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49 protocols using cryotome

1

Cryosectioning and Immunostaining of Mouse Femurs

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Femurs were dissected and cleaned from muscle, and placed immediately in 4% PFA at 4°C for 30 min. Subsequently, femurs were washed three times in 1X PBS before incubating with 15% sucrose for 2 h, followed by 30% sucrose for another 2 hours. All incubations were performed at 4 °C. Femurs were placed in OCT and frozen at -80 °C until sectioning.
For sectioning, a cryotome (ThermoFisher) was used to generate 12 μm sections at -20 to -22 °C, which were then transferred to slides using the CryoJane Tape-Transfer System (Leica Biosystems). Slides were post-fixed with 4% PFA for 1 min to enhance the adherence of sections to the slide, then washed for 2 min by dipping in PBS. Sections were stained with antibodies in blocking buffer (PBS containing 10% goat serum and 0.2% Triton X100, see table S4 for antibodies used) at 4°C overnight, then washed by dipping into PBS for 1 min. Secondary antibody staining was done in blocking buffer at room temperature for 2 h. Sections were imaged using an LSM710 microscope (Zeiss) equipped with a polychromatic META detector (Lasers: 458, 488, 514, 561, 594, and 633nm), and an Olympus FV3000 Confocal laser scanning microscope with 4 GaAsP spectral detectors, FRAP and FRET (Lasers: 405, 445, 488, 514, 561, 594 and 640 nm). Imaris software (v8.41) was used for data analysis and representation.
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2

Intracerebral Amyloid-β Infusion in Rats

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Infusion of Aβ(1–42) was performed as described earlier.23 (link) Male Sprague-Dawley rats (300–380 g) were anesthetized by injecting a mixture of xylazine–ketamine and placing them on a stereotaxic frame. Injection was carried out by using a 27-gauge Hamilton syringe. A volume of 5 μl of 100 mM Aβ1–42 in PBS was infused in the right cerebral cortex at stereotaxic co-ordinates from bregma: AP: −4.1, L: 2.5, DV: 1.3 mm, according to a previous report.51 (link) An equal volume of Aβ42–1 in PBS was injected in control animals. Animals were killed 21 days after injection. The brains were dissected out, following cardiac perfusion, and fixed in 4% PFA for 24 h. They were then incubated in a 30% sucrose solution for another 24 h before proceeding with cryosectioning (Cryotome; Thermo).
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3

Immunohistochemical and Western Blot Analyses of Mouse Brain

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The mice were anesthetized using a zoletil (12.5 mg/kg) and rompun (17.5 mg/kg) mixture and transcardially perfused with saline-containing heparin. Furthermore, their brains were isolated for immunohistochemical and Western blot analyses. For immunohistochemistry, the brains were fixed using 4% paraformaldehyde at 4 °C for 24 h. Thereafter, they were dehydrated in 30% sucrose solution at 4 °C for 3 days. The brain tissues were frozen into optimal cutting temperature compound (Sakura Finetek, Tokyo, Japan), coronally sectioned into 20-μm-thick slices using cryotome (Thermo Fisher, Waltham, MA, USA), and stored in a cryoprotectant solution at 4 °C. For Western blotting, the ST and SN were dissected from non-perfused brains, snap-frozen in liquid nitrogen, and stored at −80 °C for later use.
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4

Cryosectioning and Immunostaining of Mouse Femurs

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Femurs were dissected and cleaned from muscle, and placed immediately in 4% PFA at 4°C for 30 min. Subsequently, femurs were washed three times in 1X PBS before incubating with 15% sucrose for 2 h, followed by 30% sucrose for another 2 hours. All incubations were performed at 4 °C. Femurs were placed in OCT and frozen at -80 °C until sectioning.
For sectioning, a cryotome (ThermoFisher) was used to generate 12 μm sections at -20 to -22 °C, which were then transferred to slides using the CryoJane Tape-Transfer System (Leica Biosystems). Slides were post-fixed with 4% PFA for 1 min to enhance the adherence of sections to the slide, then washed for 2 min by dipping in PBS. Sections were stained with antibodies in blocking buffer (PBS containing 10% goat serum and 0.2% Triton X100, see table S4 for antibodies used) at 4°C overnight, then washed by dipping into PBS for 1 min. Secondary antibody staining was done in blocking buffer at room temperature for 2 h. Sections were imaged using an LSM710 microscope (Zeiss) equipped with a polychromatic META detector (Lasers: 458, 488, 514, 561, 594, and 633nm), and an Olympus FV3000 Confocal laser scanning microscope with 4 GaAsP spectral detectors, FRAP and FRET (Lasers: 405, 445, 488, 514, 561, 594 and 640 nm). Imaris software (v8.41) was used for data analysis and representation.
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5

