GEO DataSets

(Submitter supplied) We generated single-cell RNAseq profiles of microglia and brain myeloid cells (1922 total; 1816 cells passed quality control) from different developmental stages (E14.5, P7 and P60) to study their heterogeneity. Cells were isolated from either the whole developing brain (for the E14.5 stage) or six separate regions (for P7 and P60 stages): Cortex (CTX), Cerebellum (CB), Hippocampus (HIP), Striatum (STR), Olfactory bulb (OB), Choroid plexus (CP). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

1922 Samples

Download data: CSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

2446 Samples

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(Submitter supplied) We generated single-cell RNAseq profiles of 143 microglia, sorted in the gate CD45lowCD11+Gpnmb+Clec7a+, from postnatal day 7 cerebellum to validate the newly identified “proliferative region-associated microglia (PAM)” (Gpnmb and Clec7a are PAM surface markers). Single cells were FACS index sorted followed by Smart-seq2 library preparation and Illumina Nextseq (sequence depth > 1 million per cell). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

143 Samples

Download data: CSV

(Submitter supplied) We generated single-cell RNAseq profiles of 369 microglia (183 from wild type and 186 from Trem2 knock-out), sorted in the gate CD45lowCD11+ or CD45lowCD11+Gpnmb+Clec7a+ (PAM enrichment), to compare gene expression of wild type vs. Trem2 knock-out microglia on the postnatal day 7. Single cells were FACS index sorted from the whole brain followed by Smart-seq2 library preparation and Illumina Nextseq (sequence depth > 1 million per cell). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

369 Samples

Download data: CSV

(Submitter supplied) To compare microglial regional heterogeneity, we generated bulk RNA-seq profiles of postnatal day 60 microglia, sorted by TMEM119+ (also CD45lowCD11b+), from cortex (CTX), cerebellum (CB), hippocampus (HIP), striatum (STR) regions. For each sample, 3000 microglia were FACS sorted into RLT lysis buffer for total RNA extraction, followed by Smart-seq library preparation and Illumina Nextseq (sequence depth 10-20 million per sample). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

12 Samples

Download data: CSV

(Submitter supplied) Recently we demonstrated that amoeboid microglia in white matter regions are essential for proper oligodendrocyte homeostasis and myelinogenesis in the first postnatal week of mice. Amoeboid microglia in the corpus callosum change their activation profile already within few days after postnatal day (P)7 and microglia of the cerebellum show similar features to callosal microglia. Here we expanded our previous transcriptional analysis and performed bulk RNA sequencing of microglia during development in a detailed way in P7, P10 and P42 microglia from corpus callosum, cortex and cerebellum. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15103

33 Samples

Download data: TXT

(Submitter supplied) Preparation of primary microglial cultures from postnatal mice is tedious with a low yield, high variability and risk of astrocytic contamination. Microglia derived from embryonic stem cells (ESdM) have been suggested as alternative source, but it is unclear how closely ESdM resemble the molecular phenotype of primary microglia. Here, we performed a whole transcriptome analysis of ESdM in comparison to primary cultured and flow cytometry-sorted microglia and compared the microglial transcriptome to other cell types. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

27 Samples

Download data: TXT

(Submitter supplied) Whereas microglia involvement in virtually all brain diseases is well accepted their role for the control of homeostasis in the central nervous system (CNS) is mainly thought to maintain neuronal function through the formation, refinement and monitoring of synapses in both the developing and adult brain. Although the prenatal origin and the neuron-centered function of cortical microglia has recently been elucidated much less is known about a distinct amoeboid microglia population formerly described as “fountain of microglia” that appear only postnatally in the myelinating regions such as corpus callosum and cerebellum. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL16570

18 Samples

Download data: CEL

(Submitter supplied) Resident tissue macrophages such as microglia in the retina and the brain inhabit tissues providing specific environmental cues. We therefore intened to compare the expression profiles of these two microglial subpopulations. Additionally, we included other resident tissue macrophages from the eye, like the cornea, that are supposed to underly a turnover with peripheral monocytes. Overall, we compared two long-lived microglial populations with two short-lived populations, cornea macrophages and bone marrow-derived monocytes. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15103

