Identification and characterization analysis of the different genes in primary mouse microglia response to circDYM using RNA-seq.
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA670850 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Whole RNA-sequencing analysis was performed and analyzed by Lc. Biotech Co. Ltd. (Hangzhou, China). Primary mouse microglia from the Con + circCon group, Con + circDYM group, LPS + circCon group, and LPS + circDYM group were collected in TRIzol. Total RNAs were extracted from Trizol. UMI technology was used to label each sequence fragment with sequence tags, which minimized the interference of duplication caused by PCR amplification on the quantitative accuracy of the transcriptome. RNA sequencing reads were aligned to the mouse genome (GRCh37/hg19) using the software Hisat2 (2.0.4). Transcript abundance was evaluated by calculating fragments per kilo base of exon per million fragments mapped (FPKM).
2022-01-31 | GSE159904 | GEO
Project description:Poly(ADP-ribose) polymerases (PARPs) modify target proteins with ADP-ribose by using nicotinamide adenine dinucleotide as a substrate, and contribute to various signaling pathways. PARP14 is the largest member of PARP superfamily. Whole RNA-sequencing analysis was performed and analyzed by Lc. Biotech Co., Ltd. (Hangzhou, China). Primary mouse microglia from the Con + ACT-Con group, Con + ACT-PARP14 group, OGD + ACT-Con group, and OGD + ACT-Con group were collected in TRIzol. Total RNAs were extracted from Trizol. UMI technology was used to label each sequence fragment with sequence tags, which minimized the interference of duplication caused by PCR amplification on the quantitative accuracy of the transcriptome. RNA sequencing reads were aligned to the mouse genome (GRCh37/hg19) using the software Hisat2 (2.0.4). Transcript abundance was evaluated by calculating fragments per kilo base of exon per million fragments mapped (FPKM).
2023-06-05 | GSE152000 | GEO
Project description:phosphopeptides were isolated from primary microglia, and identified by LC-MS/MS analysis.
2023-02-24 | PXD040217 | JPOST Repository
Project description: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. Cultured microglia and ESdM were related to sorted microglia, but clearly distinct from other myeloid cell types, T cells, astrocytes and neurons. ESdM and primary cultured microglia showed strong overlap in their transcriptome. Only 144 gene transcripts were differentially expressed between both cell types, mainly derived from immune-related genes with a higher activation status of pro-inflammatory and immune defense genes in primary microglia compared to ESdM. Flow cytometry analysis of cell surface markers CD54, CD74 and CD274 selected from the microarray confirmed the close phenotypic relation between ESdM and primary cultured microglia. Thus, assessment of genome-wide transcriptional regulation demonstrates that microglia are distinct from other macrophage cell types and that mouse pluripotent stem cell-derived microglia are closely related to cultured postnatal microglia. Comparison of different primary neuronal cells with ES-cell derived microglial cells
2013-07-11 | E-GEOD-43808 | biostudies-arrayexpress
Project description:We report the transcriptome analysis by RNAseq for primary microglia defecting ASD-related genes by siRNA treatment.
2021-09-08 | GSE172014 | GEO
Project description:Transcriptome analysis of primary microglia defecting ASD-related genes.
| PRJNA721700 | ENA
Project description:The study of microglia biology and the development of microglia-based gene therapies are in urgent need of efficient and safe vehicles for microglia transgene delivery. To address this, we developed adeno-associated virus (AAV) variants that mediate efficient in vitro and in vivo microglia transduction via directed evolution of the AAV capsid protein. To assess the effect of AAV transduction on microglia, we carried out bulk RNAseq in primary microglia and found that microglia transduced by AAV remain close to homeostatic state. Furthermore, single-cell RNA sequencing showed that the AAV-MG variants mediate safe in vivo transgene delivery without inducing microglia immune activation. These AAV variants should facilitate the applications of various genetically-encoded sensors and effectors in studying microglia-related biology and therapeutic interventions.
2022-04-06 | GSE197743 | GEO
Project description:Microglia, the resident immune cells of the brain, can exhibit a broad range of activation phenotypes, many of which have been implicated in several diseases and disorders of the central nervous system including alcohol use disorders and disorders. By utilizing a method optimized for sensitive and rapid quantitative proteomic analysis of microglia involving suspension trapping (S-Trap), we were able to produce efficient and reproducible protein extraction from low cell yielding primary mouse brains. Using a ~2 h gradient on a 75 cm UPLC column with a modified data dependent acquisition method on a hybrid quadrupole-Orbitrap mass spectrometer (QE Plus), 5,062 total proteins were identified where 4,928 of those proteins were quantifiable by label-free quantitation (with 5 biological replicates). This analysis resulted in the most comprehensive proteomic dataset for ethanol- and LPS-treated primary mouse microglia to date and even expanded upon the well-characterized macrophage/microglia response to LPS treatment. This study also highlights the subtle, yet significant changes ethanol exposure can induce when compared to control. Interestingly, these changes are not consistent with the robust classical activation induced by LPS treatment, but instead align with the emerging theory that ethanol-treated microglia yield an alternative activation response. The contrast to LPS-treated microglia leads us to conclude that ethanol does not elicit a strong inflammatory response but rather might have a general inhibitory effect on multiple pathways such as phagocytosis and cell migration.
2020-04-07 | PXD014466 | Pride
Project description:In the brain the cells that control inflammation are called a type of white blood cell called microglia. Microglia are located throughout the brain and spinal cord and account for 10–15% of all cells found within the brain. As the resident white blood cells, they are the main active immune defence in the central nervous system (CNS). Microglia are part of an important class of cells known as macrophages that have two main states: M1 and M2. M1 cells are pro- inflammatory, leading to more inflammation, while M2 are anti-inflammatory, and drive wound healing. In this study, we will collect primary microglia from surgical biospies of 100 individuals.
This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
| EGAS00001002494 | EGA
Project description:Whole RNA-sequencing analysis was performed by LC-Bio. Day-10 neurons from the Vector or circSCMH1 overexpression groups were collected in Trizol. Total RNAs were extracted from Trizol. UMI technology was used to label each sequence fragment with sequence tags, which minimizes the interference of duplication generated by PCR amplification on the quantitative accuracy of transcriptome. RNA-seq reads were aligned to the mouse genome (GRCh37/hg19) using the software Hisat2 (2.0.4). Transcript abundance was quantified as fragments per kilo base of exon per million fragments mapped (FPKM). Differentially expressed genes were determined by DESeq2 (DOI: 10.1186/s13059-014-0550-8).
2021-07-28 | GSE135121 | GEO