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13 protocols using fisherbrand superfrost plus slides

1

Mice Tissue Preparation for Immunofluorescence and RNA In Situ Hybridization

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Mice were euthanized by isoflurane overdose. For immunofluorescence assays, super cervical ganglia were collected and fixed overnight at 4˚C. The next day the tissues were cryoprotected in 15% sucrose 0.05% sodium azide in 1xPBS. The following day, the tissues were incubated in 30% sucrose 0.05% sodium azide in 1xPBS until they no longer floated in the solution. Cryoprotected tissues were embedded in Tissue-Tek Optimum Cutting Temperature compound (Sakura Finetek, Torrance, CA, USA) and cryosectioned using a Leica CM1950 (Wetzlar, Germany) cryostat at 10 μm onto Fisherbrand Super Frost Plus slides (Fisher Scientific, Hampton, NH, USA). Slides were stored at −80˚C until use.
For RNA in situ hybridization, brain and superior cervical ganglion were harvested and fresh frozen on dry ice. The tissues were cryosectioned using a Leica CM1950 (Wetzlar, Germany) cryostat at 10 μm onto Fisherbrand Super Frost Plus slides (Fisher Scientific, Hampton, NH, USA). Slides were stored at −80˚C until use.
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2

Claudin 1 Immunohistochemistry Protocol

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Tumor sections (5 μm) were cut from paraffin-embedded tissue, mounted on Fisherbrand Superfrost/plus slides (ThermoFisher Scientific) and stained with the rabbit polyclonal claudin 1 antibody (Life Technologies) at a dilution of 1:150. This antibody has been previously validated for specificity and sensitivity in our laboratory [18 (link)]. IHC was performed as recently reported [25 ] using an automated tissue immunostainer (Discovery Staining Module, Ventana Medical Systems, AZ, USA). Briefly, sections were dewaxed in two xylene baths, taken through a series of alcohols, rehydrated and then submitted to heat-induced antigen retrieval for 8 min in the presence of a citrate buffer (CC1, Ventana Medical Systems) using the automated tissue immunostainer (Discovery Staining Module, Ventana Medical Systems). Primary antibodies were applied for 60 min and secondary antibodies for 32 min.
Positive staining for claudin 1 protein was assessed using semi-quantitative scoring (H-scores). H-scores were derived from both staining intensity (scale 0–3) and percentage of positive cells (0–100%), which when multiplied, generated a score ranging from 0–300. Tissue microarray (TMA) staining was evaluated independently by two investigators (AB, CP) and where discordant, cases were re-evaluated jointly.
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3

Tissue Fixation and Bladder Analysis in Mice

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Anesthetized mice were perfused transcardially with ice-cold saline followed by 4% paraformaldehyde (PFA) in 0.1M phosphate-buffered saline. Brains were removed whole and post-fixed overnight in 4% PFA, then transferred into a 30% sucrose solution for 72 h. Brains were then embedded in Neg50 (Richard-Allan Scientific, Thermo Fisher Scientific, Kalamazoo, MI) for storage at −80°C. Coronal sections spanning the entire cortex were cut at 40 µm on a Leica cryostat and collected serially onto Fisherbrand Superfrost* Plus slides (Thermo Fisher Scientific). As scent marking behavior may be dependent upon urinary output, and bladder function may be altered after TBI [55] (link), bladders were collected for post-mortem examination prior to perfusion. Dissected bladders were expressed to empty residual urine, blotted dry and weighed, and measurements of length (major axis) and width (minor axis) were used to estimate volume based upon the shape of a prolate spheroid of major axis L and minor axis W, as previously described (V = 4/3πL[W/2]2) [56] (link), [57] (link).
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4

RNA Expression Profiling in Ovarian Tissue

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Samples for RNAscope were fixed in 4% paraformaldehyde overnight at 4 °C and dehydrated in gradients of ethanol. Ovaries were embedded in paraffin, sectioned at 5 μm and mounted on Fisherbrand Superfrost Plus slides (Thermo Fisher Scientific, Waltham, MA, USA). RNAscope was conducted according to RNAscope Multiplex Fluorescent Reagent Kit V2 protocol for FFPE tissue (ACD bio, Newark, CA, USA), with an Rspo1 (479591-C2) probe. Slides were imaged under a Leica DMI4000 confocal microscope the following day.
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5

