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Series GSE128854 Query DataSets for GSE128854
Status Public on Mar 27, 2019
Title A single-cell atlas of mouse brain macrophages reveals unique transcriptional identities shaped by ontogeny and tissue environment. [scRNA-Seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary While the roles of parenchymal microglia in brain homeostasis and disease are fairly clear, other brain-resident myeloid cells remain less understood. By dissecting border regions and combining single-cell RNA sequencing with high-dimensional cytometry, bulk RNA-sequencing, fate-mapping and microscopy, we reveal the diversity of non-parenchymal brain macrophages. Border-associated macrophages (BAMs) residing in the dura mater, subdural meninges and choroid plexus consisted of distinct subsets with tissue-specific transcriptional signatures, and their cellular composition changed during postnatal development. BAMs exhibited a mixed ontogeny and subsets displayed distinct self-renewal capacities upon depletion and repopulation. Single-cell and fate-mapping analysis both suggested there is a unique microglial subset residing on the apical surface of the choroid plexus epithelium. Finally, gene network analysis and conditional deletion revealed IRF8 as a master regulator that drives the maturation and diversity of brain macrophages. Our results provide a framework for understanding host-macrophage interactions in the healthy and diseased brain.
Overall design sample of WT choroid plexus, sample of WT dura mater, sample of WT enriched SDM, sample of WT whole brain, sample of 9 months old APP/PS1 mice, sample of 16 months old APP/PS1 mice, sample of 16 months old WT mice, sample of Irf8 KO whole brain, sample of Irf8 KO choroid plexus, sample of Irf8 WT whole brain, sample of Irf8 WT choroid plexus, sample of dura mater with standard protocol and with ActD protocol, sample of choroid plexus with standard protocol and ActD protocol.
Contributor(s) Van Hove H, Martens L, Scheyltjens I, De Vlaminck K, Pombo Antunes AR, De Prijck S, Vandamme N, De Schepper S, Van Isterdael G, Scott CL, Aerts J, Berx G, Aerts J, Boeckxstaens GE, Vandenbroucke RE, Vereecke L, Moechars D, Guilliams M, Van Ginderachter JA, Saeys Y, Movahedi K
Citation(s) 31061494
Submission date Mar 26, 2019
Last update date Aug 25, 2022
Contact name Liesbet Martens
Organization name VIB-University of Ghent
Department VIB Inflammation Research Center
Street address Technologiepark 927
City Zwijnaarde
ZIP/Postal code 9052
Country Belgium
Platforms (1)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
Samples (15)
GSM3687213 WT dura
GSM3687214 WT choroid plexus
GSM3687215 WT enriched subdural meninges
This SubSeries is part of SuperSeries:
GSE128855 A single-cell atlas of mouse brain macrophages reveals unique transcriptional identities shaped by ontogeny and tissue environment.
BioProject PRJNA529095
SRA SRP189661

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE128854_RAW.tar 121.9 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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