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6 protocols using superfrost plus slides

1

Immunohistochemical Analysis of Vaginal T Cell Subsets

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At the end of the study (70 dpi), the animals were sacrificed. Vaginal tract was excised and then frozen in OCT compound (Sakura Finetek USA). OCT-embedded 8-μm cryostat sections mounted onto Superfrost Plus Slides (Electron Microscopy Sciences) were fixed with cold acetone before being blocked in 0.1 m Tris-HCl buffer with 1% fetal bovine serum. Phycoerythrin-conjugated anti-CD8 antibody (clone: CT6, Bio-Rad) or PE-conjugated anti CD4 antibody (clone: CT7, Bio-Rad) staining was followed by a secondary antibody, Rhodamine conjugated anti-R Phycoerythrin (Abcam). Slides were stained with 4′,6-diamidino-2-phenylindole (Sigma) and mounted with Prolong Gold Antifade reagent (Thermo fisher). All slides were analyzed by fluorescence microscopy (BX51; Olympus) with 10x lens. Imaging data were analyzed with Imaris 7.2 (Bitplane) and ImageJ 1.46r (NIH).
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2

Brain Tissue Preparation and Immunostaining

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Animals were perfused transcardially with phosphate buffered saline (PBS) followed by 4% paraformaldehyde (PFA). Brains were dissected, post-fixed in 4% PFA for 12–24 hours, and placed in 30% sucrose for 24–48 hours. They were then embedded in Optimum Cutting Temperature (OCT, Tissue Tek) and stored at −80°C until sectioning. 60 μm floating sections were collected into PBS. For Cre line characterization and layer analysis, sections were incubated in 0.3% PBST and 10% donkey serum for 1 hour and then stained with mouse anti-NeuN (Millipore MAB377, 1:1,000), rat anti–Ctip2 (Abcam ab18465, 1:200), or rabbit anti-Cux1 (Santa Cruz SC-13024, 1:500) for 1–4 nights at 4°C in 0.3% PBST and 5% donkey serum. All sections washed 3×10 min in PBS and additionally stained with NeuroTrace Blue (1:1,000) in 0.3% PBST for 2 hours, followed by DAPI (1:10,000 of 5 mg/mL, Sigma-Aldrich) in PBS for 10–15 min, and then washed once more with PBS prior to mounting onto Superfrost Plus slides and coverslipping with Fluorogel (Electron Microscopy Sciences). The sections were imaged at 5× using a Leica Ariol Slide Scanner microscope with an SL200 slide loader, and scanner images were processed with custom software55 (link).
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3

Cryopreservation and Immunostaining of Forebrain Organoids

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Forebrain organoids were fixed for 30 min in PFA at room temperature, washed three times with PBS, and cryopreserved in 30% sucrose/PBS at 4°C overnight. Fixed organoids were embedded in O.C.T. compound (Sakura Finetek, Torrance, CA, USA), frozen in an isopropanol/dry ice slurry, and sectioned at 14 μm on a cryotome. Sections were attached to Superfrost Plus slides (Electron Microscopy Sciences, Hatfield, PA, USA) and stored at −20°C until staining. Prior to staining, sections were rehydrated in PBS for 5 min, and detergent extracted in 0.5% Triton X-100 (Roche, Indianapolis, IN, USA) for 3 min.
Immunofluorescence was performed as previously described (Clemson et al., 1996 (link); Byron et al., 2013 (link)). Fixation with 4% paraformaldehyde was performed prior to detergent extraction. The primary antibodies used in this study are provided in Table 2. The conjugated secondary antibodies used in this study were Alexa Fluor 488, 594, and 647 (ThermoFisher, Waltham, MA, USA).
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4

Brain Tissue Preparation and Immunostaining

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Animals were perfused transcardially with phosphate buffered saline (PBS) followed by 4% paraformaldehyde (PFA). Brains were dissected, post-fixed in 4% PFA for 12–24 hours, and placed in 30% sucrose for 24–48 hours. They were then embedded in Optimum Cutting Temperature (OCT, Tissue Tek) and stored at −80°C until sectioning. 60 μm floating sections were collected into PBS. For Cre line characterization and layer analysis, sections were incubated in 0.3% PBST and 10% donkey serum for 1 hour and then stained with mouse anti-NeuN (Millipore MAB377, 1:1,000), rat anti–Ctip2 (Abcam ab18465, 1:200), or rabbit anti-Cux1 (Santa Cruz SC-13024, 1:500) for 1–4 nights at 4°C in 0.3% PBST and 5% donkey serum. All sections washed 3×10 min in PBS and additionally stained with NeuroTrace Blue (1:1,000) in 0.3% PBST for 2 hours, followed by DAPI (1:10,000 of 5 mg/mL, Sigma-Aldrich) in PBS for 10–15 min, and then washed once more with PBS prior to mounting onto Superfrost Plus slides and coverslipping with Fluorogel (Electron Microscopy Sciences). The sections were imaged at 5× using a Leica Ariol Slide Scanner microscope with an SL200 slide loader, and scanner images were processed with custom software55 (link).
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5

Luxol Fast Blue Staining for Myelin

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To examine demyelination in cuprizone treatment mice, brain cryosections
(30um) were mounted on Superfrost Plus slides and stained with 0.1% luxol fast
blue solution (#26681–01, Electron Microscopy Sciences) in 56 °C
oven overnight. Sections were then rinsed sequentially in 95% ethanol, water and
0.05% lithium carbonate solution (#26681–04,
Electron Microscopy Sciences) until the white matter sharply defined. When
differentiation is complete, cryosections were dehydrated in 100% ethanol,
cleared in xylene and mounted with cytoseal 60 mounting
medium.
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6

Immunocytochemistry of Retinal Organoids

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For immunocytochemistry, organoids were fixed in 4% paraformaldehyde (Electron Microscopy Sciences) for 40 min at room temperature, washed with PBS, cryopreserved in 30% sucrose, and sectioned on a cryostat. 15 μm sections were collected on Superfrost Plus slides (Electron Microscopy services), blocked for 1 hr at RT in 10% normal donkey serum, 5% BSA, and 0.5% Triton, then incubated overnight at 4°C with primary antibodies diluted in block. Primary antibodies, sources and dilutions are listed in key resources table. Slides were incubated with species-specific fluorophore-conjugated secondary antibodies diluted 1:500 in block, for 30 minutes in the dark at RT (donkey anti-mouse Alexa Fluor 488, donkey anti-rabbit AF546 and donkey anti goat-AF633: Thermo Fisher) and mounted with Prolong Gold antifade + DAPI to counterstain nuclei (Thermo Fisher). Sections were imaged on a Nikon A1R-HD laser scanning confocal microscope. For cone and rod counts, sections of the outer nuclear layer-like region of at least 4 individual organoids per line were immunostained with NR2E3 and cone ARR3, imaged, and rods and cones from at least 6 images were counted using Nikon Elements Analysis D software (Capowski et al., 2019 ; Kallman et al., 2020 (link)).
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