| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| aSMA, polyclonal | Abcam | Cat# ab5694; RRID: AB_2223021 |
| Vimentin, clone RV202 | BD Biosciences | Cat# 550513; RRID: AB_393716 |
| S100A4 (FSP1), clone S100A4 | Biolegend | Cat# 810101; RRID: AB_2564748 |
| PDGFRa, clone 16A1 | Abcam | Cat# ab96569; RRID: AB_10687154 |
| FAP, polyclonal | Millipore Sigma | Cat# SAB2900181; RRID: AB_10600445 |
| IL-6, clone 1.2-2B11-2G10 | Abcam | Cat# ab9324; RRID: AB_307175 |
| IL-1, polyclonal | Abcam | Cat# ab9722; RRID: AB_308765 |
| MGP, clone OTI8D6 | Abcam | Cat# ab273657; RRID: N/A |
| YAP, clone EPR19812 | Abcam | Cat# ab223126; RRID: N/A |
| CXCL-12 (SDF-1), polyclonal | Abcam | Cat# ab9797; RRID: AB_296627 |
| CD26, polyclonal | R&D AF1180 | Cat# AF1180; RRID: AB_354651 |
| CD56, clone MRQ-42 | Cell Marque | Custom; RRID: N/A |
| HLA Class I, clone EP1395Y | Abcam | Cat# ab216653; RRID: N/A |
| Collagen I, polyclonal | Abcam | Cat# ab34710; RRID: AB_731684 |
| Collagen IV, polyclonal | Abcam | Cat# ab6586; RRID: AB_305584 |
| Fibronectin, polyclonal | Abcam | Cat# ab23751; RRID: AB_447656 |
| PD-1, clone D4W2J | Cell Signaling Technologies | Custom; RRID: N/A |
| PD-L1, clone E1L3N | Cell Signaling Technologies | Custom; RRID: N/A |
| CTLA-4, clone CAL49 | Abcam | Cat# ab237712; RRID: AB_2905652 |
| Ki67, clone B56 | BD Biosciences | Cat# 556003; RRID: AB_396287 |
| CD4, clone EPR6855 | Abcam | Cat# ab181724; RRID: AB_2864377 |
| CD8, clone C8/144B | Biolegend | Cat# sc-53212; RRID: AB_1120718 |
| CD11c, clone EP1347Y | Abcam | Cat# ab216655; RRID: AB_2864379 |
| CD20, clone rIGEL/773 | Novus Biologicals | Cat# NBP2-54591; RRID: AB_2864380 |
| CD31, clone C31.3 + 31.7+31.10 | Novus Biologicals | Cat# NBP2-47785; RRID: AB_2864381 |
| CD68, clone KP-1 | Biolegend | Cat# 916104; RRID: AB_2616797 |
| HLA DR, clone EPR3692 | Abcam | Cat# ab215985; RRID: AB_2864390 |
| Pan Cytokeratin, clone AE-1+AE-3 | Biolegend | Cat# 914204; RRID: AB_2616960 |
| E-cadherin, clone 4A2C7 | Thermo Fisher | Cat# 33–4000; RRID: AB_2533118 |
| Biological samples | ||
| Archival tumor specimens | Stanford University, University of Virginia pathology repositories | Deidentified |
| Tissue microarrays | US Biomax, Inc. | Cat# PA2082a, PA806, PA1921a, PA501, PA803, PA961f |
| Critical commercial assays | ||
| CODEX Staining Kit | Akoya Biosciences | Cat# 7000008 |
| CODEX Antibody Conjugation Kit | Akoya Biosciences | Cat# 7000009 |
| Chemicals, peptides, and recombinant proteins | ||
| Assay Reagent for CODEX | Akoya Biosciences | Cat# 7000002 |
| Nuclear Stain for CODEX | Akoya Biosciences | Cat# 7000003 |
| CODEX Barcode/Reporter RX046 | Akoya Biosciences | Cat# 6150016 |
