Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches (spatial)
Dataset ID: STDS0000128
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24,179 Spots
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32,738 Genes
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Dataset information
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Dataset information
Summary:
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.
Technology:
10x Visium
Platform:
GPL24247, GPL24676
Species:
Mus musculus(mm10)
Homo sapiens(hg19)
Citation:
Habenicht, Livia K L et al. “The C1q-ApoE complex: A new hallmark pathology of viral hepatitis and nonalcoholic fatty liver disease.” Frontiers in immunology vol. 13 970938. 6 Oct. 2022, doi:10.3389/fimmu.2022.970938
Submission date: 2021-12-29Update date: 2022-01-13
Sample number: 15Section number: 15
Contributors
Guilliams, Martin; Bonnardel, Johnny; Haest, Birthe; Vanderborght, Bart; Wagner, Camille; Remmerie, Anneleen; Bujko, Anna; Martens, Liesbet; Thoné, Tinne; Browaeys, Robin; De Ponti, Federico F; Vanneste, Bavo; Zwicker, Christian; Svedberg, Freya R; Vanhalewyn, Tineke; Gonçalves, Amanda; Lippens, Saskia; Devriendt, Bert; Cox, Eric; Ferrero, Giuliano; Wittamer, Valerie; Willaert, Andy; Kaptein, Suzanne F; Neyts, Johan; Dallmeier, Kai; Geldhof, Peter; Casaert, Stijn; Deplancke, Bart; ten Dijke, Peter; Hoorens, Anne; Vanlander, Aude; Berrevoet, Frederik; Van Nieuwenhove, Yves; Saeys, Yvan; Saelens, Wouter; Van Vlierberghe, Hans; Devisscher, Lindsey; Scott, Charlotte L
Contact: liesbet.martens@irc.vib-ugent.be
Accessions
GEO Series Accessions: GSE192741