baseline mean, or (2) mean GCaMP3 fluorescence during the stimulation period exceeded three standard deviations above the baseline mean. Response analysis was performed blind to neuron identity.
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8

NR4A3 Rearrangement Detection in Tumor Cells

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FISH was performed on freshly cut sections from tumor tissue blocks using the ZytoLight SPEC NR4A3 Dual Color Break Apart Probe (ZytoVision GmbH, Bremerhaven, Germany) with standard protocols according to the manufacturer’s instructions. Fifty tumor cells were visually inspected using a fluorescence microscope and a cut-off of >20% tumor cells with aberrant signals was used to classify samples as NR4A3-rearranged. All cases were independently scored by two pathologists (F.H., A.A.) and revealed concordant results. The image presented in Supplemental Figure S2 was obtained with Leica SP5 II, Software Revision 2.6.3.1873 using a glycerol objective lens (×63, NA 1.3), detection with PMTs. Nyquist criterion matched for xy and z for all three channels, super critical pinhole with 0.8 Airy Units each channel. Stacks were post processed using Huygens Prof. Vers. 18.04 with deconvolution parameters: CMLE algorithm, SNR:20, 40 iterations.
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9

Immunofluorescence Staining of Adherent Cells

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Adherent cells in 6‐well plates culture slides were fixed with 4% paraformaldehyde for 15 minutes; 0.5% Triton X‐100 (CWBIO, China) was used to permeabilize the cells, which were blocked with 3% BSA for 2 hours. Cells were incubated with primary antibody in 3% BSA at 4°C overnight, washed in PBS three times and incubated with Alexa Fluor 488‐labeled goat anti–rabbit IgG secondary antibody (Invitrogen) for 1 hour; nuclei were stained with DAPI solution and then captured by fluorescence microscope (Leica SP5II).
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10

Quantitative Analysis of Bassoon Signals

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For the quantitative measurements of Bassoon immunofluorescent signals, four or five optical images from two independent beads-neuron co-cultures were obtained using a confocal microscope (SP5II, Leica). Bassoon signal intensities on the beads were measured as the fluorescence mean density within a 7 μm diameter circle enclosing a coated bead. The fluorescent mean densities of the surrounding regions within a 14-μm diameter circle were then measured and subtracted as background signals. Statistical significance of difference was evaluated by one-way ANOVA followed by post hoc Tukey’s test (n = 28–33 beads).
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