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3 protocols using opal reagents

1

Multiplex IHC Staining of Tumor Samples

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Tumors were harvested and fixed overnight in 10% neutral buffered formalin (NBF). Fixed samples were embedded in paraffin, and 4 μm sections were cut. Samples were dewaxed in xylene and antigens retrieved at 125 °C for 3 min in 10 mm citrate buffer (Sigma‐Aldrich) pH 6. Endogenous peroxidases were inactivated with 3% H2O2. CD31 staining was performed using DAB IHC. Primary CD31 antibody (abcam, ab28364, 1:1000) was incubated overnight at 4 °C, secondary ImmPress antibody (Vector Laboratories) for 1 h at room temperature, followed by DAB peroxidase (HRP) substrate kit for 6 min. For multiplexing experiments, Perkin Elmer OPAL reagents were used as per kit instructions. The following order was used: CD8 (ebioscience 4SM15, 5 μg mL−1) 570, PD‐1 (abcam EPR20665, 0.8 μg mL−1) 620, CK8 (abcam EP1628Y, 0.2 μg mL−1) 520 and DAPI (Perkin Elmer). DAB IHC was visualised on the Olympus BX51 and VS120 slide scanner and quantified using HALO v2.3 (Indica Labs). Multiplexing IHC was visualised using the Perkin Elmer Vectra 3 microscope and analysed using InForm v2.4.0 (Perkin Elmer) and HALO v2.3.
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2

Multiplex Immunofluorescence for Cerebellar Analysis

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Multiplex immunofluorescence was performed on small cerebellar sections from FFPE
tissue blocks with OPAL reagents from PerkinElmer as described in the
PerkinElmer Multiplex IHC manual. Primary antibodies used are summarized in
eTable 1 (links.lww.com/NXI/A726, method: IF). Pretreatment (heating) in a
Braun household vegetable cooking device was performed in AR9 antigen retrieval
buffer from PerkinElmer for 40 minutes before the first antibody and with AR6
antigen retrieval buffer from PerkinElmer for 30 minutes between each antibody
staining.
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3

Multicolor Immunohistochemistry for Cellular Phenotyping

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We performed tyramide signal amplification labeling with the Opal reagents (PerkinElmer, Waltham, Massachusetts) using the Opal 4‐color automation IHC method. The primary antibodies used were as follows; LOX‐1 (ab126538, 1:800, Abcam, Cambridge, UK), CD15 (Carb‐3, 1:400, Dako, Glostrup, Denmark), CD11b (ab52478, 1:400, Abcam, Cambridge, UK), CD45 (1:400, #13917, Cell Signaling Technology, Inc., Danvers, Massachusetts), CD3 (ab16669, 1:300, Abcam, Cambridge, UK), CD20 (L26, 1:400, Dako, Glostrup, Denmark), CD163 (1:1000, #93498, Cell Signaling Technology, Inc., Danvers, Massachusetts), and α‐SMA (M0851, 1:100, Dako, Glostrup, Denmark). Antigens were retrieved from the tissue sections using ImmunoSaver (Nisshin EM, Tokyo, Japan). Tissue sections were incubated with fluorophores Opal 520, 570, and 690 for 10 minutes at room temperature. Antigen retrieval was performed using 10 mM sodium citrate buffer pH 6 in a microwave for 15 minutes. Finally, all sections were counterstained with DAPI. Images were captured using the BZ‐X700 microscope (Keyence). We analyzed 10 cases from the stromal LOX‐1 high group using triple‐labeled high‐power fields.
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