Cryo-Sectioning Mouse Embryos and Tissues

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Mouse embryos and tissues were collected and rinsed in ice-cold Dulbecco’s PBS and fixed by incubation for 15–20 minutes in PBS containing 4% PFA (Santa Cruz, sc-281692) at 4°C. They were rinsed twice in ice-cold PBS and incubated for 24 hours in 30% sucrose/PBS at 4°C, followed by Tissue-Tek OCT compound (catalog 4583) in plastic molds and allowed to freeze on dry-ice and stored at –80°C. The tissue submerged in OCT compound was sectioned onto 5 μm–10 μm slices in a cryostat and dried on Fisherbrand Superfrost Plus slides (Fisher Scientific, catalog 22-037-246) 12 to 16 hours at room temperature. P0.5 mice tissue were collected after anesthesia. Hearts were then removed and treated as described above.
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6

Immunofluorescence of Mouse Brain Sections

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Immunofluorescence was performed on coronal brain section (16 μm thick) fixed with 4% formaldehyde and mounted on Fisherbrand superfrost plus slides (Fisher Scientific) according to the protocol established by Cell Signaling Technology for STEP (23E5: 1:100) and GFP (D5.1: 1:100) antibodies using Alexa Fluor 488 conjugated secondary antibodies (1:1000) and prolong gold antifade reagent with DAPI (Cell Signaling). Immunofluorescence was visualized using a Zeiss Axio Observer.Z1 microscope.
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7

Transcardial Perfusion and Cryosectioning

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Mice of the appropriate age were anesthetized and perfused transcardially with 4% paraformaldehyde/PBS. For cryoprotection, subdissected samples were incubated in a graded series of 10%, 20%, and 30% sucrose/PBS at 4°C before embedding in O.C.T. compound and freezing. Cryostat sections were collected on Fisherbrand Superfrost/Plus slides (Fisher Scientific) and air-dried prior to staining. For some experiments, brains were dissected, postfixed, and mounted in agarose prior to vibratome sectioning.
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8

Histopathological Analysis of Liver Biopsies

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The liver biopsy specimens that were immersion fixed in 10% neutral buffered formalin were dehydrated in ascending grades of reagent alcohol, cleared in xylenes, infiltrated, and embedded into Paraplast X-TRA paraffin (McCormick Scientific, LLC, St Louis, MO) on a Tissue-Tek VIP tissue processor (Sacura Finetek Japan Co., Tokyo, Japan). Sections of 5 µm thickness were cut on a Leica microtome and mounted onto Fisherbrand Superfrost Plus Slides (Fisher Scientific, Pittsburgh, PA). Slides were stained with modified hematoxylin and eosin, Masson trichrome, and Gordon-Sweets reticulin stains according to standard methods.28 Immunohistochemistry for the macrophage-specific marker, CD68, was performed using a mouse anti-human CD68 antibody (Dako; clone PG-M1, cat# M0876) at a concentration of 0.4 μg/mL. Slides were stained with Dako diaminobenzidine chromagen solution and a hematoxylin counterstain (Dako).
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9

Cryosectioning and Immunostaining Protocol

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Blocks were sectioned on a Leica CM3050S cryostat (Leica Biosystems) at 25μm. Sections were collected on Fisherbrand Superfrost Plus slides (Fisher Scientific). Eight consecutive sections were collected in two rows on each slide (Figures 1J and 1K). Slides were washed in Wheaton staining dishes filled with PBS, for 5 min on an orbital shaker, to dissolve OCT and SpineRack material. Sections were incubated with primary antibodies in PBS containing 0.1% Triton X-100 at 4°C overnight, then washed in PBS and incubated with secondary antibodies, DAPI and/or Neurotrace in PBS for 1-2h at room temperature. tdTomato signal was amplified using anti RFP or anti dsRed antibodies. See key resources table for material details.
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10

Immunohistochemistry Staining Protocol

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Blocks were sectioned on a Leica CM3050S cryostat (Leica Biosystems) at 25μm. Sections were collected on Fisherbrand Superfrost Plus slides (Fisher Scientific). Eight consecutive sections were collected in two rows on each slide (Figures 1J and 1K). Slides were washed in Wheaton staining dishes filled with PBS, for 5 min on an orbital shaker, to dissolve OCT and SpineRack material. Sections were incubated with primary antibodies in PBS containing 0.1% Triton X-100 at 4°C overnight, then washed in PBS and incubated with secondary antibodies, DAPI and/or Neurotrace in PBS for 1-2h at room temperature. tdTomato signal was amplified using anti RFP or anti dsRed antibodies. See key resources table for material details.
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