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Series GSE118948 Query DataSets for GSE118948
Status Public on Jan 25, 2019
Title Single-cell profiling of the myeloid landscape identifies cell subsets with distinct fates during neuroinflammation
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The innate immune cell compartment is highly diverse in the healthy central nervous system (CNS) including parenchymal and non-parenchymal macrophages. However, this complexity is increased in inflammatory settings by the recruitment of circulating myeloid cells. It is unclear which disease-specific myeloid subsets exist and what their transcriptional profiles and dynamics during CNS pathology are. By combining deep single-cell transcriptome analysis, fate mapping, in vivo imaging, clonal analysis, and transgenic lines, we comprehensively characterized unappreciated myeloid subsets in several CNS compartments during neuroinflammation. During inflammation, CNS macrophage subsets undergo self-renewal, and random proliferation shifted towards clonal expansion. Finally, functional studies demonstrated that endogenous CNS tissue macrophages are redundant for antigen presentation. Our results highlight myeloid cell diversity and provide insights into the brain’s innate immune system.
Overall design CD45+ cells isolated from different CNS compartments (including leptomeninges, perivascular space and parenchyma, and choroid plexus) and Ly6Chigh and Ly6Clow monocytes from blood were FACS-sorted in 384-well plates and used for scRNAseq. All myeloid cells were sorted from C57BL/6N mice with 8-10 weeks of age at naive stage or at different stages of Experimental Autoimmune Encephalomyelitis (preclinical, onset and peak of the disease). Data are representative of 16-18 mice from three independent experiments. mCEL-Seq2 protocol was used for single cell sequencing (Hashimshony et al. 2016, Herman et al. 2018).
Contributor(s) Costa Jordão MJ, Sankowski R, Sagar -, Gruen D, Prinz M
Citation(s) 30679343
Submission date Aug 22, 2018
Last update date Feb 11, 2019
Contact name Sagar -
Organization name University Medical Center Freiburg
Department Department of Internal Medicine II
Lab Sagar
Street address Hugstetter Straße 55
City Freiburg
ZIP/Postal code 79106
Country Germany
Platforms (1)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (55)
GSM3351706 Blood_Naive_5
GSM3351707 Blood_Onset_18
GSM3351708 Blood_Precl4d_6
BioProject PRJNA487465
SRA SRP158633

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Supplementary file Size Download File type/resource
GSE118948_RAW.tar 20.5 Mb (http)(custom) TAR (of CSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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