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| Status |
Public on Aug 18, 2020 |
| Title |
Osteopontin expression identifies a subset of recruited macrophages distinct from Kupffer cells in the fatty liver. [Bulk RNA Seq] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
CITE-seq analysis on total CD45+ cells isolated from the livers of mice fed a standard diet (SD) or western diet (WD; fat, cholesterol and sugar) for 12, 24 and 36 weeks. We also performed single cell RNA sequencing analysis of the CD45- cells isolated from the livers of the mice fed the SD or WD for 24 and 36 weeks.
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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) for 12, 24 and 36 weeks.
Bulk RNA Seq = Kupffer cells, moKCs and Clec4f- macrophages derived from mice fed a standard diet (SD) or western diet (WD; fat, cholesterol and sugar) for 12 and 24 weeks.
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| Contributor(s) |
Remmerie A, Martens L, Thone T, Castoldi A, Seurnick R, Pavie B, Roels J, Vanneste B, De Prijck S, Vanhockerhout M, Latib MB, Devisscher L, Hoorens A, Bonnardel J, Vandamme N, Kremer A, Borghgraef P, Van Vlierberghe H, Lippens S, Pearce E, Saeys Y, Scott C |
| Citation(s) |
32888418, 36304458 |
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| Submission date |
Aug 11, 2020 |
| Last update date |
Nov 02, 2022 |
| 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 (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (35)
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| GSM4721386 |
Kupffer cells derived from mice fed a standard diet for 12 weeks, 1 |
| GSM4721387 |
Kupffer cells derived from mice fed a standard diet for 12 weeks, 2 |
| GSM4721388 |
Kupffer cells derived from mice fed a standard diet for 12 weeks, 3 |
| GSM4721389 |
Kupffer cells derived from mice fed a standard diet for 12 weeks, 4 |
| GSM4721390 |
Kupffer cells derived from mice fed a standard diet for 12 weeks, 5 |
| GSM4721391 |
Kupffer cells derived from mice fed a standard diet for 12 weeks, 6 |
| GSM4721392 |
Kupffer cells derived from mice fed a standard diet for 12 weeks, 7 |
| GSM4721393 |
Kupffer cells derived from mice fed a western diet for 12 weeks, 1 |
| GSM4721394 |
Kupffer cells derived from mice fed a western diet for 12 weeks, 2 |
| GSM4721395 |
Kupffer cells derived from mice fed a western diet for 12 weeks, 3 |
| GSM4721396 |
Kupffer cells derived from mice fed a western diet for 12 weeks, 4 |
| GSM4721397 |
Kupffer cells derived from mice fed a western diet for 12 weeks, 5 |
| GSM4721398 |
Kupffer cells derived from mice fed a standard diet for 24 weeks, 1 |
| GSM4721399 |
Kupffer cells derived from mice fed a standard diet for 24 weeks, 2 |
| GSM4721400 |
Kupffer cells derived from mice fed a standard diet for 24 weeks, 3 |
| GSM4721401 |
Kupffer cells derived from mice fed a standard diet for 24 weeks, 4 |
| GSM4721402 |
Kupffer cells derived from mice fed a standard diet for 24 weeks, 5 |
| GSM4721403 |
Kupffer cells derived from mice fed a standard diet for 24 weeks, 6 |
| GSM4721404 |
Kupffer cells derived from mice fed a western diet for 24 weeks, 1 |
| GSM4721405 |
Kupffer cells derived from mice fed a western diet for 24 weeks, 2 |
| GSM4721406 |
Kupffer cells derived from mice fed a western diet for 24 weeks, 3 |
| GSM4721407 |
Kupffer cells derived from mice fed a western diet for 24 weeks, 4 |
| GSM4721408 |
Kupffer cells derived from mice fed a western diet for 24 weeks, 5 |
| GSM4721409 |
Kupffer cells derived from mice fed a western diet for 24 weeks, 6 |
| GSM4721410 |
moKCs derived from mice fed a western diet for 24 weeks, 1 |
| GSM4721411 |
moKCs derived from mice fed a western diet for 24 weeks, 2 |
| GSM4721412 |
moKCs derived from mice fed a western diet for 24 weeks, 3 |
| GSM4721413 |
moKCs derived from mice fed a western diet for 24 weeks, 4 |
| GSM4721414 |
moKCs derived from mice fed a western diet for 24 weeks, 5 |
| GSM4721415 |
Clec4f- macrophages derived from mice fed a western diet for 24 weeks, 1 |
| GSM4721416 |
Clec4f- macrophages derived from mice fed a western diet for 24 weeks, 2 |
| GSM4721417 |
Clec4f- macrophages derived from mice fed a western diet for 24 weeks, 3 |
| GSM4721418 |
Clec4f- macrophages derived from mice fed a western diet for 24 weeks, 4 |
| GSM4721419 |
Clec4f- macrophages derived from mice fed a western diet for 24 weeks, 5 |
| GSM4721420 |
Clec4f- macrophages derived from mice fed a western diet for 24 weeks, 6 |
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| This SubSeries is part of SuperSeries: |
| GSE156059 |
Osteopontin expression identifies a subset of recruited macrophages distinct from Kupffer cells in the fatty liver. |
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| Relations |
| BioProject |
PRJNA656542 |
| SRA |
SRP277074 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE156052_RAW.tar |
8.1 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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