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18 protocols using wga alexa fluor 555

1

Anterograde Tracing of Cerebellar Mossy Fibers

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Anterograde neuroanatomical tracing of mossy fibers to the cerebellum was performed as described previously (Lackey and Sillitoe, 2020 (link); Sillitoe, 2016 (link)). P12 pups were anesthetized with isoflurane on a surgery rig. Hair was removed and an incision was made in the skin over the lower thoracic/upper lumbar spinal cord, using the curvature of the spine as a guide. We used a Nanoject II to inject 0.2–1 µl of 2% WGA-Alexa Fluor 555 (Thermo Fisher Scientific; #W32464) and 0.5% Fast Green (Sigma-Aldrich; #F7252, used for visualization) diluted in 0.1 M phosphate-buffered saline (PBS; Sigma-Aldric; #P4417; pH 7.4). Tracer was injected 1 mm below the surface of the spinal cord, on the right side of the dorsal spinal vein. After tracer injection, we applied antibiotic ointment and closed the incision using VetBond (3M; #1469 SB) and wound clips (Fine Science Tools; #12032–07). Pups were placed back with the mom after waking up from anesthesia. We placed soft food and hydrogel on the cage floor and monitored behavior closely for whether the mom accepted the pups back into the litter. Tissue was collected (see section on Tissue processing above) for tracer visualization 2 days after the surgery, at P14.
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2

Tracking Lactobacillus Rhamnosus Gut Localization

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A single dose of fluorescently labelled (WGA-Alexa Fluor 555; Thermo Fisher) living Lactobacillus Rhamnosus (LR) was given to naïve rats, and the gut tissue isolated after 30 minutes. Serial 10 μm thick cryosections of Peyer's patches were co-stained with mouse anti-vimentin mAb (Dako) and sections of villi were counterstained with mouse anti-cytokeratin mAb (Dako), followed by goat anti-mouse Ab Alexa Fluor 488 conjugated. Nuclei were stained with DAPI. Single z-scan images were captured via confocal microscopy (20x objective).
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3

Platelet Spreading on Fibrinogen

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Washed platelets in DMEM were incubated on fibrinogen (50–230–4925, Fisher Scientific, Waltham, MA) coated chamber slides for 1 hour under static conditions. Spreading was then stopped by the addition of 2 % paraformaldehyde. Slides were then washed, permeabilized and stained with WGA-Alexa Fluor 555 (W32464, ThermoFisher, Waltham, MA), and phalloidin-Alexa Fluor 488 (A12379, ThermoFisher), and imaged.
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4

Targeted neural circuit manipulation

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ALM (AP 2.5 mm; ML 1.5mm; diameter 1.5 mm) is the cortical area that produced behavioral effects with photoinhibition during the delay epoch 3 (link),24 (link). For the thalamic reticular nucleus the coordinate was AP -0.7, ML 1.6, DV 3.7 - 3.3 mm, as retrograde labeling from thalALM showed labeling in this sector of the thalamic reticular nucleus (Extended Data Fig. 9). Virus and tracer were injected through the thinned skull using a volumetric injection system (modified from Mo-10 Narishige) 48 (link). Glass pipettes (Drummond) were pulled and beveled to a sharp tip (outer diameter ∼ 20 - 30 μm), back-filled with mineral oil and front-loaded with viral suspension immediately before injection. The injection rate was 15 nl/min. See Supplementary Table 2 for description of viruses and injection coordinates used for each experiment. We used the following viruses and tracers: AAV2/1-CAG-EGFP (Penn vector Core, University of Pennsylvania), AAV2/10 CAG-flex-ChR2(H134R)-tdTomato (Penn vector Core, University of Pennsylvania), AAV1-CAG-mRuby2-FLAG49 , WGA-Alexa Fluor® 555 (Thermo Fisher Scientific)50 (link) (WGA555), and Red RetroBeads (Lumafluor).
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5

Targeted neural circuit manipulation

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ALM (AP 2.5 mm; ML 1.5mm; diameter 1.5 mm) is the cortical area that produced behavioral effects with photoinhibition during the delay epoch 3 (link),24 (link). For the thalamic reticular nucleus the coordinate was AP -0.7, ML 1.6, DV 3.7 - 3.3 mm, as retrograde labeling from thalALM showed labeling in this sector of the thalamic reticular nucleus (Extended Data Fig. 9). Virus and tracer were injected through the thinned skull using a volumetric injection system (modified from Mo-10 Narishige) 48 (link). Glass pipettes (Drummond) were pulled and beveled to a sharp tip (outer diameter ∼ 20 - 30 μm), back-filled with mineral oil and front-loaded with viral suspension immediately before injection. The injection rate was 15 nl/min. See Supplementary Table 2 for description of viruses and injection coordinates used for each experiment. We used the following viruses and tracers: AAV2/1-CAG-EGFP (Penn vector Core, University of Pennsylvania), AAV2/10 CAG-flex-ChR2(H134R)-tdTomato (Penn vector Core, University of Pennsylvania), AAV1-CAG-mRuby2-FLAG49 , WGA-Alexa Fluor® 555 (Thermo Fisher Scientific)50 (link) (WGA555), and Red RetroBeads (Lumafluor).
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6

