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13 protocols using vectamount mounting media

1

Histological and Biochemical Analysis of Liver in AOM-Treated Mice

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Paraffin-embedded livers from vehicle and AOM-treated mice were sectioned into 3 µm sections and mounted onto positively charged slides (VWR, Radnor, PA). Slides were deparaffinized and stained with Hematoxylin QS (Vector Laboratories, Burlingame, CA) for one minute followed by staining for one minute with eosin Y (Amresco, Solon, OH) and rinsed in 95% ethanol. The slides were then dipped into 100% ethanol and subsequently through 2 xylene washes. Coverslips were mounted onto the slides using Vectamount mounting media (Vector Laboratories). The slides were viewed and imaged using an Olympus BX40 microscope with an Olympus DP25 imaging system (Olympus, Center Valley, PA).
Serum ALT and bilirubin were assessed using commercially available kits. Alanine aminotransferase measurement was performed using a fluorometric activity assay (Sigma-Aldrich, St. Louis, MO). Total bilirubin was assayed using a total bilirubin ELISA (CusaBio, Wuha, China). All assays and subsequent analyses were performed according to the manufacturer’s instructions.
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2

Immunohistochemistry of Synaptophysin

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Unstained sections were de-paraffinized, rehydrated, and placed in Target Retrieval Solution (Dako, Carpinteria, CA) for 10 min at 100 °C. After cooling for 20 min, slides were quenched with 3% hydrogen peroxide for 5 min, followed by blocking with 3% goat serum and primary antibody incubation (Synaptophysin, 1:200, Sigma/Cell Marque #336R-95/clone MRQ-40, St. Louis, MO) overnight at 4 °C. Sections were then incubated with anti-biotin secondary antibodies (1:1000) and labeling was then detected with the Vectastain ABC kit (Vector Laboratories). Slides were mounted using Vectamount mounting media (Vector Laboratories).
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3

Immunohistochemical Staining of Paraffin Embedded Tissue

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2 µm thick slides of paraffin embedded tissue were used for immunohistochemical staining. Antigen retrieval was performed by cooking the slides in DAKO Antigen retrieval buffer (DAKO, Santa Clara, CA) for 30 min. Endogeneous peroxidase activity was blocked by 3% H2O2. Slides were blocked with PBS containing 5% bovine serum albumine (BSA) and 0.3% Triton X-100 for 1 h. Antibodies were diluted in PBS containing 1% BSA and 0.3% Triton X-100 and added on the slides and incubated over night at 4 °C. Anti-mouse secondary antibody was used from DAKO. DAB staining kit was used from Vector Laboratories (Burlingame, CA). After DAB reaction the slides were counterstained with Hematoxylin and mounted with VectaMount mounting media from Vector Laboratories.
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4

Immunohistochemical Analysis of Neuroinflammation

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MPTP, tamoxifen, MPP+, normal goat serum (NGS), diaminobenzidine, H2O2, carbenoxolone and ethidium bromide were purchased from Sigma-Aldrich. Vectastain Avidin-biotin peroxidase ABC kit, Vectashield and Vectamount mounting media were purchased from Vector. RNeasy Lipid Tissue Mini Kit was purchased from Qiagen. Superscript III reverse transcriptase kit and mouse ELISA TNF-α kit were purchased from InVitrogen. Iba-1 antibody was obtained from Wako. S100-beta and GFAP antibodies were purchased from Sigma-Aldrich; tyrosine hydroxylase (TH) and NeuN antibodies from Merck Millipore; GR antibodies from Santa Cruz (M20) and AbCam. Secondary biotinylated antibodies were purchased from Vector, whereas fluorescent secondary antibodies, anti-mouse Alexa 488, anti-rabbit Cy3 and anti-rabbit Alexa 633 were purchased from InVitrogen. Cx43-mimetic peptide Gap26 and  TAT-Gap19 were obtained from Pepnome Inc. and synthesized at >95% purity.
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5

Histopathological Analysis of Tissue Samples

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Tissue samples were fixed in 10% phosphate-buffered formalin and embedded in paraffin. Formalin-fixed, paraffin-embedded sections were cut 4-μm thick, mounted on poly-l-lysine–coated slides (Sigma), and dried overnight at 37°C. Sections were then dewaxed in xylene, rehydrated according to standard histopathologic procedures, and stained with H&E. Immunodetection was done using the DakoCytomation LSAB+Kit according to manufacturer's protocol (Dako, Denmark). The slides were then counterstained with Hematoxylin and covered with VectaMount Mounting Media (Vector Labs, Burlingame, CA). Each stained section was then evaluated by microscopy.
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6

Multi-Modal Tissue Staining and Analysis

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Cryosections were permeabilized, blocked, and incubated with primary antibodies (see Supplementary material online, Table S1) or isotype controls followed by Alexa-647 conjugated secondary antibodies, and nuclei counterstained with DAPI before mounting in RapiClear 1.52 (Sunjin Lab). FFPE sections were dewaxed, antigen retrieval-treated, and blocked before staining with first anti-FBLN2 or isotype control, visualized with HRP-conjugated anti-Rabbit (Cell Signalling Technology, 8114) and DAB peroxidase substrate (SignalStain), and subsequently with anti-αSMA (DAKO, M0851), visualized with biotin-coupled anti-Mouse (DAKO, E0433), and Vectastain avidin-coupled alkaline phosphatase with Blue AP substrate solution (Vector Labs) before mounting in VectaMount mounting media (Vector Labs). RNA in situ hybridization of Hs-LUM-C1 probes coupled to Opal™ 690 was performed using RNA Scope® Multiplex Fluorescent v2 kits (ACD), according to the manufacturer’s instructions and imaged using a ZEISS Axioscan slide scanner.
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7

