KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal anti-CD9 | Santa Cruz Biotechnology | Cat# sc-13118, RRID: AB_631471 |
| Mouse monoclonal anti-CD63 | Santa Cruz Biotechnology | Cat# sc-5275, RRID: AB_627877 |
| Goat polyclonal anti-HSP70 | Santa Cruz Biotechnology | Cat# sc-1060, RRID: AB_631685 |
| Mouse monoclonal anti-TSG101 | Santa Cruz Biotechnology | Cat# sc-7964, RRID: AB_671392 |
| Mouse monoclonal anti-GM130 | Santa Cruz Biotechnology | Cat# sc-55591, RRID: AB_1124984 |
| Rabbit polyclonal anti-cytochrome c | Thermo Fisher Scientific | Cat# 10993–1-AP, RRID: AB_2090467 |
| Mouse monoclonal anti-actin | Sigma-Aldrich | Cat# A5441, RRID: AB_476744 |
| Mouse monoclonal anti-Rab27a | Santa Cruz Biotechnology | Cat# sc-74586, RRID: AB_2176724 |
| Rabbit monoclonal anti-LATS2 (D83D6) | Cell Signaling Technology | Cat# 5888S, RRID: AB_10835233 |
| Mouse monoclonal anti-YAP | Santa Cruz Biotechnology | Cat# sc-101199, RRID: AB_1131430 |
| Rabbit monoclonal anti-phospho-YAP (Ser127) | Cell Signaling Technology | Cat# 13008, RRID: AB_2650553 |
| Mouse monoclonal anti-lamin B1 | Santa Cruz Biotechnology | Cat# sc-374015, RRID: AB_10947408 |
| Mouse monoclonal anti-CYR61 | Novus Biologicals | NB100-356, RRID: AB_10000986 |
| Rat monoclonal anti-F4/80 | Thermo Fisher Scientific | Cat# 14–4801, RRID: AB_2314387 |
| Mouse monoclonal anti-human CD206 | R&D Systems | Cat# MAB25341, RRID: AB_10890782 |
| Goat polyclonal anti-mouse CD206 | R&D Systems | Cat# AF2535, RRID: AB_2063012 |
| Rabbit monoclonal anti-CD68 | Abcam | Cat# ab213363, RRID: AB_2801637 |
| Goat anti-rabbit IgG-biotin | Thermo Fisher Scientific | Cat# 31820, RRID: AB_228340 |
| Goat anti-mouse IgG-biotin | BD Bioscience | Cat# 553999, RRID: AB_395196 |
| Donkey anti-goat antibody-Alexa 568 | Thermo Fisher Scientific | Cat# A11057, RRID: AB_2534104 |
| Goat anti-mouse antibody-Alexa 488 | Thermo Fisher Scientific | Cat# A11001, RRID: AB_2534069 |
| Goat anti-Rabbit antibody-Alexa 568 | Thermo Fisher Scientific | Cat# A11011, RRID: AB_143157 |
| Donkey anti-rat antibody-Alexa 488 | Thermo Fisher Scientific | Cat# A21208, RRID: AB_2535794 |
| Mouse monoclonal anti-αSMA, Clone 1A4 | Novus Biologicals | Cat# NBP2-34522, RRID: N/A |
| Mouse monoclonal anti-CD31, Clone C31.3 | Abcam | Cat# ab187377, RRID: AB_2756834 |
| Mouse monoclonal anti-galectin-9, Clone 1G3 | EMD Millipore | Cat# MABT833, RRID: N/A |
| Rabbit monoclonal anti-YAP1, Clone EP1674Y | Abcam | Cat# ab52771, RRID: AB_2219141 |
| Mouse monoclonal anti-CD14, Clone EPR3653 | Fluidigm | Cat# 3144025D, RRID: N/A |
| Mouse monoclonal anti-CK19, Clone RCK108 | Abcam | Cat# ab9221, RRID: AB_307088 |
| Mouse monoclonal anti-CD163, Clone EDHu-1 | Fluidigm | Cat# 3147021D, RRID: AB_2892115 |
| Rabbit polyclonal anti-NKG2D | Novus Biologicals | Cat# NBP2-43645, RRID: N/A |
| Rabbit monoclonal anti-PDL1, Clone 28–8 | Abcam | Cat# ab205921, RRID: AB_2687878 |