Perfusion and Sectioning of RSA59-Infected Mouse Brains

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RSA59 infected WT and Ifit2-/- mice (day 5 p.i.) were perfused transcardially with PBS, followed by cold PBS containing 4% PFA. Brains were harvested in 4% PFA for 6 h and then placed at 4°C for 4 h in 10% sucrose, followed by 30% sucrose overnight. Tissues were embedded with OCT medium (Tissue Tek, Hatfield, PA), sectioned sagitally with the help of a Cryotome (Thermo Scientific) to 5-10-μm thickness, and mounted on charged glass slides. Frozen tissue sections were washed with PBS at RT to remove cryomatrix. Tissues then were incubated for 1 h at RT with 1 M glycine in PBS to reduce nonspecific cross-linking, followed by a 10-min incubation at RT with 1 mg/ml NaBH4 in PBS to reduce autofluorescence. The slides were then washed with PBS and scanned for EGFP fluorescence. A Leica Aperio AT2 slide scanner (Leica Microsystems, GmbH, Wentzler, Germany) was used to scan images of whole slides at 20x magnification. High resolution images were acquired using a Leica SP8 confocal microscope (Leica Microsystems, GmbH, Wetzlar, Germany) that was purchased with funding from National Institutes of Health SIG grant 1S10OD019972-01.
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6

Immunohistochemical Analysis of Mouse Brain

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Control and SA treated mice were anesthetized and perfused initially with cold PBS followed by 4% paraformaldehyde. The brain was dissected out and kept overnight in the same solution. For cryosectioning brain was washed with PBS and then kept in 15% and 30% sucrose solution for 1 day each respectively. Coronal sections of brain were cut from the posterior side till midbrain using a cryotome (Thermo scientific) and kept in PBS in a 12 well plate. Sections were treated with 0.3% hydrogen peroxide in methanol for 30 min at −20 °C. Brain sections were kept in blocking buffer (2% FBS and 0.1% Triton X-100 in PBS) for 1 h. Following overnight incubation at 4 °C with primary antibody (1:500 in blocking buffer) cells were washed with the same buffer 3 times for 15 min each. Sections were incubated with appropriate secondary antibodies for 2 h at RT. Nuclei were stained with DAPI (1 μg/ml) for 2 min, washed and sections were mounted on glass slides using the antifade mounting medium (Invitrogen). Slides were observed under Nikon Eclipse 90i microscope (Nikon, Kawasaki, Japan).
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7

Fetal Tissue Sampling and Preservation

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To collect foetal tissue samples, the sow was first sedated by intramuscular administration of ketamine/azaperone (Intervet), then killed by intravenous injection of T61 (Intervet). Tissue samples from bladder, brain, colon, heart, liver, lung, skin, pancreas and spleen were embedded in OCT embedding compound, frozen on dry ice and stored at −80°C. 5 µm sections were cut using a cryotome (Thermo Fisher Scientific) and fluorescence detected by fluorescence microscopy (Zeiss).
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8

Cryosectioning and Alcian Blue Staining

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The OCT blocks of the half constructs were sectioned to 10 µm thickness using a cryotome (Fischer Scientific, Waltham, MA, USA). The sections were mounted on superfrost slides and stored in a −20 °C freezer until we used them for histological and immunofluorescence staining.
Alcian blue staining was used to visualize deposition of GAGs. To this end, frozen sections were first washed with 70% ethanol in 3% acetic acid solution for 15 min. Then, the slides were stained with 0.25% Alcian blue in 3% acetic acid solution for 4 h followed by destaining with graded ethanol solutions in 3% acetic acid over 3 h (50%, 75%, and 100% ethanol). The destained slides were washed with xylene, permount mounting medium was added on the slides, and images were taken at different magnifications using light microscopy (Nikon, Eclipse E600, SPOT Insight™ Camera, Melville, NY, USA).
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9

Quantifying Dystrophin in Frozen GM Muscle

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OCT embedded frozen GM muscle was cut with cryotome (ThermoFischer, Waltham, MA, USA) at 4-micron cross-sections, which were fixed with ice-cold acetone. Immuno-blocking was performed with 10% normal goat serum in 1% BSA. Dystrophin was detected using primary anti-dystrophin (1:200, MANDYS8, Abcam, Cambridge, MA, USA) antibody and secondary goat Alexa Fluor (AF) 555 conjugated secondary antibody. Nuclei were counterstained with DAPI Vector Laboratories, CA, USA. A Zeiss Meta confocal microscope with ZEN software (Carl Zeiss, Oberkochen, Germany) was used for fluorescence signal detection and analysis. The number of dystrophin-positive muscle fibers in five standardized regions of each cross-section were counted and normalized to total nuclei numbers; three, non-serial cross-sections were quantified for each animal (n = 6/group).
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10

Histological Evaluation of Graft Rejection

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After standard euthanasia, grafted tissue was harvested and fixed in optimal cutting temperature compound (Sakura Fineteck USA Inc., Torrance, CA). Eight days after VCA, 9-μm-thick graft sections were obtained using a cryotome (Thermo Fisher Scientific, Waltham, MA). Each section underwent hematoxylin-eosin (H&E) (Sigma-Aldrich) staining and examination for rejection grade by microscopy (Olympus, Hamburg, Germany). Image capture was performed with a SPOT RT color camera (Diagnostic instruments Inc, Sterling Heights, MI).
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