Histological Liver Analysis and Serum Biomarkers

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Paraffin-embedded livers were cut into 3-μm sections and mounted onto positively charged slides (VWR, Radnor, PA). Slides were deparaffinized and stained with Hematoxylin QS (Vector Laboratories, Burlingame, CA) for 1 min, followed by staining for 1 min with eosin Y (Amresco, Solon, OH), and rinsed in 95 % ethanol. The slides were then dipped into 100 % ethanol and subsequently through two xylene washes. Coverslips were mounted onto the slides using Vectamount mounting media (Vector Laboratories). The slides were viewed and imaged using an Olympus BX40 microscope with an Olympus DP25 imaging system (Olympus, Center Valley, PA).
Serum alanine aminotransferasase (ALT) and bilirubin were assessed using commercially available kits. Alanine aminotransferase measurement was performed using a fluorimetric activity assay. Total bilirubin was assayed using a total bilirubin ELISA. All assays and subsequent analyses were performed according to the instructions provided by the manufacturers.
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8

Multiplex RNA Analysis of WNT-MB Tumors

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Paraffin-embedded tissue sections from two WNT-MB tumours of the single-cell cohort (SJ99 and SJ129) were obtained from St. Jude Children’s Research Hospital. Sections were mounted on glass slides and stored at −80°C. Slides were stained using the RNAscope 2.5 HD Duplex Detection Kit (Advanced Cell Diagnostics (ACD), 322430). Slides were baked for 1 hour at 60°C, deparaffinized and dehydrated with xylene and ethanol. The tissue was pretreated with RNAscope Hydrogen Peroxide (ACD, 322335) for 10 minutes at room temperature and RNAscope Target Retrieval Reagent (ACD, 322000) for 15 minutes at 98°C. RNAscope Protease Plus (ACD, 322331) was then applied to the tissue for 30 minutes at 40°C. Hybridization probes were prepared by diluting the C2 probe (red) 1:50 into the C1 probe (green). Advanced Cell Technologies RNAscope Target Probes used included Hs-MKI67 (ACD, 591771 and 591771-C2), Hs-DKK2 (ACD, 531131-C2), Hs-STMN2 (ACD, 525211-C2), Hs-ZFP36 (ACD, 427351) and Hs-EGR1 (ACD, 457671). Probes were added to the tissue and hybridized for 2 hours at 40°C. A series of 10 amplification steps were performed using instructions and reagents provided in the RNAscope 2.5 HD Duplex Detection Kit. Tissue was counterstained with Gill’s hematoxylin for 25 seconds at room temperature followed by mounting with VectaMount mounting media (Vector Laboratories).
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9

Multiplex RNA Detection in Paraffin Tissues

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Paraffin-embedded tissue sections were mounted on glass slides and stored at −80 °C. Slides were stained using the RNAscope 2.5 HD Duplex Detection Kit (Advanced Cell Diagnostics, #322430), as previously described (Filbin et al., 2018 (link)). Briefly, slides were baked for 1 h at 60 °C, deparaffinized and dehydrated with xylene and ethanol. The tissue was pretreated with RNAscope Hydrogen Peroxide (Cat. No. 322335) for 10 min at room temperature and RNAscope Target Retrieval Reagent (Cat. No. 322000) for 15 min at 98 °C. RNAscope Protease Plus (Cat. No. 322331) was then applied to the tissue for 30 min at 40 °C. Hybridization probes were prepared by diluting the C2 probe (red) 1:50 into the C1 probe (green). Advanced Cell Technologies RNAscope Target Probes used included Hs-CD24 (#313021-C2), Hs-CD44 (#311271-C2), Hs-CD14 (#418801-C1). Probes were added to the tissue and hybridized for 2 h at 40 °C. A series of 10 amplification steps were performed using instructions and reagents provided in the RNAscope 2.5 HD Duplex Detection Kit. Tissue was counterstained with Gill’s hematoxylin for 25 s at room temperature followed by mounting with VectaMount mounting media (Vector Laboratories).
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10

RNA ISH Analysis of PDX Tumor Samples

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Formalin-fixed, paraffin-embedded PDX tumors and mouse organs were sliced into 5-μm sections and subjected to standard H&E staining or IHC to detect GFP expression. RNAscope technology [Advanced Cell Diagnostics (ACD)] was used for RNA ISH according to the manufacturer’s instructions as described previously (42 (link)). Briefly, tissue sections on slides were baked for 1 hour at 60°C, deparaffinized, and dehydrated. The tissues were pretreated with hydrogen peroxide for 10 min at room temperature and with target retrieval reagent for 15 min at 98°C. Protease Plus was then applied for 30 min at 40°C. EPHB2 probe (ACD) was hybridized for 2 hours at 40°C, followed by signal amplification. Tissue was counterstained with Gill’s hematoxylin followed by mounting with VectaMount mounting media (Vector Laboratories). Images were taken with a Hamamatsu NanoZoomer S60 Digital slide scanner, at ×40 magnification.
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