PMCID stringclasses 24
values | Title stringclasses 24
values | Sentences stringlengths 2 40.7k |
|---|---|---|
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | P0F4QLilra5Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | P0M7NItgaxResolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | P1C1RDcnResolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | P1E4SMmrn1Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | P1F4RLplResolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | P1M7PCd79aResolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | P2662Cd36Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | P2A5YGpnmbResolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | P2H7TMarcoResolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | P2M7QCd19Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | P3663PdgfrbResolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | P3E4VAdgre1Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | P3F4TAdamtsl2Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | P3K7SMfap4Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | P3M7RLyve1Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | P4961AxlResolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | P4C1VOlfml3Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | P4E2TAtp6v0d2Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | P4K7TMmp12Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | P4M7SC5ar1Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | P5K7VMslnResolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | P5M7TLhx6Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | P5T2FFn1Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | P6952Ccr7Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | P6K7WCd14Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | P7K7XNrxn1Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | P7M7WActa2Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | P8668Cd207Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | P8K7YCd5lResolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | P9K7ZRspo3Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | P9M7YCcr2Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PAF40Slc40a1Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PAM7ZGls2Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PAN7YSdsResolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PCG40Clec10aResolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PCK70Spon2Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PCM7LPck1Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PCN7ZSirpaResolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PDH73Clec4fResolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PDK71Stab2Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PDM70Krt19Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PE07NSiglechResolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PEF43Clic5Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PEK72Svep1Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PEM71Cd9Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PFH75Col1a1Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PFK73Timd4Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PFM72Pecam1Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PFP5ZCx3cr1Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PG35JNcam1Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PGE46Colec11Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PGK74Tmem119Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PGM73PdgfraResolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PHG45Cox6a2Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PHK75Upk3bResolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PHM74Cxcl12Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PJK76Wnt2Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PJM75RelnResolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PK54JFcgr1Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PK86HMyh11Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PK95FDesResolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PKK77Wnt9bResolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PKM76Sox9Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PKT6LChil3Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PMH7ADptResolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PMK78Grip1Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PND2AMs4a7Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PNH7CF13a1Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PNK79Vsig4Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PPH7DFlt3Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PPK7ASpp1Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PQD4FFlt4Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PQK7CEpcamResolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PRD4GPlpp1Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PRE4FFolr2Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PRK7DCd3eResolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PS56TClec9aResolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PS66SGhrResolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PSF4FMafbResolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PSS66Gja5Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PTK7FCyp2e1Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PVF4HSept3Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PW66WVwfResolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PWE4KLgr5Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PWF4JHalResolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PWK7HProx1Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PWS25Xcr1Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PX86VHgfResolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PXK7JItgaeResolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PY86WSpnResolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PYE7RIgfbp3Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PYK7KCd209aResolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PYM6HGlulResolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PZ81RItgb7Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | PZK7MMgl2Resolve Bio. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | 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). |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | This study did not generate new unique reagents. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | WT C57Bl/6J mice (Janvier) were used for this study. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | Male and Female mice were used for all experiments, with the exception of NAFLD experiments were only male mice were used. |
PMC8809252 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. | 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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