Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Bulk RNA-seq of FACS sorted astrocytes upon microglial depletion

ABSTRACT: Bulk RNA-seq of FACS sorted astrocytes upon microglial depletion

PROVIDER: PRJNA719128 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR14130163_1.fastq.gz	Fastqsanger.gz
	SRR14130163_2.fastq.gz	Fastqsanger.gz
	SRR14130164_1.fastq.gz	Fastqsanger.gz
	SRR14130164_2.fastq.gz	Fastqsanger.gz
	SRR14130165_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 20

Similar Datasets

Bulk RNA-seq of FACS sorted astrocytes upon microglial depletion

Project description:As the professional phagocyte in the central nervous system (CNS), microglia are the primary scavenger removing cell corpses. The failure of microglia in debris clearance influences the normal CNS function. Meanwhile, microglia undergo turnover during the whole lifespan. If dead microglia are not timely removed, accumulated corpses may influence the CNS function. The microglial corpse clearance is hereby crucial for CNS homeostasis. However, the underlying mechanism remains obscure. In this study, we investigated how microglial corpses are removed. We found that microglial corpses are mainly phagocytosed by astrocytes, mediated by C4b opsonization. Then engulfed microglial fragments are degraded in astrocytes via the RUBICON-dependent LC3-associated phagocytosis (LAP), a form of non-canonical autophagy. The interference of the C4b-mediated engulfment and its subsequent LAP disrupt the microglial debris removal and degradation, respectively. Together, we elucidated cellular and molecular mechanisms of microglial debris removal, extending the knowledge on how the CNS homeostasis is maintained.

2022-09-01 | GSE171321 | GEO

Comparison of microglial proteomes of MACS and FACS-based purified CD11b+ microglia

Project description:Background Proteomic characterization of microglia has been limited by low yield and contamination by non-microglial proteins by magnetic-activated cell sorting (MACS) enrichment strategies. To determine whether a fluorescent-activated cell sorting (FACS)-based strategy overcomes these limitations, we compared microglial proteomes of MACS and FACS-based purified CD11b+ microglia in order to identify core sets of microglial proteins in adult mouse brain tissue. Results Quantitative multiplex proteomics by tandem mass tag mass spectrometry (TMT-MS) of MACS-enriched (N = 5) and FACS-purified (N = 5) adult wild-type CD11b+ microglia identified 1,791 proteins, of which 953 were differentially expressed indicating significant differences between both approaches. While the FACS-purified microglia proteome was enriched with cytosolic, endoplasmic reticulum and ribosomal proteins involved in protein metabolism and immune system functions, the MACS-enriched microglia proteome was enriched with proteins related to mitochondrial function and synaptic transmission. As compared to MACS, the FACS microglial proteome showed strong enrichment for canonical microglial proteins while neuron, astrocyte, and oligodendrocyte proteins were decreased. Interestingly, we observed enrichment of endothelial specific proteins in the FACS microglia proteome. By comparing FACS-purified microglia proteomes with transcriptomes, we observed highly concordant as well as highly discordant proteins that were abundant at the protein level but low at the transcript level. Conclusions We demonstrate that TMT-MS proteomics of FACS-purified adult microglia is superior to column-based enrichment approaches, resulting in purer and highly-enriched microglial proteomes. We also define core sets of highly-abundant adult microglial proteins including Moesin (Msn) that can guide future studies.

2020-05-11 | PXD015652 | Pride

RNA-seq profiling of astrocytes after microglial ablation

Project description:Astrocytes become activated in a mouse model of microglial ablation. We isolated astrocytes from hippocampus after microglial ablation, and performed RNA-seq analyses to reveal gene expression profile of activated astrocytes.

2020-09-22 | GSE142022 | GEO

Tau-P301S sorted neurons and astrocytes

Project description:Mice of indicated genotypes were perfused and their brains dissected and dissociated. Cells were fixed, immunolabeled and FACS sorted. RNA was extracted from neuron, astrocyte, and microglial cell populations. Typical RIN=4-5 for neurons, 6-8 for astrocytes, and 5-7 for microglia. Typical RNA yields 200-300ng for neurons, ~20ng for microglia, and ~5ng for astrocytes. cDNA was generated from up to 25 ng of total RNA using Nugen’s RNA-Seq method for low-input RNA samples, Ovation RNA-Seq System V2 (NuGEN). (Per manufacturers instructions, total RNA was neither depleted of rRNA nor polyA-selected.) 1 μg of sheared cDNA was taken into further processing, starting at end repair step, using Illumina’s TruSeq RNA Sample Preparation Kit v2 (Illumina). The SAMPLE_ID sample characteristic is a sample identifier internal to Genentech. The ID of this project in Genentech's ExpressionPlot database is PRJ0025262

2019-07-25 | GSE129797 | GEO

FACS sorted podocytes, mesangial cells

Project description:FACS sorted glomerular kidney cells from a single mouse were subjected to proteomics.

2022-10-13 | PXD016237 | Pride

RNA-seq profiling of astrocytes after microglial ablation

Project description:RNA-seq profiling of astrocytes after microglial ablation

| PRJNA595592 | ENA

A novel FACS-based method to isolate enriched populations of neurons, astrocytes, and microglia

Project description:We developed a novel FACS-based method to isolate enriched populations of neurons, astrocytes, and microglia. Whole mouse brains were digested, and populations of neurons, astrocytes, and microglia were subsequently enriched by FACS using a combination of positive gating on cell-type specific markers and stringent negative selection against markers of oligodendrocytes and endothelial cells. We confirmed a strong enrichment of corresponding cell-type specific genes in isolated populations and a reduction in gene markers of endothelial cells and oligodendrocytes, demonstrating that highly pure populations of neurons, astrocytes, and microglia were obtained.

2020-09-16 | GSE139000 | GEO

The RNA sequencing of brain after microglial depletion and repopulation

Project description:The RNA sequencing of brain after microglial depletion and repopulation

2018-02-24 | GSE108269 | GEO

Expression data from FACS sorted astrocytes FMR1 KO mice vs control

Project description:Fmr1 mutation results in autistic behaviors and the FMR1 KO mice model is one of the popular methods to study autism spectrum disorders. In this dataset, we include the expression data obtained from astrocytes isolated from cortex of control and FMR1-KO mice.

2017-11-30 | GSE99277 | GEO

Cortical diurnal rhythms remain intact with microglial depletion

Project description:Cortical diurnal rhythms remain intact with microglial depletion

| PRJNA780947 | ENA