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2 protocols using red 610 kit

1

Multiplex IHC Staining and Analysis

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All samples for IHC were FFPE into blocks. FFPE blocks were sectioned at 4 mm. IHC was run on a Ventana Discovery Ultra. Primary antibodies used are listed in Supplementary Methods. The Chromomap DAB detection kit (Ventana; 760-159) and OmniMap anti-Rabbit HRP (Ventana; 760-4311) were used for rabbit primary antibodies. DABMap detection kit (Ventana; No. 760-124) and biotinylated antirat secondary antibody-mouse adsorbed (Vector Labs; No. BA9401)were used for rat primary antibodies. All chromogenic staining was done using DAB as a substrate and counterstained using Hematoxylin II (Ventana; No. 790-2208) and Bluing Reagent (Ventana; No. 760-2037). For fluorescent multiplexing, Ki67, granzyme B, and CD8 primary antibodies were sequentially stained, with a CC2 denaturation step in between. The following substrates were used for a fluorescence Red 610 kit (Ventana; No. 760-245), DCC kit (Ventana; No. 760-240), and FAM (Ventana; No. 760-243), and the counterstain used was QD DAPI (Ventana; No. 760-4196). Chromogenic slides were scanned using an Aperio AT2 (Leica), and fluorescent slides were scanned with an Aperio Versa (Leica). Image analysis was performed on the HALO platform (Indica Labs).
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2

Immunohistochemical Profiling of Organoid Structures

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Four-micron sections of formalin-fixed paraffin embedded organoids were stained with hematoxylin and eosin (Ventana Medical Systems, Tucson, AZ). Immunohistochemistry was performed with an automated, validated, and accredited staining system (Ventana Benchmark ULTRA) using the UltraView or OptiView universal DAB detection Kit (Ventana Medical Systems). After deparaffinization and heat-induced antigen retrieval, the tissue samples were incubated with WT1 (Cell Marque, Rocklin, CA), ECAD (Ventana Medical Systems), Villin-1 (Abcam, Cambridge, UK), CD31 (Cell Marque), renin (Abcam), NKCC2 (StressMarq Biosciences, Victoria, BC, Canada), NHE3 (StressMarq), CD34 (Cell Marque), COL1A1 (Novus Biologicals, Littleton, CO), or PDGFRa (R&D systems). Incubation was followed by hematoxylin II counterstaining. Double stainings of PDGFRa and renin were performed by incubating the samples with PDGFRa for 32 minutes at 37 C followed by detection with Red610 kit (#760-245, Ventana) and renin for 32 minutes at 37 C followed by detection with FAM kit (#760-243, Ventana). An AF488-conjugated anti-human mitochondria antibody MAB1273A4 (Millipore, Billerica, MA) was used to detect
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