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22 protocols using excelsior as

1

Bone Tissue Preparation and Histological Analysis

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After being fixed in 4% polyoxymethylene for 24 h and then decalcified in 10% EDTA for 2 weeks at 4 °C, femurs and tibiae were dehydrated in ethanol and xylene by Excelsior AS (Thermo Scientific). Embedded in paraffin, bone specimens were cut into 5-µm-thick sections with a paraffin microtome (RM2255; Leica)3 (link),5 (link).
Sections of decalcified bone specimens were mainly processed for hematoxylin and eosin (HE) staining, tartrate-resistant acid phosphatase (TRAP) staining, IHC staining, and IF staining. The VOI was defined as the distal end of femurs. According to the IHC and IF staining protocol, slides were incubated in sodium citrate antigen retrieval solution at 100 °C for 10 min and then incubated with rabbit anti-CHD7 antibody (Abcam, ab117522, 1:200). IF staining slides were imaged by laser scanning confocal microscopy (FV3000; Olympus), and other staining slides were photographed by microscopy (BX53; Olympus) and analyzed with OsteoMeasure software (OsteoMetrics; Decatur, GA)5 (link),26 .
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2

Femur Decalcification and Embedding

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Femurs were dissected and fixed in 4% paraformaldehyde in phosphate-buffered saline (PBS) for 24 hours at 4 °C. Bones were decalcified for 5 days in 10% EDTA (Sigma) in PBS pH 7.5 with 2 changes of EDTA. Bones were processed using a Thermo Fisher Scientific Excelsior AS with 2× 70% ethanol, 2× 95% ethanol, 3× 100% ethanol, 3× Xylene, and 3× Paraffin, with 1 hour for each step. A Leica tissue embedder was used for embedding. Bones were sectioned at 5-μm thickness on an HM 355s microtome (Thermo Fisher Scientific) and mounted onto Leica Bond Plus microscope slides.
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3

Histological Analysis of Spleen and Liver

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Mice were anesthetised under 5% isoflurane. The spleen and liver were dissected and fixed in 4% paraformaldehyde. Prior to processing, spleens were blotted dry and weighed. Spleen and liver were processed overnight using an Excelsior AS tissue processor (Thermo-fisher, Waltham, MA), embedded in paraffin and sectioned using a microtome (4μm sections). Sections were stained with haematoxylin and eosin and subsequently imaged using a BX-51 light microscope (Olympus).
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4

Intestinal Morphometry Analysis Protocol

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The method described by Daneshmand et al.59 (link) was used to prepare samples for morphometry analysis. In summary, jejunal and ileal samples were stored in a 10% formaldehyde phosphate buffer for 48 h. Then, the samples were trimmed and processed on a tissue processor (Excelsior™ AS, Thermo Fisher Scientific, Loughborough, UK), fixed in paraffin using an embedder (Thermo Fisher Histo Star Embedder, Loughborough, UK) and cut with a microtome (Leica HI1210, Leica Microsystems Ltd., Wetzlar, Germany) to a slice of 3 μm, placed on a slide and dehydrated on a hotplate (Leica ASP300S, Leica Microsystems Ltd., Wetzlar, Germany). Then, the prepared samples were dyed with hematoxylin and eosin and examined under a microscope (Olympus BX41, Olympus Corporation, Tokyo, Japan). A total of 8 slides were prepared from the jejunal segment per bird, and 10 individual well-oriented villi were measured per prepared slide (80 villi/bird). The average of slide measurements per sample was stated as a mean for each bird. Villus width (VW) was measured at the base of each villus; villus height (VH) from the top of the villus to the villus-crypt junction, crypt depth (CD) from the base of the adjacent villus to the sub-mucosa, the ratio of VH to CD and villus surface area were calculated.
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5

Sunstar Gonad Histology Sexing Protocol

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Gonadal tissue from sunstars which could not be sexed through gross visual examination were dissected and fixed in Davidson’s fixative for at least 24 h. Following fixation, samples were processed in a Thermo Scientific Excelsior AS tissue processor following standard overnight routine processing schedule, where tissues were dehydrated through ethanol series, placed in xylene substitute, and then embedded in paraffin wax. Sections 3 µm thick were taken using a Leica HistoCore Multicut semiautomated rotary microtome, stained with hematoxylin and eosin, mounted and coverslipped. Sunstar gonads were sexed via light microscopy using a Nikon Eclipse E800 microscope and compared to images from [121 ]. Figure 11 illustrates male and female sunstar gonads.
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6