| Sheep polyclonal anti-FAP antibody | R&D Systems | Cat# AF3715, RRID: AB_2102369 |
| Mouse monoclonal anti-CD11c, Clone ITGAX/1242 | Abcam | Cat# ab212508, RRID: N/A |
| Rabbit monoclonal anti-LAG3, Clone D2G40 | Fluidigm | Cat# 3153028D, RRID: N/A |
| Mouse monoclonal anti-HepPar1, Clone V3109 | NSJ Bioreagents | Cat# V3109SAF, RRID: N/A |
| Mouse monoclonal anti-FoxP3, Clone 236A/E7 | Fluidigm | Cat# 3155016D, RRID: N/A |
| Mouse monoclonal anti-CD4, Clone EPR6855 | Fluidigm | Cat# 3156036D, RRID: N/A |
| Mouse monoclonal anti-CD68, Clone KP1 | Fluidigm | Cat# 3159035D, RRID: AB_2810859 |
| Rabbit monoclonal anti-VISTA, Clone D1L2G | Fluidigm | Cat# 3160025D, RRID: AB_2811070 |
| Mouse monoclonal anti-CD20, Clone H1 | Fluidigm | Cat# 3161029D, RRID: AB_2811016 |
| Mouse monoclonal anti-CD8a, Clone C8/144B | Fluidigm | Cat# 3162034D, RRID: AB_2811053 |
| Rabbit monoclonal anti-TIM3, Clone D5D5R | Cell Signaling Technology | Cat# 45208, RRID: AB_2716862 |
| Mouse monoclonal anti-PD1, Clone NAT105 | Abcam | Cat# ab201811, RRID: N/A |
| Rabbit monoclonal anti-iNOS, Clone SP126 | Abcam | Cat# ab239990, RRID: N/A |
| Rabbit monoclonal anti-CDX2, Clone 2951R | Novus Biologicals | Cat# NBP3-08738, RRID: N/A |
| Rabbit polyclonal anti-CD3 | Fluidigm | Cat# 3170019D, RRID: AB_2811048 |
| Mouse monoclonal anti-CD15, Clone HI98 | Biolegend | Cat# 301902, RRID: AB_314194 |
| Rabbit monoclonal anti-CD11b, Clone EPR1344 | Abcam | Cat# ab209970, RRID: N/A |
| Mouse monoclonal anti-Ki67, Clone B56 | BD Biosciences | Cat# 556003, RRID: AB_396287 |
| Rabbit monoclonal anti-histone H3, Clone EPR16987 | Abcam | Cat# ab238971, RRID: N/A |
| Rabbit monoclonal anti-CD453, Clone D9M8I | Cell Signaling Technology | Cat# 47937, RRID: N/A |
| Mouse monoclonal anti-HLA-ABC, Clone EMR8-5 | Abcam | Cat# ab70328, RRID: AB_1269092 |
| Mouse monoclonal anti-HLA-DR, Clone L243 | Fluidigm | Cat# 3174023D, RRID: AB_2811059 |
| – | – | – |
| Bacterial and virus strains | ||
| Scrambled-shRNA with GFP adenovirus | Vector Biolabs | Cat# 1122 |
| Mouse RAB27A shRNA silencing adenovirus | Vector Biolabs | Cat# shADV-269969 |
| Mouse RAB27A adenovirus | Vector Biolabs | Cat# ADV-269969 |
| Mouse GFP-CYR61 adenovirus | Vector Biolabs | Cat# ADV-256579 |
| – | – | – |
| Biological samples | – | – |
| Human CRC liver metastasis samples | Cedars-Sinai Medical Center | N/A |
| – | – | – |
| – | – | – |
| – | – | – |
| – | – | – |
| Chemicals, peptides, and recombinant proteins | ||
| Palmitate | Sigma-Aldrich | Cat# P9767 |
| TRIzol | Thermo Fisher Scientific | Cat# 15596–018 |
| DAPI | Thermo Fisher Scientific | Cat# D1306 |
| Oil Red O | VWR | Cat# AAA12989-14 |
| DMEM, high glucose | Thermo Fisher Scientific | Cat# 11965118 |
| 1x DPBS | Thermo Fisher Scientific | Cat# 21600069 |
| Fetal bovine serum | Sigma-Aldrich | Cat# F0926 |
| Fetal bovine serum, exosome-depleted | Thermo Fisher Scientific | Cat# A2720801 |
| Trypsin EDTA | Thermo Fisher Scientific | Cat# 15400054 |