| CODEX Barcode/Reporter RX049 | Akoya Biosciences | Cat# 6150017 |
| CODEX Barcode/Reporter RX035 | Akoya Biosciences | Cat# 6250010 |
| CODEX Barcode/Reporter RX042 | Akoya Biosciences | Cat# 6550023 |
| CODEX Barcode/Reporter RX043 | Akoya Biosciences | Cat# 6150015 |
| CODEX Barcode/Reporter RX016 | Akoya Biosciences | Cat# 6150006 |
| CODEX Barcode/Reporter RX027 | Akoya Biosciences | Cat# 6550019 |
| CODEX Barcode/Reporter RX020 | Akoya Biosciences | Cat# 6250005 |
| CODEX Barcode/Reporter RX010 | Akoya Biosciences | Cat# 6150004 |
| CODEX Barcode/Reporter RX005 | Akoya Biosciences | Cat# 6250002 |
| CODEX Barcode/Reporter RX040 | Akoya Biosciences | Cat# 6150014 |
| CODEX Barcode/Reporter RX034 | Akoya Biosciences | Cat# 6150012 |
| CODEX Barcode/Reporter RX002 | Akoya Biosciences | Cat# 6250001 |
| CODEX Barcode/Reporter RX030 | Akoya Biosciences | Cat# 6550020 |
| CODEX Barcode/Reporter RX045 | Akoya Biosciences | Cat# 6550024 |
| CODEX Barcode/Reporter RX037 | Akoya Biosciences | Cat# 6150013 |
| CODEX Barcode/Reporter RX036 | Akoya Biosciences | Cat# 6550022 |
| CODEX Barcode/Reporter RX041 | Akoya Biosciences | Cat# 6250011 |
| CODEX Barcode/Reporter RX004 | Akoya Biosciences | Cat# 6150002 |
| CODEX Barcode/Reporter RX047 | Akoya Biosciences | Cat# 6250012 |
| CODEX Barcode/Reporter RX003 | Akoya Biosciences | Cat# 6550025 |
| CODEX Barcode/Reporter RX026 | Akoya Biosciences | Cat# 6250007 |
| CODEX Barcode/Reporter RX024 | Akoya Biosciences | Cat# 6550018 |
| CODEX Barcode/Reporter RX007 | Akoya Biosciences | Cat# 6150003 |
| CODEX Barcode/Reporter RX001 | Akoya Biosciences | Cat# 6150001 |
| CODEX Barcode/Reporter RX021 | Akoya Biosciences | Cat# 6550028 |
| CODEX Barcode/Reporter RX015 | Akoya Biosciences | Cat# 6550027 |
| CODEX Barcode/Reporter RX033 | Akoya Biosciences | Cat# 6550021 |
| CODEX Barcode/Reporter RX019 | Akoya Biosciences | Cat# 6150007 |
| CODEX Barcode/Reporter RX014 | Akoya Biosciences | Cat# 6250003 |
| Deposited data | ||
| Trichrome Histological Images | Github | Github: HageyLab/PDAC2023 |
| CODEX Phenotyping Data | Github | Github: HageyLab/PDAC2023 |
| Software and algorithms | ||
| R | R Foundation for Statistical Computing | 4.1 |
| RStudio | Posit PBC | 1.4.1106.0 |
| AdjacencyScore | Govek et al.50 | 0.1.0 |
| Batchelor | Haghverdi et al.51 | 1.6.3 |
| DDRTree | Mao et al.23 | 0.1.5 |
| Monocle3 | Trapnell et al.24 | 1.2.9 |
| RANN | Github | jefferislab/RANN (2.6.1) |
| Seurat | Hao et al.52 | 4.1.1 |
| STvEA | Govek et al.50 | 1.0 |
| MATLAB (Image Processing Toolbox, Statistics and Machine Learning Toolbox) | The MathWorks, Inc. | R2021a |
| Akoya Multiplex Analysis Viewer | Akoya Biosciences | 1.5 |
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