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10 protocols using pfa pb

1

Immunohistochemical Analysis of Spinal Cord in SOD1 Mouse Model

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Isotype control or anti-HMGB1 antibody-treated SOD1G93A mice at mid-symptomatic stage (n = 4 per treatment group) were euthanized by intraperitoneal injection of zolazapam (50 mg/kg; Zoletil, Lyppard) and xylazine (10 mg/kg; Xylazil, Lyppard). Mice were then fixed by transcardiac perfusion with 2% sodium nitrite in 0.1 M phosphate buffer (pH 7.4; Sigma-Aldrich, St Louis, MO, USA) followed by 4% paraformaldehyde in 0.1 M phosphate buffer (4% PFA-PB, pH 7.4; Sigma-Aldrich, St Louis, MO, USA). Lumbar spinal cords were collected and placed into 4% PFA-PB for 2 h at 4 °C. Following this incubation, spinal cords were washed 3 × 5 min in phosphate-buffered saline (PBS; pH 7.4), followed by submersion in sucrose solution at 15% then 30% in PBS (pH 7.4). Lumbar spinal cords were then embedded in optimal cutting temperature compound (Sakura, Finetek, Torrance, CA, USA) then snap frozen in liquid nitrogen. Lumbar spinal cords were sectioned into 16-μm-thick transverse and coronal sections and dry mounted onto Superfrost Plus slides (Menzel-Glaser, Braunschweig, Germany) for quantitation of astrocytes and microglia as detailed below.
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2

Profiling Lumbar Spinal Cord of TDP-43 Transgenic Mice

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Female NTg, TDP-43WT and TDP-43Q331K mice (n = 4 per genotype) were euthanized by intraperitoneal injection of zolazapam (50 mg/kg; Zoletil, Lyppard) and xylazine (10 mg/kg; Xylazil, Lyppard). Mice were then fixed by transcardiac perfusion with 2% sodium nitrite in 0.1 M phosphate buffer (pH 7.4; Sigma-Aldrich, St Louis, MO, USA) followed by 4% paraformaldehyde in 0.1 M phosphate buffer (4% PFA-PB; pH 7.4; Sigma-Aldrich, St Louis, MO, USA) at the previously mentioned ages. Lumbar spinal cords were collected and placed into 4% PFA-PB for 2 h at 4 °C. Following this incubation, the spinal cords were washed 3 × 5 min in phosphate-buffered saline (PBS; pH 7.4), followed by submersion in sucrose solution at 15% then 30% in PBS (pH 7.4). Lumbar spinal cords were then embedded in optimal cutting temperature compound (Sakura, Finetek, Torrance, CA, USA) then snap frozen in liquid nitrogen. Lumbar spinal cords were sectioned into 16-μm-thick transverse and coronal sections and dry mounted onto Superfrost Plus slides (Menzel-Glaser, Braunschweig, Germany) for estimation of astrocytes, microglia and immunohistochemistry as detailed below.
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3

Mandibular Development in Miniature Pigs and Human Embryos

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Mandible samples from miniature pigs and human embryos were fixed in 4% paraformaldehyde in phosphate‐buffered saline (PFA‐PBS; Sigma‐Aldrich, St. Louis, MO) at 4°C overnight. The pig mandible slice containing a canine or third incisor as well as the human mandible slice containing a canine was dissected. After rinsing with PBS for 10 min twice, pig mandible slices from embryonic days 50 (E50), E55, E60, and E70 were decalcified in 10% EDTA‐PBS for 2, 4, 7, and 14 days, respectively. Pig mandible slices from E85, E90, E100, PN0, and PN10 were decalcified in 10% EDTA‐PBS for 30 days. Human mandible slices aged 18–19 weeks were decalcified in 10% EDTA‐PBS for 30 days. The decalcification media were refreshed every 2 days.
Samples were dehydrated in serial alcohol dilutions (30, 50, 70, 90, 95, and 100%) and embedded in paraffin, after which the samples were sectioned (5–7 μm thickness) for staining. H&E staining was used for morphological examination. Detailed ISH, TUNEL, RNAscope, and quantification methods are provided in the Appendix Supplementary Methods.
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4

DAPI Staining for Nuclear Visualization

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Morphological changes in the cell nucleus were examined by DAPI staining. Cells treated with 3OTPCA were washed with PBS and fixed with 4% paraformaldehyde (PFA/PBS (v/v); Sigma-Aldrich, St. Louis, MO, USA) for 15 min at 4°C. Then, cells were stained with 2 μg/mL DAPI (Molecular Probes, Invitrogen, Carlsbad, CA, USA) for 5 min for nuclear visualization and thoroughly washed before observation under a fluorescent microscope (GE Healthcare Delta Vision Elite) [16 (link)].
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5

Embryonic Development in Swiss Mice

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Animal use was approved by the Animal Ethics Committee, Faculty of Science, University of Melbourne. Experimental work on mice was conducted in accordance with the Prevention of Cruelty to Animals Act 1986 and the Australian code of practice for the care and use of animals for scientific purposes, 7th edition (2004). Swiss mice were used throughout. Embryos were collected from pregnant mice on days 6.5, 7.5, 8.5, and 9.5 of gestation. Embryos to be used for wholemount in situ hybridization (WISH) were fixed in 4% paraformaldehyde in phosphate-buffered saline (PFA/PBS) (Sigma Aldrich) for 30 min, washed in PBS, dehydrated through a graded methanol series, and stored in 100% methanol at −20°C. Embryos that were to be used for horseradish peroxidase (HRP) endocytosis assay were transferred into assay medium immediately after dissection.
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6