| Bovine serum albumin | Gold Biotechnology | Cat# A421-100 |
| Puromycin dihydrochloride | Thermo Fisher Scientific | Cat# A1113803 |
| Antibiotic-antimycotic | Thermo Fisher Scientific | Cat# 15240–062 |
| Lipofectamine 3000 | Thermo Fisher Scientific | Cat# L3000015 |
| UltraPure low melting point agarose | Thermo Fisher Scientific | Cat# 16520050 |
| Rat collagen I | Corning | Cat# 354236 |
| Collagenase D | Roche | Cat# 11088866001 |
| Pronase E | Sigma-Aldrich | Cat# 10165921001 |
| Nycodenz | Axis-Shield | Cat# Axs-1002424 |
| – | – | – |
| – | – | – |
| Critical commercial assays | ||
| RNeasy Mini Kit | Qiagen | Cat# 74104 |
| iScript Reverse Transcription Supermix | Bio-Rad Laboratories | Cat# 1708841 |
| iTaq Universal SYBR Green Supermix | Bio-Rad Laboratories | Cat# 1725122 |
| Exosome Isolation Reagent (serum) | Thermo Fisher Scientific | Cat# 4478360 |
| Exosome Isolation Reagent (culture media) | Thermo Fisher Scientific | Cat# 4478359 |
| miScript II RT Kit | Qiagen | Cat# 218161 |
| miScript SYBR Green PCR Kit | Qiagen | Cat# 218075 |
| miScript miRNA PCR Array Human Liver miFinder | Qiagen | Cat# 331221 |
| miScript miRNA PCR Array Mouse Liver miFinder | Qiagen | Cat# 331221 |
| miScript PreAMP PCR Kit | Qiagen | Cat# 331452 |
| exoRNeasy Serum/Plasma Starter Kit | Qiagen | Cat# 77023 |
| exoRNeasy Midi Kit (50) | Qiagen | Cat# 77144 |
| PKH67 Green Fluorescent Cell Linker | Sigma-Aldrich | Cat# MIDI67 |
| PKH26 Red Fluorescent Cell Linker | Sigma-Aldrich | Cat# MIDI26 |
| Nuclear Extraction Kit | Abcam | Cat# ab113474 |
| SuperSignal West Femto Maximum Sensitivity Substrate | Thermo Fisher Scientific | Cat# PI34096 |
| DAB Substrate Kit, Peroxidase | Vector Laboratories | Cat# SK4100 |
| M.O.M. (Mouse on Mouse) Immunodetection Kit | Vector Laboratories | Cat# BMK2202 |
| ABC Peroxidase Standard Staining Kit | Thermo Fisher Scientific | Cat# 32020 |
| Luc-Pair Duo-Luciferase Assay Kit 2.0 | GeneCopoeia | Cat# LF001 |
| Transwell polycarbonate-membrane cell culture insert | Corning | Cat# CLS3422 |
| BioCoat Matrigel Invasion Chambers with 8.0 μm PET Membrane | Corning | Cat# 354480 |
| Bicinchoninic acid protein assay kit | Thermo Fisher Scientific | Cat# 23225 |
| – | – | – |
| Deposited data | ||
| Raw and processed sequencing data | This paper | NCBI Bioproject: GEO: GSE227913; GEO: GSE227914 |
| scRNAseq data | Yu et al. 53 | GSE157600 |
| Data S1. Unprocessed source data underlying all blots and graphs | This paper | N/A |
| – | – | – |
| – | – | – |
| Experimental models: Cell lines | ||
| Mouse MC38 colorectal adenocarcinoma | Gift from Michael Karin 64 | RRID: CVCL_B288 |
| Mouse CMT93 colorectal adenocarcinoma | ATCC | Cat# CCL223, RRID: CVCL_1986 |
| Human HCT116 colon cancer | ATCC | Cat# CCL-247, RRID: CVCL_0291 |
| Human Huh7 hepatocellular carcinoma | CLS | Cat# 300156/p7178_HuH7, RRID: CVCL_0336 |
| Human HEK293T | ATCC | Cat# CRL-3216, RRID: CVCL_0063 |
