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6 protocols using anti ki 67 clone 30 9

1

Immunohistochemistry of Ki-67 in Myx2 Tumors

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IHC studies using the streptavidin-biotin peroxidase complex method were carried out on histological slides from MUG-Myx2a and MUG-Myx2b mice tumours, employing a rabbit monoclonal primary antibody against the anti-Ki-67 (clone 30–9) (Ventana Medical Systems) using the BenchMark Ultra instrument (Ventana Medical Systems). Slides were photographed using an Olympus BX51 microscope with an Olympus DP71 microscope digital camera. The stained slides were scanned digitally and positive and negative cells were quantified using the ImageScope software (ImageScope Virtual Slide, version 6.25, Aperio Technol., Vista, US). Positivity was determined by assessing the number of positive cells / number of total cells.
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2

Multiplex Immunohistochemistry for Tissue Analysis

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Tissue sections were prepared from formalin-fixed paraffin embedded tissue blocks and cut to 4 μm serial sections and mounted on Superfrost Plus (VWR). The procedure for multiplex immunohistochemistry (mIHC) was followed by a manufacturer’s protocol for Opal7-color automation IHC kit (Akoya Bioscience), and the staining was performed with Autostainer DISCOVERY ULTRA (Ventana). Antibodies used in mIHC are anti-CD3 (clone 2GV6, Ventana), anti-CD20 (clone L26, Ventana), anti-Ki67 (clone 30-9, Ventana), anti-FOXP3 (clone SP97, Spring), anti-pan cytokeratin (CK; clone AE1/AE3, DAKO), anti-CD117 (clone c-kit, DAKO). The molecular markers of immune panel (CD3, CD20, Ki67, CKs, FOXP3, and CD117) were visualized with Opal520, Opal540, Opal570, Opal620, Opal650, and Opal690, respectively. DAPI counterstaining was performed with Discovery QD DAPI (Roche). ProLong Diamond Antifade Mounting (ThermoScientific) was used for mounting the coverslip. Detailed staining conditions and autostainer’s protocols are reported in our recent report86 (link).
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3

FGF9 Signaling Pathway Evaluation

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AZD4547 (#S2801) was purchased from Selleck Chemicals. Recombinant FGF9 protein was purchased from Peprotech. Antiphospho-p44/42 MAPK (Tyr202/Tyr204; #3126), anti-total p44/42 MAPK (#3127), anti-RB1 (#9309) anti-phospho-AKT (Ser473; D9E; #4060), and anti-total AKT (#9272) antibodies were purchased from Cell Signaling Technologies. An anti-actin antibody produced in mice (#A5441) and rabbit polyclonal antibodies against CGRP (#C8198) were purchased from Sigma-Aldrich. An anti-chromogranin antibody (#412751) and anti-synaptophysin antibody (#413831) were purchased from Nichirei Biosciences Inc. An anti-FGF9 antibody was purchased from R&D Systems (#AF-273NA) and Abcam (#ab71395). A goat anti-GFP polyclonal antibody (#600-101-215) was purchased from Rockland. A rabbit polyclonal antibody against FGFR1 (#sc-121) was purchased from Santa Cruz Biotechnology. Anti-EGFR (clone 3C6) and anti-Ki67 (clone 30-9) antibodies (CONFIRM kits) were obtained from Ventana-Roche.
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4

Multimodal Evaluation of Tissue Markers

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Human tissues were fixed in formalin and mouse tissues were fixed in 4% paraformaldehyde for 24 h before paraffin embedding. Immunostaining was performed on 5-μm sections via standardized automated protocols on a Ventana Discovery XT machine with the following antibodies: anti-L1CAM (clone 14.10, BioLegend), anti-Ki67 (clone 30–9, Roche) and anti-E-cadherin (clone 24E10, Cell Signaling). For dual LGR5 FISH and L1CAM immunofluorescence, freshly cut 3-μm paraffin sections were stained with the RNAscope 2.5 LS Brown kit (ACD, 322100) for FISH and the Bond Polymer Refine Detection kit (Leica, DS9800) for immunofluorescence on a Leica Bond RX instrument following routine manufacturer protocol ACD 2.5 DAB and Protocol F, using RNAscope 2.5 LS probe for human LGR5 (ACD, 311028) and anti-L1CAM antibody (clone 14.10, BioLegend) with Tyramide Alexa Fluor 594 (Life Technologies, B40957) instead of the DAB step. An Ultra-High-Def mouse-on-mouse kit (StatLab) was used for mouse L1CAM staining. For Ki67 and L1CAM scoring, stained serial sections with overlapping morphology were aligned with the SIFT algorithm and the extent of immunostaining was scored with ImageJ software. L1CAM staining in Extended Data Fig. 4l,m was scored with ImageJ software. All other immunostaining was visually scored in a blinded fashion.
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5

Molecular Subtyping of Breast Tumors

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Systematic assessment of samples in 10% neutral buffered formalin blocks was performed using a tissue microarray (TMA). The approximate molecular subtypes were assessed by immunohistochemistry. The tumor markers anti-ER SP1, anti-PR 1E2, anti-HER2/neu (clone 4B5), and anti-Ki-67 (clone 30-9) were used (Roche Diagnostics). Tumors were rated ER/PR-positive when nuclear labeling was evident in more than 1% of tumor cells. A semi-quantitative score was used for HER2 staining. A score of 0, 1+, or 2+ was considered negative staining, and a score of 3+ was considered positive staining. Fluorescence in situ hybridization (FISH) was performed for samples with a 2+ score. The approximate molecular subtypes were clustered as a function of the immunohistochemical results as follows: luminal A (ER/PR-positive, HER2-negative, and Ki-67<14), luminal B/HER-negative (ER/PR-positive, HER2-negative, and Ki-67 ≥14), luminal B/HER-positive (ER/PR-positive and HER2-positive), HER2 (ER/PR-negative and HER2-positive), and triple negative (ER/PR-negative and HER2-negative). In the absence of TMA information, the primary immunohistochemical lamina was reviewed. Discrepancies were discussed until reaching consensus. To evaluate the analysis, luminal A and luminal B/HER-negative samples were grouped into the luminal/HER-negative group.
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6

Postn and Ki67 Immunohistochemistry Protocol

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Immunohistochemistry (IHC) for Postn was performed using the Ventana Discovery automation system (Roche, Switzerland) according to the manufacturer's protocol. A rabbit polyclonal anti-Periostin antibody (ab14041, 1: 2,000, Abcam, UK) was used according to the manufacturer's instructions on 3-μm sections. Anti-Ki67 (clone 30-9, Roche) staining was also performed using the same system.
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