Testis Histology and RNA Extraction

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Testes were removed at necropsy. Two transverse slices were taken from the centre of the left testis, fixed overnight in 10% neutral buffered formalin (Thermo Scientific – 16499713), then transferred to 70% ethanol (VWR – 20821.330) prior to processing, and embedding in paraffin wax for histology (Excelsior AS, Thermo Scientific). A 5mm thick transverse slice was taken from the centre of the right testis and frozen on dry ice prior to storage at −80°C until RNA extraction.
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7

Comparative Cytological Analysis of Wax Gourd Seeds

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To compare the cytological characteristics of the seeds between the two parents, seeds with the same growth based on the maximum cross-section of wax gourd fruit (30 DAP) were sampled. They were immediately fixed in a formalin/acetic acid/alcohol fixative solution with 70% ethanol for 24 h and dewaxed using a dehydrator (Excelsior AS; Thermo Fisher Scientific, Waltham, MA, USA). Wax blocks were sliced into sections using a paraffin slicer (Histocore Arcadia h; Leica Biosystems, Nussloch, Germany), and 4–7 μm thick tissue slices were prepared using a slicer (RM2235; Leica). Subsequently, the sections were rehydrated and stained using the safranin O/fast green staining method, and finally dewaxed with xylene. Tissue sections were scanned using a fluorescence microscope (AxioVert.A1; Zeiss, Oberkochen, Germany), and the images were observed using the NDP.view.2 software (https://nanozoomer.hamamatsu.com/eu/en/products/product-for-research/U12388-01.html). Cell sizes and numbers were determined using the ImageJ software (https://imagej.net/downloads), and the experiment was repeated three times.
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8

Tissue Processing Protocol

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The harvested tissues were processed with the following reagents and respective soaking duration. The stages are formalin, 3.5 hrs; formalin, 0.5 hr; six ascending gradient of alcohols (75%, 90%, 95%, 100%, 100%, 100%), each step for 1 hr; three changes of xylene at 1 hr per step and lastly wax infiltration in three changes of wax at 1.5 hrs per step. This stage was performed using Excelsior™ AS tissue processor (Thermo Scientific™, USA).
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9

Kidney Tissue Sectioning and Preparation

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Kidney cross-sections of the cortex and medulla were dehydrated with isopropyl alcohol and infiltrated with paraffin in a tissue processor (Excelsior AS, Thermo Scientific, Inc.). Tissues were allowed to solidify in a base mold and then snapped into plastic tissue cassettes using a paraffin molding processor (HistoStar, Thermo Scientific, Inc.). Samples were cut to 5 μm thickness sections with a microtome (HM 355 S, Thermo Scientific, Inc.), and continuous “ribbon” of the sections were formed. Sections were carefully transferred onto a 40°C water dish for about 3–5 min to flatten and avoid wrinkles in the sectioned tissues.
Tissue slices were placed on the charged microscope slides, and deparaffinization was performed by placing the slides in a 60°C oven for 30 min in order to melt any extra paraffin. Slides were rinsed twice with a xylene solution for 5 min each, followed by hydration through a series of washing for 1 min each in decreasing alcohol concentrations (100, 95, 80, 70%). Slides were then submerged in the distilled water for 3 min for the staining process.
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10

Liver Enzyme Activity and Histopathology Analysis

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The serum ALT activity, AST activity, and ALP activity were determined using a microplate reader (PerkinElmer 2030), according to the instructions of the manufacturers. Briefly, for ALT activity analysis, ALT reacted with alanine and α-ketoglutarate and produced pyruvic acid. Pyruvic acid was then reacted with 2,4-dinitrophenylhydrazine (DNPH) to form phenylhydrazone, which could be dissolved in sodium hydroxide and then detected at 505nm . For AST activity analysis, AST catalyzed aspartate and α-ketoglutarate to form oxalacetate and glutamate. Oxalacetate could decarboxylate automatically to pyruvic acid, which could react with DNPH and then be detected at 510 nm . For ALP activity analysis, ALP catalyzed disodium phenyl phosphate to form phenol, which could react with 4-aminoantipyrine and potassium ferricyanide and could be detected at 520 nm . For pathological analysis, the mice liver tissues were fixed in 10% neutral buffered formaldehyde solution for 24 h, paraffin-processed (Excelsior AS and HistoStar; Thermo Scientific) and sectioned at 4μm (Leica RM2125RTS). The sections were stained with hematoxylin-eosin (HE) and examined for histopathological changes under the microscope (Olympus DX45). The images were taken by the built-in software installed in the microscope.
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