Extracellular Protein Extraction from Mouse Brains

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Four months post-injection, mice were deeply euthanized with isoflurane and transcardially perfused with 25 ml of ice-cold PBS, followed by 4% PFA/PBS (Sigma-Aldrich). The brains were rapidly removed. The left hemisphere was dissected and immediately frozen in dry ice for biochemical testing. The right hemisphere was immersed in freshly depolymerized 4% paraformaldehyde for 48 hours at 4 °C, and protected by successive 24-hour immersions in 15% and 30% sucrose in 1 × PBS. Fixed, cryopreserved brains were sectioned coronally using a Cryostat (Leica, Bannockburn, IL, USA) with sections serially collected and stored at −80 °C for immunohistochemical tests. For biochemical testing, protein extraction of an extracellular-enriched fraction was extracted as described (Lesne et al., 2006 (link)). After separation of extracellular-enriched fraction, protein pellet was homogenized in ice-cold RIPA buffer (Thermo Fisher Scientific, Waltham, MA, USA) with protease inhibitor cocktail (Sigma, St. Louis, MO, USA). Protein concentration was determined using Micro BCA Protein Assay (Thermo Fisher Scientific, Waltham, MA, USA).
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7

HOXA1-ERα Protein Interaction Assay

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Seventy-five thousand COS7 cells were seeded on glass coverslips in 24-well plates and were transfected 16 h growth later with 250 ng of pEXP-VC155(Nter) and 250 ng of pEXP-VN173(Nter) plasmids encoding HOXA1 and ERα fusion proteins, respectively. Empty pDEST-VC155(Nter) and pDEST-VN173(Nter) vectors were used as negative controls. Twenty-four hours post-transfection, cells were washed twice with PBS and fixed for 20 min with 4% PFA-PBS (#441244, Sigma-Aldrich) at room temperature. Cells were then rinsed twice for 5 min in TBS-T buffer (50 mM Tris-HCl, pH 7.5, 155 mM NaCl, 0.1% Triton X-100 (#10789704001, Merck)) and once for 10 min with TB buffer (50 mM Tris-HCl, pH 7.5). Cells on coverslips were stained in a mounting medium containing DAPI and Vectashield (#H-1200, Labconsult, Brussels, Belgium), and pictures were taken under an epifluorescence microscope (Axioskop 2, Zeiss, Oberkochen, Germany). Fluorescence was quantified with the IMAGEJ software and tested interactions were considered as positive when the emitted fluorescence was at least three times higher than in the negative control conditions. pEXP-VN173(Nter)-hHOXA1 with pEXP-VC155(Nter)-mHOXA1 was used as a positive BiFC control in each experiment.
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8

Immunofluorescence Analysis of Tissue Samples

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Tissues were embedded in Tissue‐Tek OCT medium and snap frozen in liquid nitrogen. For immunofluorescence, 10‐μm cryosections were rehydrated to water, postfixed with 4% PFA/PBS (Sigma‐Aldrich), blocked and permeabilized for 30 min in .25% Triton X‐100/5% normal donkey serum (NDS)/PBS (Vector Laboratories). Antibodies were diluted in 5% NDS/.1% Tween‐20/PBS. The following primary antibodies were incubated at 4°C overnight: anti‐FAPα (AF3715, R&D Systems), anti‐CXCL12 (MA5‐23759, Thermo Fisher Scientific), anti‐THBD (hpa002982, Atlas Antibodies), anti‐NPM1 (FC61991, Thermo Fisher Scientific), anti‐FBLN1(hpa001612, Atlas Antibodies), anti‐CD90 (AF2067, R&D Systems), anti‐c‐Myc (MAB36961, R&D Systems) and anti‐c‐Fos (PC05L, Merck). Staining was visualized with secondary antibodies (IgG‐NL493 (NL006) and IgG‐NL557 (NL010), 1:200, R&D Systems). Nuclei were visualized using ProLong Gold Antifade Mountant (P36931, Thermo Fisher Scientific). Stains were evaluated with a Leica DM6000 fluorescence microscope and using LAS AF Lite software.
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9

Isolation of Equine Hoof Progenitor Cells

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Hooves were obtained from horses that were not euthanized for research purposes. Horse hooves were collected from the abattoir 1 h post euthanasia following ethical approval by The School of Veterinary Medicine and Science, University of Nottingham. For three-dimensional imaging and histological sampling, PBS was injected through the medial and lateral palmar digital arteries to remove the blood, and tissues were fixed by replacing PBS with a 4% PFA/PBS (Sigma, UK) fixative solution under manual pressure. When needed, biopsies were taken from the dorsal and quarter parts of the coronary band and placed into a 4% PFA/PBS solution fixative solution prior processing. For primary cell isolation, hooves were aseptically cleaned and progenitor keratinocyte cells obtained as described below. All primary cell cultures were performed at 37°C in 5% CO2.
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10

Visualizing Endothelial Cell Activation

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HGMVECs and BOECs were seeded in a black 96-well plate with a clear bottom (Falcon Corning Incorporated, Corning, NY, USA). Cells were incubated with either control medium or medium with 10 ng/mL of TNFα (Roche Diagnostics GmbH, Mannheim, Germany) for 24 h and fixed with 2% paraformaldehyde (PFA)/PBS (Sigma Aldrich) at room temperature for 15 min. Mouse anti-CD31 (BD Biosciences, San Jose, CA, USA) primary and corresponding species-specific Alexa Fluor 568 were used as antibodies. Alexa 488-labeled Stx-B at a concentration of 5 μg/mL and the fluorescent DNA stain DAPI (Invitrogen, Carlsbad, CA, USA) were added, and images were taken with the use of a Zeiss LSM900 confocal microscope (Zeiss, Oberkochen, Baden-Württemberg, Germany).
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