{"database": "metadata", "table": "run_metadata", "rows": [[67833, "SRR17375071", "SRX13549230", "SRS11443004", "SRP352824", "PRJNA793009", "Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches single cells", "GSE192740", "Other", "Analysis of CITE seq data   Nuclei RNA seq data and single cell RNA seq data on CD45+ and CD45  cells isolated from the livers of mice fed a standard diet SD or western diet WD; fat  cholesterol and sugar  from healthy and steatotic human livers  from hamster liver  pig liver  chicken liver  monkey liver and zebrafish liver. We also performed Spatial Transcriptomics analysis on heatlhy mouse livers  NAFLD mouse livers  healthy human livers and steatotic human livers. Overall design: Single cell RNA Seq = Liver CD45+ and CD45  cells derived from mice fed a standard diet SD or western diet WD; fat  cholesterol and sugar. Liver CD45+ and CD45  cells derived from healthy and obese humans. 10 Visium Spatial Seq = mouse StSt liver  mouse StSt capsule  mouse NAFLD liver   human non steatotic liver  human steatotic liver", "parent bioproject:PRJNA793005", "pubmed:35021063;pubmed:36304458", null, "Zebrafish 001 Whole Liver Cells Zebrafish", "GSM5764412", null, "tissue:Liver|shortfilename:CS130|strain:Tgmpeg1:EGFPgl22|platform:10x Genomics \u2013 v3|digestion method:Ex Vivo|number of added abs:0|number of cells:2256", "Zebrafish 001 Whole Liver Cells Zebrafish", "Raw data bcl files were first demultiplexed using Cell Ranger mkfastq version 3.1.0 or version 3.0.2 Demultiplexed data was then processed using the Cell Ranger count pipeline version 3.1.0 or version 3.0.2. Cite seq samples were mapped against the TotalSeqA whitelist. Genome build: mm10 Mouse  hg19 Human  GRCz10 Zebrafish  MesAur1.0.100 Hamster  GRCg6a.96 Chicken  Sscrofa11.1.96 Pig or Macaca facicularis 5.0.100 Macaque Supplementary files format and content: h5 or txt files including raw gene \u2013 and if present \u2013 antibody counts output CellRanger Count Supplementary files format and content: rds file: Seurat object", "Liver", null, "All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022.", null, "shortfilename:CS130|strain:Tgmpeg1:EGFPgl22|platform:10x Genomics \u2013 v3|digestion method:Ex Vivo|number of added abs:0|number of cells:2256", "GSM5764412", "GSM5764412: Zebrafish 001 Whole Liver Cells Zebrafish; Danio rerio; RNA Seq", "GSM5764412", null, "1", "All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. 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