| – | – | – |
| Experimental models: Organisms/strains | ||
| C57BL/6J | The Jackson Laboratory | – |
| – | – | – |
| – | – | – |
| – | – | – |
| – | – | – |
| – | – | – |
| Oligonucleotides | ||
| Human miR-25-3p primers Forward: CATTGCACTTGTCTCGGTCTGA Reverse: CTCAACTGGTGTCGTGGAGTCGG |
Integrated DNA Technologies | N/A |
| Human miR-92a-3p primers Forward: TATTGCACTTGTCCCGGCCTG Reverse: CTCAACTGGTGTCGTGGAGTCGG |
Integrated DNA Technologies | N/A |
| Human miR-103-3p primers Forward: AGCAGCATTGTACAGGGCTATGA Reverse: CTCAACTGGTGTCGTGGAGTCGG |
Integrated DNA Technologies | N/A |
| Human RNU6-1 primers Forward: CGCAAGGATGACACGCAAATTC Reverse: CTCAACTGGTGTCGTGGAGTCGG |
Integrated DNA Technologies | N/A |
| Mouse miR-25-3p primers Forward: CATTGCACTTGTCTCGGTCTGA Reverse: CTCAACTGGTGTCGTGGAGTCGG |
Integrated DNA Technologies | N/A |
| Mouse miR-92a-3p primers Forward: TATTGCACTTGTCCCGGCCTG Reverse: CTCAACTGGTGTCGTGGAGTCGG |
Integrated DNA Technologies | N/A |
| Mouse miR-103-3p primers Forward: AGCAGCATTGTACAGGGCTATGA Reverse: CTCAACTGGTGTCGTGGAGTCGG |
Integrated DNA Technologies | N/A |
| Mouse RNU6-1 primers Forward: TGACACGCAAATTCGTGAAG Reverse: CTCAACTGGTGTCGTGGAGTCGG |
Integrated DNA Technologies | N/A |
| Mouse miR-151a-3p primers Forward: CTAGACTGAGGCTCCTTGAGG Reverse: CTCAACTGGTGTCGTGGAGTCGG |
Integrated DNA Technologies | N/A |
| Mouse miR-222-3p primers Forward: CTCAGTAGCCAGTGTAGATCC Reverse: CTCAACTGGTGTCGTGGAGTCGG |
Integrated DNA Technologies | N/A |
| Mouse miR-221-3p primers Forward: AGCTACATTGTCTGCTGGGTTTC Reverse: CTCAACTGGTGTCGTGGAGTCGG |
Integrated DNA Technologies | N/A |
| Human ANKRD1 primers Forward: AGAGGCACGTCTGTGTTTTGG Reverse: ATCTTGGCCCCTGAGTTTACC |
Integrated DNA Technologies | N/A |
| Human AXL primers Forward: GTGGGCAACCCAGGGAATATC Reverse: GTACTGTCCCGTGTCGGAAAG |
Integrated DNA Technologies | N/A |
| Human CTGF primers Forward: ACCGACTGGAAGACACGTTTG Reverse: CCAGGTCAGCTTCGCAAGG |
Integrated DNA Technologies | N/A |
| Human CYR61 primers Forward: ACCGCTCTGAAGGGGATCT Reverse: ACTGATGTTTACAGTTGGGCTG |
Integrated DNA Technologies | N/A |
| Human GAPDH primers Forward: GGAGCGAGATCCCTCCAAAAT Reverse: GGCTGTTGTCATACTTCTCATGG |
Integrated DNA Technologies | N/A |
| Human LATS2 primers Forward: ACCCCAAAGTTCGGACCTTAT Reverse: CATTTGCCGGTTCACTTCTGC |
Integrated DNA Technologies | N/A |
| Human Rab27a primers Forward: GCTTTGGGAGACTCTGGTGTA Reverse: TCAATGCCCACTGTTGTGATAAA |
Integrated DNA Technologies | N/A |
| Human Rab27b primers Forward: TAGACTTTCGGGAAAAACGTGTG Reverse: AGAAGCTCTGTTGACTGGTGA |
Integrated DNA Technologies | N/A |
| Human SMPD3 Forward: GCTGCCCTTTGCGTTTCTC Reverse: TCCAGCCGTGAATAGATGTAGG |
Integrated DNA Technologies | N/A |
| Human YAP1 primers Forward: TAGCCCTGCGTAGCCAGTTA Reverse: TCATGCTTAGTCCACTGTCTGT |
Integrated DNA Technologies | N/A |
| Mouse ARG1 primers Forward: TTTTTCCAGCAGACCAGCTT Reverse: AGAGATTATCGGAGCGCCTT |
Integrated DNA Technologies | N/A |