16 Samples

Download data: TXT

(Submitter supplied) Similar to the brain, the eye is considered an immune-privileged organ where tissue-resident macrophages provide the major immune cell constituents. However, little is known about spatially restricted macrophage subsets within different eye compartments with regard to their origin, function and fate during health and disease. Here, we combined single-cell analysis, fate mapping, parabiosis and computational modelling to comprehensively examine myeloid subsets in distinct parts of the eye during homeostasis. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21493

20 Samples

Download data: CSV

(Submitter supplied) Microglia are myeloid cells of the central nervous system (CNS) that participate both in normal CNS function and disease. We investigated the molecular signature of microglia and identified 239 genes and 8 microRNAs that were uniquely or highly expressed in microglia vs. myeloid and other immune cells. Out of 239 genes, 106 were enriched in microglia as compared to astrocytes, oligodendrocytes and neurons. more...

Organism:

Mus musculus

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platforms:

GPL6096 GPL17871 GPL17873

77 Samples

Download data: CEL, RCC

(Submitter supplied) Using RNA-seq, we report here that primary microglia (PM) cells have a distinct transcriptomic signature and express a unique cluster of transcripts in response to 2hrs or 4 hrs with LPS.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

9 Samples

Download data: TXT

(Submitter supplied) Using RNA-seq, we report that jumonji H3K27 demethylase inhibitor, GSK-J4, exerts potent anti-inflammatory effects on LPS-stimulated BV-2 microglial cells.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

15 Samples

Download data: TXT

(Submitter supplied) Expression profiling by high throughput sequencing Microglial cells have a double life as the immune cells of the brain in times of stress but have also specific physiological functions in homeostatic conditions. In pathological contexts, microglia undergo a phenotypic switch called “reaction” ’that promotes the initiation and the propagation of neuro-inflammation. Reaction is complex, molecularly heterogeneous and still poorly characterized, leading to the concept that microglial reactivity might be too diverse to be molecularly defined. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

10 Samples

Download data: TXT

(Submitter supplied) Microglia, the resident immune cells of the central nervous system (CNS), have two distinct phenotypes in the developing brain: amoeboid form, known to be amoeboid microglial cells (AMC) and ramified form, known to be ramified microglial cells (RMC) alongside several intermediate forms. The AMC are characterized by being proliferative, phagocytic and migratory whereas the RMC are quiescent and exhibit a slow turnover rate. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL1355

6 Samples

Download data: CEL, TXT

(Submitter supplied) Single-cell RNA sequencing (scRNA-seq) methods generate sparse gene expression profiles for thousands of single cells in a single experiment. The information in these profiles is sufficient to classify cell types by distinct expression patterns but the high complexity of scRNA-seq libraries prevents full characterization of transcriptomes from individual cells. To generate more focused gene expression information from scRNA-seq libraries, we developed a strategy to physically recover the DNA molecules comprising transcriptome subsets, enabling deeper interrogation of the isolated molecules by another round of DNA sequencing. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

5 related Platforms

13 Samples

Download data: JSON, TSV, TXT

(Submitter supplied) To understand the molecular mechanisms of neural commitment from mouse ESCs, we selected very dense time points during neural differentiation based on qPCR results and performed mRNA-sequencing at both of cell population and single cell levels.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

113 Samples

Download data: TXT

(Submitter supplied) Analysis of gene expression changes during mouse salivary gland development using RNA-Seq

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

13 Samples

Download data: CSV

(Submitter supplied) The goal of this study is to discover fibroblast subpopulations relevant to recessive dystrophic epidermolysis bullosa

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15520

543 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Expression profiling by array

Platforms:

GPL16686 GPL20301

21 Samples

Download data: CEL, RDS