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| Status |
Public on Jan 11, 2022 |
| Title |
Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches (spatial) |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| 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.
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| 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.
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| Web link |
https://livercellatlas.org
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| Contributor(s) |
Guilliams M, Bonnardel J, Haest B, Vanderborght B, Wagner C, Remmerie A, Bujko A, Martens L, Thoné T, Browaeys R, De Ponti FF, Vanneste B, Zwicker C, Svedberg FR, Vanhalewyn T, Gonçalves A, Lippens S, Devriendt B, Cox E, Ferrero G, Wittamer V, Willaert A, Kaptein SF, Neyts J, Dallmeier K, Geldhof P, Casaert S, Deplancke B, ten Dijke P, Hoorens A, Vanlander A, Berrevoet F, Van Nieuwenhove Y, Saeys Y, Saelens W, Van Vlierberghe H, Devisscher L, Scott CL |
| Citation(s) |
35021063, 36304458 |
| Submission date |
Dec 29, 2021 |
| Last update date |
Apr 06, 2024 |
| Contact name |
Liesbet Martens |
| E-mail(s) |
liesbet.martens@irc.vib-ugent.be
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| Organization name |
VIB-University of Ghent
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| Department |
VIB Inflammation Research Center
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| Street address |
Technologiepark 927
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| City |
Zwijnaarde |
| ZIP/Postal code |
9052 |
| Country |
Belgium |
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| Platforms (2) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (15)
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| GSM5764414 |
Healthy Mouse Liver_Mouse_001_Sample_001 |
| GSM5764415 |
Healthy Mouse Liver_Mouse_001_Sample_002 |
| GSM5764416 |
Healthy Mouse Liver_Mouse_001_Sample_003 |
| GSM5764417 |
Healthy Mouse Liver_Mouse_001_Sample_004 |
| GSM5764418 |
Healthy Mouse Liver Capsule_Mouse_002_Sample_001 |
| GSM5764419 |
Standard diet fed (36 weeks) Mouse Liver_Mouse_001_Sample_001 |
| GSM5764420 |
Western diet fed (36 weeks) Mouse Liver_Mouse_001_Sample_001 |
| GSM5764421 |
Western diet fed (36 weeks) Mouse Liver_Mouse_002_Sample_001 |
| GSM5764422 |
Western diet fed (36 weeks) Mouse Liver_Mouse_002_Sample_002 |
| GSM5764423 |
Healthy Mouse Liver_ with Abs_Mouse_002_Sample_001 |
| GSM5764424 |
Whole Liver_Visium of Human H35 (sample1) |
| GSM5764425 |
Whole Liver_Visium of Human H35 (sample2) |
| GSM5764426 |
Whole Liver_Visium of Human H36 |
| GSM5764427 |
Whole Liver_Visium of Human H37 |
| GSM5764428 |
Whole Liver_Visium of Human H38 |
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| This SubSeries is part of SuperSeries: |
| GSE192742 |
Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches |
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| Relations |
| BioProject |
PRJNA793008 |
| SRA |
SRP352825 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE192741_RAW.tar |
179.6 Mb |
(http)(custom) |
TAR (of CSV, H5, JSON, PNG) |
| GSE192741_sampleInfo_spatialRNAseq.tsv.gz |
579 b |
(ftp)(http) |
TSV |
| GSE192741_seuratObj_humanVisium.rds.gz |
339.8 Mb |
(ftp)(http) |
RDS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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