| Mouse AXL primers Forward: GGAACCCAGGGAATATCACAGG Reverse: AGTTCTAGGATCTGTCCATCTCG |
Integrated DNA Technologies | N/A |
| Mouse ANKRD1 primers Forward: AAACGGACGGCACTCCACCG Reverse: CGCTGTGCTGAGAAGCTTGTCT |
Integrated DNA Technologies | N/A |
| Mouse BTG2 primers Forward: ATGAGCCACGGGAAGAGAAC Reverse: GCCCTACTGAAAACCTTGAGTC |
Integrated DNA Technologies | N/A |
| Mouse CPEB2 primers Forward: TTGGAGCAACCATCAGAACAG Reverse: TACCCGAGAACGGCTTCTTCA |
Integrated DNA Technologies | N/A |
| Mouse CTGF primers Forward: GGCCTCTTCTGCGATTTCG Reverse: GCAGCTTGACCCTTCTCGG |
Integrated DNA Technologies | N/A |
| Mouse CYR61 primers Forward: TAAGGTCTGCGCTAAACAACTC Reverse: CAGATCCCTTTCAGAGCGGT |
Integrated DNA Technologies | N/A |
| Mouse FBXW7 primers Forward: GTTCCGCTGCCTAATCTTCCT Reverse: CCCTTCAGGGATTCTGTGCC |
Integrated DNA Technologies | N/A |
| Mouse KLF4 primers Forward: GGCGAGTCTGACATGGCTG Reverse: GCTGGACGCAGTGTCTTCTC |
Integrated DNA Technologies | N/A |
| Mouse GAPDH primers Forward: TGGATTTGGACGCATTGGTC Reverse: TTTGCACTGGTACGTGTTGAT |
Integrated DNA Technologies | N/A |
| Mouse LATS2 primers Forward: GGACCCCAGGAATGAGCAG Reverse: CCCTCGTAGTTTGCACCACC |
Integrated DNA Technologies | N/A |
| Mouse LATS1 primers Forward: AATTTGGCACACATCATAAAGCC Reverse: ACGAGGGTCTTGGTAACTCATT |
Integrated DNA Technologies | N/A |
| Mouse MRC2 primers Forward: CCTGGCTGAAGATGAGGAAG Reverse: GTCTTGCTTCTCGGGGGACT |
Integrated DNA Technologies | N/A |
| Mouse NOS2 primers Forward: ACATCGACCCGTCCACAGTAT Reverse: CAGAGGGGTAGGCTTGTCTC |
Integrated DNA Technologies | N/A |
| Mouse IL-4 primers Forward: GGTCTCAACCCCCAGCTAGT Reverse: GCCGATGATCTCTCTCAAGTGAT |
Integrated DNA Technologies | N/A |
| Mouse IL-13 primers Forward: CACACAAGACCAGACTCCCC Reverse: TCTGGGTCCTGTAGATGGCAAT |
Integrated DNA Technologies | N/A |
| Mouse CD163 primers Forward: TGGGTGGGGAAAGCATAACT Reverse: AAGTTGTCGTCACACACCGT |
Integrated DNA Technologies | N/A |
| Mouse TGF-b1 primers Forward: CAGCTCCTCATCGTGTTGGTG Reverse: GCACATACAAATGGCCTGTCTC |
Integrated DNA Technologies | N/A |
| Mouse IFN-g primers Forward: ATGAACGCTACACACTGCATC Reverse: CCATCCTTTTGCCAGTTCCTC |
Integrated DNA Technologies | N/A |
| Mouse Rab27a primers Forward: TCGGATGGAGATTACGATTACCT Reverse: TTTTCCCTGAAATCAATGCCCA |
Integrated DNA Technologies | N/A |
| Mouse Rab27b primers Forward: TGGCTGAAAAATATGGCATACCA Reverse: CCAGAAGCGTTTCCACTGACT |
Integrated DNA Technologies | N/A |
| Mouse SMPD3 primers Forward: ACACGACCCCCTTTCCTAATA Reverse: GGCGCTTCTCATAGGTGGTG |
Integrated DNA Technologies | N/A |
| Mouse TCF21 primers Forward: CTCCCTGAAAGTGGACTCCAA Reverse: CGGGCTTTTCTTAGTGGGC |
Integrated DNA Technologies | N/A |
| Mouse TGIF1 primers Forward: TGAAGCTGCAATGGGTATCAAA Reverse: GGTATGGCAGATCACTGACGG |
Integrated DNA Technologies | N/A |
| Mouse YAP1 primers Forward: ACCCTCGTTTTGCCATGAAC Reverse: TGTGCTGGGATTGATATTCCGTA |
Integrated DNA Technologies | N/A |
