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8 protocols using view2

1

Evaluation of Bone Invasion in Oral Tumors

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After scanning with CBCT, specimens were immediately fixed in 4% formaldehyde and preserved for at least 48 h. Subsequently, they were decalcified in a mixture of formic acid, acetic acid, and hydrochloric acid. During decalcification, the superficial bone became soft and was removed. This process was repeated until a 3-mm-thick bone slice with the three GP points exposed on the surface was acquired (Fig. 1c). The whole decalcification process took 7–14 days. Finally, the specimens were sliced into 4-μm-thick sections and stained with hematoxylin–eosin. The GP points dissolved during the staining process, and blank circles served as markers of their original positions.
The stained sections were scanned using a digital slice scanning device (NanoZoomer S60, Japan), and the boundary of bone invasion was delineated using NDP. View 2.7 software (Hamamatsu, Japan). The distances between the GP points were measured for specimens embedded in paraffin and specimens stained with hematoxylin–eosin. For histopathological specimens, bone invasion was defined as replacement of bone by an advancing tumor front. The presence of tumor cells in the inferior alveolar nerve fibers indicated positive nerve invasion. A senior pathologist determined the diagnostic result and delineated the boundary of bone invasion with NDP. View 2.7 software (Hamamatsu, Japan).
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Histological Analysis of Glabrous Skin

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A hematoxylin and eosin stain was performed to assess the general morphology of the glabrous skin of PIEZO1cKO and wild-type littermate controls. Glabrous skin of PIEZO1cKO and wild-type animals was dissected, and the tissue was fixed in 4% formaldehyde. The skin was processed, embedded in paraffin, sectioned into 4 μm sections and dried at RT until subsequent staining at the MCW Histology Core. Rehydrated sections were stained in hematoxylin for 3 min, washed in Richard-Allan Scientific Signature Series Clarifier 1,2 (for 45 sec, dipped for 30 sec in 0.1% ammonia water (bluing agent)), stained in eosin for 30 s, washed four times using 100% EtOH and lastly rinsed in Xylene. Slides were scanned using a Hamamatsu Nanozoomer HT slide scanner (Hamamatsu Photonics, K.K., Hamamatsu City, Japan) and images were assessed using NDP.View 2 software (Hamamatsu Photonics).
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3

Histological Tissue Processing and Staining

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Tissues were embedded in Optimal Cutting Temperature compound, and frozen histological sections were cut at 30 µm, mounted on polyethylene naphthalate (PEN) slides and fixed in 70% ethanol for 5 min, followed by two washes with PBS for 1 min each. Slides were manually stained in hematoxylin and eosin (H&E) using a conventional staining protocol. A subset of samples (PD44594c–h and PD44589f) were fixed in PAXgene Tissue FIX (Qiagen) according to the manufacturer’s instructions. Fixed tissue samples were embedded in paraffin using a Tissue-Tek tissue-processing machine (Sakura). No formalin was used in the preparation, storage, fixation or processing of samples. Processed tissue blocks were embedded in paraffin wax, sectioned to 10-µm thickness and mounted onto PEN slides (Leica). Tissue slides were stained using a standard H&E protocol. Slides were temporarily coverslipped and scanned on a NanoZoomer S60 Slide Scanner (Hamamatsu); images were viewed using NDP.View2 software (Hamamatsu).
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4

Tissue Preparation and Staining Protocol

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Tissues were embedded in Optimal Cutting Temperature (OCT) compound, frozen histological sections were cut at 25–30 µm and mounted on polyethylene naphthalate (PEN) slides and fixed in 70% ethanol for 5 minutes followed by two washes with phosphate buffered saline for 1 min each. Slides were manually stained in haematoxylin and eosin using a conventional staining protocol. A subset of samples were fixed in RNAlater (Sigma Aldrich) according to manufacturer’s instructions. Fixed tissue samples were embedded in paraffin using a Tissue-Tek tissue processing machine (Sakura). No formalin was used in the preparation, storage, fixation or processing of samples. Processed tissue blocks were embedded in paraffin wax, sectioned to 10 µm thickness and mounted onto PEN slides (Leica). Tissue slides were stained using a standard haematoxylin and eosin (H&E) protocol. Slides were temporarily cover-slipped and scanned on a NanoZoomer S60 Slide Scanner (Hamamatsu), images were viewed with NDP.View2 software (Hamamatsu).
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5

