PMCID
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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P0F4QLilra5Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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P0M7NItgaxResolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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P1C1RDcnResolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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P1E4SMmrn1Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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P1F4RLplResolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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P1M7PCd79aResolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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P2662Cd36Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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P2A5YGpnmbResolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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P2H7TMarcoResolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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P2M7QCd19Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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P3663PdgfrbResolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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P3E4VAdgre1Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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P3F4TAdamtsl2Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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P3K7SMfap4Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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P3M7RLyve1Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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P4961AxlResolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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P4C1VOlfml3Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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P4E2TAtp6v0d2Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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P4K7TMmp12Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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P4M7SC5ar1Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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P5K7VMslnResolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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P5M7TLhx6Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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P5T2FFn1Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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P6952Ccr7Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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P6K7WCd14Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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P7K7XNrxn1Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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P7M7WActa2Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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P8668Cd207Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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P8K7YCd5lResolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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P9K7ZRspo3Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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P9M7YCcr2Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PAF40Slc40a1Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PAM7ZGls2Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PAN7YSdsResolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PCG40Clec10aResolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PCK70Spon2Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PCM7LPck1Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PCN7ZSirpaResolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PDH73Clec4fResolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PDK71Stab2Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PDM70Krt19Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PE07NSiglechResolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PEF43Clic5Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PEK72Svep1Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PEM71Cd9Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PFH75Col1a1Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PFK73Timd4Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PFM72Pecam1Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PFP5ZCx3cr1Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PG35JNcam1Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PGE46Colec11Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PGK74Tmem119Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PGM73PdgfraResolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PHG45Cox6a2Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PHK75Upk3bResolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PHM74Cxcl12Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PJK76Wnt2Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PJM75RelnResolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PK54JFcgr1Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PK86HMyh11Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PK95FDesResolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PKK77Wnt9bResolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PKM76Sox9Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PKT6LChil3Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PMH7ADptResolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PMK78Grip1Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PND2AMs4a7Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PNH7CF13a1Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PNK79Vsig4Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PPH7DFlt3Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PPK7ASpp1Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PQD4FFlt4Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PQK7CEpcamResolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PRD4GPlpp1Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PRE4FFolr2Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PRK7DCd3eResolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PS56TClec9aResolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PS66SGhrResolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PSF4FMafbResolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PSS66Gja5Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PTK7FCyp2e1Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PVF4HSept3Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PW66WVwfResolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PWE4KLgr5Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PWF4JHalResolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PWK7HProx1Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PWS25Xcr1Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PX86VHgfResolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PXK7JItgaeResolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PY86WSpnResolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PYE7RIgfbp3Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PYK7KCd209aResolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PYM6HGlulResolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PZ81RItgb7Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PZK7MMgl2Resolve Bio.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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PZM6JSoftware and algorithmsAdobe IllustratorAdobewww.adobe.comCell Ranger10X Genomicshttps://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-rangerFastCAR R PackageN/Ahttps://github.com/LungCellAtlas/FastCARSeurat R Package V3(Stuart et al., 2019)https://satijalab.org/seurat/Scater R Package(McCarthy et al., 2017)https://bioconductor.org/packages/release/bioc/html/scater.htmlBioMartN/Ahttps://www.ensembl.org/biomart/martview/3e2c65a5e3f783f8c9e5d648e4b64126pheatmap R packageN/Ahttps://rdrr.io/cran/pheatmap/ggplot2(Wickham 2016)https://ggplot2.tidyverse.orgScanpy(Wolf et al., 2018)https://scanpy.readthedocs.io/en/stable/PyTorchN/Ahttps://pytorch.orgTotalVI(Gayoso et al., 2021)https://docs.scvi-tools.org/en/stable/user_guide/models/totalvi.htmlScVI(Lopez et al., 2018)https://docs.scvi-tools.org/en/stable/user_guide/models/totalvi.htmlNicheNet(Browaeys et al. 2019)https://github.com/saeyslab/nichenetrEnrichr(Kuleshov et al., 2016)http://amp.pharm.mssm.edu/Enrichr/FlowJo v10.6.1FlowJohttps://www.flowjo.comGeneOntology(Ashburner et al., 2000)http://geneontology.org/GraphPad Prism 9GraphPadhttps://www.graphpad.com/Harmony(Korsunsky et al., 2019)https://www.github.com/immunogenomics/harmonyIlastik(Berg et al., 2019)https://www.ilastik.org/ImageJ(Schneider et al., 2012)https://imagej.nih.gov/ijQi-TissueQuantitative Imagining Systemshttps://www.qi-tissue.comgenexyz PolyluxResolve BiosciencesSingle-Cell Signature Explorer algorithm(Pont et al., 2019)https://sites.google.com/site/fredsoftwares/products/single-cell-signature-explorerWEB-based GEne SeT AnaLysis Toolkit(Liao et al., 2019)http://www.webgestalt.org/Venn Diagram GeneratorPSB, VIB-Ghent Universityhttps://bioinformatics.psb.ugent.be/webtools/Venn/Zen BlackZEISS Microscopywww.zeiss.comExperimental modelsMouse: B6(C)-Ccr2 The Jackson LaboratoryJAX: 027619Mouse: C57BL/6j SPFJanvier LabsN/AMouse: B6-Clec4f(Scott et al., 2016)N/AMouse: B6-Clec4f(Scott et al., 2018)N/AMouse: Alk1-flox(Park et al., 2008)N/A Further information and requests for resources and reagents should be directed to and will be fulfilled by the lead contact, Martin Guilliams (martin.guilliams@irc.vib-ugent.be).
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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This study did not generate new unique reagents.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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WT C57Bl/6J mice (Janvier) were used for this study.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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Male and Female mice were used for all experiments, with the exception of NAFLD experiments were only male mice were used.
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PMC8809252
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Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches.
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For NAFLD experiments, mice were put on the SD or WD at 5 weeks of age and sacrificed after either 24 or 36 weeks on the diet as indicated.
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