| Human miR-25-3p mimic 5′CAUUGCACUUGUCUCGGUCUGA | Bioland Scientific LLC | N/A |
| Human miR-92a-3p mimic 5′UAUUGCACUUGUCCCGGCCUGU | Bioland Scientific LLC | N/A |
| Human miR-103-3p mimic 5′AGCAGCAUUGUACAGGGCUAUGA | Bioland Scientific LLC | N/A |
| Mouse miR-25-3p mimic 5′CAUUGCACUUGUCUCGGUCUGA | Bioland Scientific LLC | N/A |
| Mouse miR-92a-3p mimic 5′UAUUGCACUUGUCCCGGCCUG | Bioland Scientific LLC | N/A |
| Mouse miR-103-3p mimic 5′AGCAGCAUUGUACAGGGCUAUGA | Bioland Scientific LLC | N/A |
| Human miR-25-3p antisense (antagomiR) | Bioneer | N/A |
| Human miR-92a-3p antisense (antagomiR) | Bioneer | N/A |
| Human miR-103-3p antisense (antagomiR) | Bioneer | N/A |
| Mouse Rab27a siRNA | Thermo Fisher Scientific | Cat# AM16706, Assay ID 161926 |
| Mouse Rab27b siRNA | Thermo Fisher Scientific | Cat# AM16706, Assay ID 174906 |
| Negative Control siRNA | Thermo Fisher Scientific | Cat# AM4638 |
| – | – | – |
| Recombinant DNA | ||
| Yap1 shRNA plasmid (mouse) | Santa Cruz Biotechnology | Cat# sc-38638-SH |
| Ccn1 shRNA plasmid (mouse) | Santa Cruz Biotechnology | Cat# sc-39332-SH |
| Control shRNA plasmid (mouse) | Santa Cruz Biotechnology | Cat# sc-108060 |
| miRNA 3′-UTR target expression clone for mouse Lats2 (NM_015771.2) | GeneCopoeia | Cat# MmiT031281-MT06 |
| Custom mutant (2 sites) miRNA 3′-UTR target for mouse Lats2 (NM_015771.2) | GeneCopoeia | Cat# CS-MmiT031281-MT06-01 |
| miRNA target clone control vector for pEZX-MT06 | GeneCopoeia | Cat# CmiT000001-MT06 |
| – | – | – |
| Software and algorithms | ||
| ImageJ | https://imagej.nih.gov/ij/ | N/A |
| GraphPad Prism 9.0 | GraphPad Software | N/A |
| TargetScan | http://www.targetscan.org | N/A |
| miRDB | http://mirdb.org | – |
| PicTar | https://pictar.mdc-berlin.de | – |
| FlowJo | BD Bioscience | – |
| R 4.1.0 | R Core Team | https://www.r-project.org |
| Rphenograph (R package) | Levin et al. 65 | https://github.com/JinmiaoChenLab/Rphenograph |
| Tidyverse (R package) | https://www.tidyverse.org/ | – |
| Data.table (R package) | https://rdatatable.gitlab.io/data.table/index.html | – |
| Pheatmap (R package) | https://github.com/raivokoldse/pheatmap | – |
| Spatstat (R package) | https://spatstat.org/ | – |
| Rstudio | Rstudio Team, 2020 | http://www.rstudio.com |
| MCD Viewer | Fluidigm, 2021 | https://www.fluidigm.com/products-services/software |
| HistocatS | Schapiro et al. 66 | https://github.com/BodenmillerGroup/histoCAT |
| STAR 2.7.3a | Dobin et al. 67 | https://github.com/alexdobin/STAR |
| GSEA | Broad Institute | https://www.gsea-msigdb.org/gsea/index.jsp |
| Cell Ranger 6.0.0 | 10xGenomics | http://10xgenomics.com/ |
| Seurat package 4.0.5 | Stuart et al. 68 | https://satijalab.org/seurat/ |
| IMCSegmentationPipeline | https://github.com/BodenmillerGroup/ImcSegmentationPipeline | – |
| – | – | – |
| – | – | – |
| Other | ||
| Diet (Normal Chow) | LabDiet | Cat# 3005740–220 |
| HFD | Bio-Serv | Cat# S3282 |
| – | – | – |
| – | – | – |
| – | – | – |