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4 protocols using goat anti rat hrp

1

SDS-PAGE Protein Analysis Protocol

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The samples for SDS-PAGE were prepared as described in [26 (link)]. Protein samples were separated on SDS-PAGE gels (Any kD, Mini-PROTEAN TGX, Bio-Rad) and transferred to PVDF membranes by electroblotting using standard techniques. The HA tagged proteins were probed using rat anti-HA high affinity clone 3F10 (Roche) diluted to 1:1500 in PBS-T containing 3% BSA for 2h at room temperature. Bound antibodies were detected with horseradish peroxidase conjugated secondary antibody (goat anti-rat HRP, Thermo Scientific) diluted 1:10000 in 3% milk. The blots were developed by using Clarity Western ECL Substrate (Bio-Rad) and images were recorded on a Chemi-Doc MP (Bio-Rad).
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2

Peptide/MHC Biotinylation Validation Assay

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To investigate the success of peptide/MHC biotinylation, a 96-well high protein binding plate (Corning) was first coated overnight at 4 °C with 4 μg/ml streptavidin (Promega) in 0.1 M sodium carbonate and then blocked (3% BSA/PBS) for 1 hr at RT. Biotinylated protein samples were diluted in block and added to wells at various dilutions and incubated at RT for 1 hr. Wells were washed extensively with PBST and then exposed to 4 μg/ml of either a MHC class I-reactive (clone M1/42; Biolegend) or rat isotype control IgG (Biolegend) antibody in block. In separate wells, a positive control biotinylated irrelevant rat antibody (Biolegend) was incorporated to validate the extent of streptavidin binding. The plate was again washed with PBST and relevant wells provided a goat anti-rat HRP (Thermo Scientific Fisher) or goat anti-mouse FcγR-specific HRP (Jackson ImmunoResearch, West Grove, PA) antibody in block for 1 hr at RT. Wells were washed with PBST and developed for 5 min after the addition of 200 μl 1-Step Ultra TMB (Thermo Scientific Fisher). Reactions were terminated with 100 μl TMB stop solution (KPL), and the absorbance immediately read at 450 nm using a Cytation 5 Imaging Reader (Biotek, Winooski, VT).
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Western Blot Analysis of Protein Markers

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Whole-cell lysates were prepared with phosphatase and protease inhibitor cocktail and loaded to 12% resolving SDS-PAGE gels with equal amount of total protein. After electrophoresis, proteins were transferred to polyvinylidene difluoride transfer membrane (PVDF) followed by blocking in 5% non-fat milk and incubated with primary antibodies. After washing with TBST (TBS with 0.1% Tween), secondary antibodies conjugated with HRP were used to incubate the membranes. Samples were developed by Chemiluminescent Substrate (Thermo Fisher) and exposed by Odyssey Imaging Systems (LI-COR). Primary antibodies used are as following: HSF1 (Enzo 10H8 #ADI-SPA-950-D 1: 1000), GAPDH (Cell Signaling 14C10 #2118 1:1000), CBS (Sigma 3E1 #WH0000875M1 1 ug per mL), β-actin (Cell Signaling 13E5 #4970 1:1000), Caspase 3 (Cell Signaling #9662 1:1000), and cleaved Caspase 3 (Cell Signaling #9661 1:1000). Secondary antibodies used were Goat anti-rat HRP (Invitrogen # 31470 1:10000), Goat anti-mouse HRP (BioRad #1721011 1.34:4000), and Goat anti-rabbit HRP (BioRad # 1706515 1.34:4000). Western blots protein levels were quantified with Image J. Unedited blots are provided in the Supplementary Information (Supplementary Fig. 10).
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4

Histopathological Assessment of Murine Brain Tumors

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Brain tissues were harvested after euthanizing mice by cervical dislocation and fixed using 10% neutral buffered formalin (Sigma). Fixed tissues were embedded in paraffin blocks and sectioned into slices of 5 μm thickness. Consecutive sections of the brain were subjected to hematoxylin and eosin (H&E) staining for evaluation of tumor morphology and cellularity, and to bright field immunohistochemistry for markers of vascularity – CD34 (EP373Y, Abcam) and hypoxia - Carbonic anhydase IX (CAIX) enzyme (NB100–417, Novus Biologicals). After deparrafinizing and dehydrating, heat-induced epitope retrieval was performed using Bond™ Epitope Retrieval Solution (pH 9.6) for 40 min at 100°C. Slides were then incubated with the primary antibody followed by secondary antibody (goat anti-rat HRP, Invitrogen, Carlsbad, CA; 1:50) for 30 min. Bond™ Mixed DAB Refine was applied for 5 min, and rinsed with deionized water to stop the DAB reaction and counter stained with hematoxylin. Slides were finally dehydrated and mounted in synthetic mounting media. Bright field images of slides were taken using Nikon NiE: Ri2 microscope with DS-Ri2 camera using NIS elements 4.5 software. Tissue sections stained for H&E and CD34 were analyzed by board-certified pathologist. % areas of sections positively stained for CAIX were analyzed using Image J.
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