Table 3 Reagents and tools table
From: Tunable PhenoCycler imaging of the murine pre-clinical tumour microenvironments
Reagent or Resource | Reference or Source | Identifier or Catalog No. |
|---|---|---|
Experimental Models | ||
BALB/C Mice | Charles River | BALB/cAnNCrl |
C57BL/6J Mice | The Jackson Laboratory | Strain #:000664 |
Tyr::CreER/BRafCA/+/Ptenlox/lox Mice | The Jackson Laboratory | Strain #:013590 |
A20 | ATCC | TIB-208 |
Eµ-Myc | Lab of Dr. Jerry Pelletier | N/A |
66cl4 | Lab of Dr. Josie Ursini-Siegel | N/A |
4T1 | ATCC | CRL-2539 |
YUMMER1.7 | Lab of Dr. Marcus Bosenberg | N/A |
Drugs and Treatments | ||
4-Hydroxytamoxifen | Sigma-Aldrich | H6278 |
IgG Control | Bio X Cell | 2A3, BE0089 |
aPD-1 | Bio X Cell | RMP1-14, BE0146 |
Chemicals and Reagents | Â | Â |
Tris | Bio Basic | TB0195 |
EDTA | Bio Basic | EB0185 |
Sodium Chloride | Bio Basic | SB0476 |
Potassium Chloride | Bio Basic | PB0440 |
Sodium Hydroxide 10Â N | VWR | BDH7247-1 |
50% H2O2 | Sigma-Aldrich | 516813-500ML |
Paraformaldehyde 16% | Electron Microscopy Sciences | 15,710 |
Tween20 | VWR | 0777-1Â L |
IHC and IF Reagents and Tools | ||
SuperFrost Plus Slides | Fisher | 22-037-246 |
Xylenes | Fisher | X5-4 |
Ethanol | Commercial Alcohols | P016EAAN |
Hydrophobic Barrier PAP Pen | Thermo Scientific | R3777 |
Harris’ Hematoxylin | Sigma-Aldrich | 638 A-85 |
Eosin Y Solution | Sigma-Aldrich | HT110116 |
Donkey Serum | Jackson ImmunoResearch | 017-000-121 |
FC Blocking Reagent | Made in house | Â |
ECL Anti-mouse IgG, Horseradish peroxidase linked whole antibody from sheep | Cytiva | NA931V |
Mouse CD45 Antibody | R&D Systems | AF114 |
Dnk pAb to Goat IgG (HRP polymer) | Abcam | Ab214881 |
ImmPACT DAB Substrate Kit, Peroxidase | Vector Laboratories | SK-4105 |
AF647 donkey anti-rabbit IgG | Invitrogen | A31573 |
Donkey anti-Rat IgG DyLight 650 | Invitrogen | SA5-10029 |
AF647 donkey anti-goat IgG | Invitrogen | A21447 |
DAPI (1Â mg/mL) | Thermo Scientific | 62,248 |
Flouromount-G | Invitrogen | 00-4958-02 |
24 × 55 mm No. 1.5 Thickness Cover Slips | Epredia | 152,455 |
PhenoCycler Antibody Conjugation and Tissue Staining | ||
Lammeli Loading Dye | Bio-Rad | #1610737EDU |
GelCode Blue Stain Reagent | Thermo Scientific | 24,590 |
1X D-PBS | Wisent | 311-425-CL |
Methanol | Commercial Alcohols | P016MEOH |
Akoya Reagents | ||
10X PhenoCycler Buffer | Akoya Biosciences | 7,000,001 |
Staining Kit | Akoya Biosciences | 7,000,008 |
Conjugation Kit | Akoya Biosciences | 7,000,009 |
Black-walled 96-well plate | Akoya Biosciences | 7,000,006 |
Adhesive foil | Akoya Biosciences | 7,000,007 |
Assay Reagent | Akoya Biosciences | 7,000,002 |
Nuclear Stain | Akoya Biosciences | 7,000,003 |
Flow Cell | Akoya Biosciences | 240,204 |
Software | ||
QuPath | Bankhead et al. (68) | Â |
StarDist | Schmidt et al. (69) | Â |
MatLab | MathWorks | Â |
CytoMAP | Stoltzfus et al. (55) Weigert et al. (70) | Â |
GraphPad Prism | Dotmatics | Â |
Other | ||
Microtome | Leica | RM2125 RTS |
PT Link for Pre-Treatment | Agilent | Â |
LED Lamps | Â | 20,000Â lx Intensity |
AxioScan 7 | Zeiss | Â |
PhenoCycler-Fusion | Akoya Biosciences |  |