Histological Analysis of Tissues

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For PAS staining, muscle tissues were fixed in 3% glutaraldehyde (EM grade, Electron Microscopy Sciences) in 0.2 M sodium cacodylate buffer for 4 hours at 4°C, washed in 0.1 M sodium cacodylate buffer, and stored at 4°C in the same buffer. For PAS staining of brain tissues, the samples were fixed in 10% neutral-buffered formalin (NBF) for 48 hours, postfixed in NBF containing 1% periodic acid for another 48 hours at 4°C, embedded in paraffin, sectioned, and stained with PAS by standard procedures. Liver tissues were fixed in 10% NBF, and serial sections were stained with hematoxylin and eosin according to the standard procedure. All stained slides were scanned and captured using a Hamamatsu NanoZoomer XR slide scanner equipped with a Plan Apochromatic 20×/0.75 NA lens (Olympus). The images were viewed, processed, and exported as.TIFF using the NDP.view2 software (Hamamatsu). The levels of glucose, bilirubin, creatine kinase, AST, and ALT in blood were measured according to the standard procedure (IDEXX BioAnalytics). The animals were starved overnight prior to the blood collection.
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6

Histological Analysis of Formalin-Fixed Carcinoma

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Formalin-fixed carcinoma samples were embedded in paraffin blocks and cut into sections 3
μm thick. The sections were deparaffinized and then stained with hematoxylin and eosin
(HE). Images of HE-stained specimens were acquired with a Nano Zoomer 2.0-RS (C10730-13,
Hamamatsu Photonics K.K., Shizuoka, Japan) and observed with NDP. View2 software
(Hamamatsu Photonics K.K.).
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7

Matrigel Plug Assay for Angiogenesis

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8‐week‐old C57Bl/6 mice were injected subcutaneously with 0.2 mL of Matrigel (Corning) containing 1 mmol·L−1 heme‐albumin or LPS (1 μg/mL). The injected Matrigel rapidly formed a single, solid gel plug. After 5 days the Matrigel plug was removed, fixed in formalin, and embedded in paraffin. Sections (3–5 μm thick) were prepared, mounted on glass slides, deparaffinized in xylene, rehydrated through graded alcohols, and stained with hematoxylin and eosin (HE) and Abs against F4/80 (Invitrogen MA5‐16363 poly R6), Lys6G (Biolegend 127602), and iNOS (EMD Millipore, ABN26). All slides were scanned using a digital slide scanner (NanoZoomer‐XR C12000, Hamamatsu, Japan), images were taken using NDP.view2 software (Hamamatsu).
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8

Quantifying CD69+ CD8+ T Cells in Liver

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IHC was performed using a Bond-Max automated immunohistochemical staining machine (Leica Microsystems, Milton Keynes, UK). Evaluation of CD69+ CD8+ T cells was performed using double fluorescent immunohistochemistry. Anti-human CD8 monoclonal Ab (Nichirei, Japan, clone C8/144B) and anti-human CD69 monoclonal antibody (Abcam, clone EPR21814) were used as primary Abs. The slides were scanned to obtain multi-colored whole-slide images using a NanoZoomer 2.0HT scanner (Hamamatsu Photonics K.K., Shizuoka, Japan) with a ×40 objective lens, according to the manufacturer’s instructions. The slides were further stained with H&E and rescanned to obtain merged images of H&E images on top of the pre-scanned multi-colored images51 (link). To quantify CD69+ CD8+ T cells, all portal areas were checked for merged CD69+ CD8+ T cells using NDP.view2 software (Hamamatsu Photonics K.K), and the highest number in 1-mm2 areas was determined as the maximum cell count. Detailed information for the antibodies used in this study is summarized in Supplementary Table 2.
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