Triple Labeling of Blood, Conduit, and Lymphatic Vessels in Murine Lymph Nodes

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To achieve triple staining of the blood vasculature, conduit channels, and lymphatic vessels in popliteal and inguinal LNs, briefly anaesthetized C57BL/6 mice were first injected with 50 μL anti-LYVE-1-Alexa Fluor 488 antibody (20 μg/mL, R&D Systems, Minneapolis, MN) into the rear right hock, an alternative injection site to the footpad, which is less invasive while allowing strong labeling [73 (link)]. After 8 h, 50 μL WGA-Alexa Fluor 647 (1 mg/mL, Invitrogen, Thermo Fisher Scientific, Waltham, MA) were injected in the same site, and after a circulation period of 1 h, the blood system of the whole body was labeled by injecting 100 μL of WGA-Alexa Fluor 555 (5 mg/mL, Invitrogen, Thermo Fisher Scientific, Waltham, MA) with 10 μL Heparin (100 units/mL) into the tail vein or vena cava of the anaesthetized mouse for a duration 2 min. Freshly excised murine tissue was fixed in 4% PFA, 3% sucrose at 4 °C overnight and embedded in LR white resin (medium grade, ProSciTech, Kirwan, Australia) for confocal imaging as described above. Standard confocal microscopy was performed using a Leica TCS SP2 equipped with a Leica HCX APO L 40.0 × 0.80 W UV water objective (Leica Microsystems, Wetzlar, Germany) at a voxel resolution of 0.36 × 0.36 × 1 μm.
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7

Viral Tracing Techniques Described

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We followed (dx.doi.org/10.17504/protocols.io.bctxiwpn) for virus and tracer injection. See Supplementary Table 1 and 2 for descriptions of viruses and injection coordinates used for each experiment. We used the following tracers: WGA-Alexa555 (WGA-Alexa Fluor® 555; Thermo Fisher Scientific) and Red RetroBeads (Lumafluor). See Supplementary Table 3 for a list of viruses used in this research.
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8

Isolation and Flow Cytometry of Lgr5+ Organoids

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For flow cytometry experiments, SI organoids were generated from crypts extracted from Lgr5-GFP mice. After 4 days of treatment, organoids were harvested and washed 5 times with cold PBS-BSA 0.1%. Organoids were disaggregated to single cells by incubating with TrypLE supplemented with DNase I for 5 min at 37 °C. Cells were incubated in Fc block (1:1000; Invitrogen, Cat. No. 14-0161-85) and Fixable Viability Dye eFluor 780 (1:1000; eBioscience, Cat. No. 65-0865-14) for 15 min at 4 °C, and subsequently stained with anti-Epcam PE-Cy7 (1:200; BioLegend, Cat. No. 118215), anti-CD24 BV421 (1:200; BioLegend, Cat. No. 101825) and WGA Alexa Fluor 555 (1:5000; Invitrogen) for 1 h at 4 °C. Flow cytometry was performed using an LSRFortessa flow cytometer (BD Biosciences, USA), and analysis was perfumed using FlowJo v10 (Treestar, USA).
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9

Mating-Induced Reproductive Tract Analysis

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Reproductive tracts of 3–4-day old females were dissected 3 h post mating (hpm) in PBS solution and fixed in PBS with 4% paraformaldehyde, washed in PBS and treated with 3% hydrogen peroxide solution (in PBS) to quench autofluorescence. Samples were washed in PBS and permeabilized for 1 h in PBS with 0.2% Triton X-100, then blocked and permeabilized over night at 4 °C in PBS with 1% BSA and 0.1% Triton X-100. Samples were incubated in 1.5 μg/ml mouse anti-5194 antibody diluted in blocking buffer, washed and then stained with anti-mouse Alexa Fluor 488 (Invitrogen). Samples were then incubated with 5 μg/ml of wheat germ agglutinin (WGA)-Alexa Fluor 555 (Invitrogen) and in 1 μg/ml of DAPI (4,6-diamidino-phenylindole, Sigma-Aldrich). All staining steps were followed by washes in PBS with 0.1% Triton X-100. Tissues were then mounted in Vectashield medium (Vector Laboratories, Inc.) and visualized using a Zeiss Axio Observer inverted fluorescent microscope with ApoTome 2. Post-imaging processing was performed with Fiji software.
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10

Cellular Uptake of CHI-PEG-PTX Nanofibers

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4T1 cells were seeded onto glass-bottom petri dishes (Mattech).
After overnight incubation, cells were incubated with CHI-PEG-PTX nanofibers
(50 μg mL−1) for 1 h at either 37°C or
4°C. Cells were washed 3 times with cold PBS, fixed with 4%
paraformaldehyde for 15 min at 37°C, stained with 5 μg
mL−1 WGA-Alexa Fluor 555 (Invitrogen, Carlsbad, CA)
for 5 min at 37°C, and washed with PBS 3 times (5 min each). Cells
were then incubated with DAPI for 5 min at 37°C, followed by washing
with PBS. After PBS washing, cells were mounted with VECTASHIELD mounting
medium (Vector Laboratories, Inc. Burlingame, CA). The images of cells were
acquired using a Leica SP8 confocal laser scanning microscope (Leica,
Germany).
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