Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Donkey anti-Rat IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 |
Thermo Fisher | RRID: AB_2535794 |
| Donkey anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 555 |
Thermo Fisher | RRID: AB_162543 |
| Donkey anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 |
Thermo Fisher | RRID: AB_162542 |
| Anti-CD3 antibody [CD3-12] | Abcam | RRID: AB_2889189 |
| Na,K-ATPase α1 (D4Y7E) Rabbit mAb | Cell Signaling Technology | Cat#: 23565 RRID: Pending |
| Monoclonal Mouse Anti-Human CD45R0 | Dako | RRID: AB_2237910 |
| Ki-67 (D3B5) Rabbit mAb (Alexa Fluor® 488 Conjugate) | Cell Signaling Technology | RRID: AB_2687824 |
| Pan Cytokeratin Monoclonal Antibody (AE1/AE3), eFluor 570, eBioscience™ | Thermo Fisher/ eBioscience | RRID: AB_11218704 |
| Alpha-Smooth Muscle Actin Monoclonal Antibody (1A4), eFluor 660, eBioscience™ | eBioscience | RRID: AB_2574362 |
| Recombinant Anti-CD4 antibody [EPR6855] (Alexa Fluor® 488) | Abcam | RRID: AB_2889191 |
| PE anti-human CD45 Antibody | Biolegend | RRID: AB_2562057 |
| Recombinant Anti-PD1 antibody [EPR4877(2)] (Alexa Fluor® 647) | Abcam | RRID: AB_2728811 |
| CD20 Monoclonal Antibody (L26), Alexa Fluor 488, eBioscience™ | eBioscience | RRID: AB_10734357 |
| CD68 (D4B9C) XP® Rabbit mAb (PE Conjugate) | Cell Signaling Technology | RRID: AB_2799935 |
| CD8a Monoclonal Antibody (AMC908), eFluor 660, eBioscience™ | eBioscience | RRID: AB_2574149 |
| Recombinant Anti-CD163 antibody [EPR14643-36] – C-terminal (Alexa Fluor® 488) | Abcam | RRID: AB_2889155 |
| FOXP3 Monoclonal Antibody (236A/E7), eFluor 570, eBioscience™ | eBioscience | RRID: AB_2573609 |
| PD-L1 (E1L3N®) XP® Rabbit mAb (Alexa Fluor® 647 Conjugate) | Cell Signaling Technology | RRID: AB_2728832 |
| E-Cadherin (24E10) Rabbit mAb (Alexa Fluor® 488 Conjugate) | Cell Signaling Technology | RRID: AB_10691457 |
| Vimentin (D21H3) XP® Rabbit mAb (Alexa Fluor® 555 Conjugate) | Cell Signaling Technology | RRID: AB_10859896 |
| Recombinant Alexa Fluor® 647 Anti-CDX2 antibody [EPR2764Y] | Abcam | RRID: AB_2728786 |
| Lamin A/C (4C11) Mouse mAb (Alexa Fluor® 488 Conjugate) | Cell Signaling Technology | RRID: AB_10997529 |
| Recombinant Alexa Fluor® 488 Anti-Lamin B1 antibody [EPR8985(B)] - Nuclear Envelope Marker |
Abcam | RRID: AB_2728786 |
| Recombinant Alexa Fluor® 555 Anti-Desmin antibody [Y66] - Cytoskeleton Marker |
Abcam | RRID: AB_2890164 |
| Recombinant Anti-CD31 antibody [EPR3094] (Alexa Fluor® 647) | Abcam | RRID: AB_2857973 |
| PCNA (PC10) Mouse mAb (Alexa Fluor® 488 Conjugate) | Cell Signaling Technology | RRID: AB_11178664 |
| Ki-67 Monoclonal Antibody (20Raj1), eFluor 570, eBioscience™ | eBioscience | RRID: AB_11220088 |
| Collagen IV Monoclonal Antibody (1042), Alexa Fluor 647, eBioscience™ |
Thermo Fisher/ eBioscience | RRID: AB_10854267 |
| CD11c (D3V1E) XP® Rabbit mAb #45581 | Cell Signaling Technology | RRID:AB_2799286 |
| Granzyme B (Concentrate) clone GrB-7 | Agilent | RRID:AB_2114697 |
| Recombinant Alexa Fluor® 647 Anti-HLA A antibody [EP1395Y] (ab199837) |
Abcam | RRID:AB_2728798 |
| Phospho-Rb (Ser807/811) (D20B12) XP® Rabbit mAb (Alexa Fluor® 555 Conjugate) #8957 | Cell Signaling Technology | RRID:AB_2728827 |
| Phospho-Tyrosine Mouse mAb (P-Tyr-100) (Alexa Fluor® 647 Conjugate) #9415 | Cell Signaling Technology | RRID:AB_10693160 |
| Alexa Fluor® 647 antiPodoplanin (Lymphatic Endothelial Marker) Antibody | Biolegend | RRID:AB_2810816 |
| CD44 (156-3C11) Mouse mAb (PE Conjugate) #8724 | Cell Signaling Technology | RRID:AB_10829611 |
| p53 Protein (Concentrate) Clone DO-7 | Agilent | RRID:AB_2206626 |
| EGF Receptor (D38B1) XP® Rabbit mAb (Alexa Fluor® 488 Conjugate) #5616 |
Cell Signaling Technology | RRID:AB_10691853 |
| CDX2 (D11D10) Rabbit mAb (Alexa Fluor® 555 Conjugate) #84638 | Cell Signaling Technology | RRID:AB_10691853 |
| Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb (PE Conjugate) #40724 | Cell Signaling Technology | RRID:AB_2799182 |
| Recombinant Alexa Fluor® 647 Anti-Histone H3 (acetyl K27) antibody [EP16602] (ab245912) | Abcam | Cat# ab245912, RRID: pending |
| Purified anti-TIF1β (KAP-1, TRIM28) Phospho (Ser473) Antibody | Biolegend | RRID:AB_2563298 |
| CD11b Monoclonal Antibody (C67F154), Alexa Fluor™ 488, eBioscience™ | Thermo Fisher | RRID:AB_2637200 |
| Alexa Fluor® 488 anti-human CD15 (SSEA-1) Antibody | Biolegend | RRID:AB_493257 |
| Anti-CD14 antibody [EPR3653] (Alexa Fluor® 647) | Abcam | RRID:AB_2890135 |
| Collagen IV Monoclonal Antibody (1042), Alexa Fluor 647, eBioscience™ |
Thermo Fisher/eBioscience | RRID: AB_10854267 |
| Biological samples | ||
| FFPE tissue block and frozen tissue (CRC1) | Cooperative Human Tissue Network, Western Division | N/A |
| FFPE tissue blocks (CRC2-93) | Department of Pathology, Brigham and Women’s Hospital | N/A |
| Software and algorithms | ||
| MCMICRO pipeline (de0d76d7cf0870f1ed979722a465de0fc246b90b) | https://doi.org/10.1101/2021.03.15.435473 | https://github.com/labsyspharm/mcmicro |
| ImageJ (1.53c) | doi:10.1038/nmeth.2019 | https://imagej.nih.gov/ij/ |
| MATLAB 2019b | Mathworks Inc. | https://www.mathworks.com/products/matlab.html |
| Minerva Story | doi: 10.1038/s41551-02100789-8 and doi: 10.21105/joss.02579 | https://github.com/labsyspharm/minerva-story |
| Deposited Data | ||
| Human Tumor Atlas Network | https://humantumoratlas.org/ | https://humantumoratlas.org/explore |