Gene expression from primary brain cell cultures and RNA mixtures.
Ontology highlight
ABSTRACT:
ORGANISM(S): Rattus norvegicus
PROVIDER: GSE19380 | GEO | 2010/12/01
SECONDARY ACCESSION(S): PRJNA121801
REPOSITORIES: GEO
Similar Datasets
Project description:Gene expression from primary neuronal, astrocytic, oligodendrocytic and microglial cultures, as well as from RNA mixtures thereof. Keywords: Primary cell cultures Primary neuronal, astrocytic, oligodendrocytic and microglial cultures (4 biological replicates of each), as well as RNA mixtures thereof (5 different mixing proportions, 2 independent replicates of each mixing proportion).
2010-12-01 | E-GEOD-19380 | biostudies-arrayexpress
Project description:Primary microglial cultures from neonatal mice were exposed to hypoxia (1% O2, 6 h) and their global gene expression profile was analyzed. This data were used to described the Hypoxic Microglia Signature, genes that were up- or down-regulated by hypoxia in microglial cells in culture.
2021-03-08 | GSE97423 | GEO
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:To test the effect of saracatinib on gene expression patterns in microglia, we treated mouse (C57BL/6) primary microglial cultures with saracatinib (1microM, 24h) versus DMSO vehicle control and quantified gene expression. Sequencing libraries were prepared using the Lexogen QuantSeq 3'Forward kit with sequencing performed on an Illumina HiSeq 4000 (single end reads 1 x 65; 5M reads per sample). For processed data, reads were aligned against GRCm38 and quantified using STAR. Samples were normalized with CQN. Batch correction was completed using ComBat from sva version 3.6.0.
2020-11-05 | GSE146865 | GEO
Project description:To test the effect of fatostatin on gene expression patterns in microglia, we treated mouse (C57BL/6) primary microglial cultures with fatostatin (5microM, 72h) versus DMSO-only control and quantified gene expression using 3' end labeling. Sequencing libraries were prepared using the Lexogen QuantSeq 3'Forward kit and sequencing of single end reads (1 x 65) was performed on an Illumina HiSeq 4000 at 5M reads per sample. For processed data, reads were aligned against GRCm38 using STAR. Transcripts were quantified and annotated against GencodeM11 using Rsubread. Samples were normalized with CQN.
2020-11-05 | GSE146864 | GEO
Project description:We undertook a survey of gene expression changes in primary microglial cultures with and without neurovirulent (FrCasE) and non-neurovirulent (Fr57E) virus infection to identify physiological changes that could be relevant to the induction of spongiform neurodegeneration. These gene expression analyses were performed using Affymetrix 430A mouse GeneChips (5 chips for each of the three experimental conditions, representing over 14,000 murine genes and ESTs. RNA from 5 separate microglial culture preparations were analyzed for Control (mock infected), Fr57E-, and FrCasE-infected microglia. Present/absent calls were based on MicroArray Suite 5.0 from Affymetrix. Affymetrix CEL files were analyzed using dChip software after normalization of the data between all 15 arrays. Statistical analyses were performed using ANOVA.
2005-05-11 | E-MEXP-459 | biostudies-arrayexpress
Project description:Saracatinib drug treatment of mouse primary microglia cultures
| PRJNA612216 | ENA
Project description:Fatostatin drug treatment of mouse primary microglia cultures
| PRJNA612217 | ENA
Project description:Glioblastoma, the most frequent and malignant adult brain tumor has been extensively studied; yet no effective treatment exists. To overcome this dismal scenario, it is essential to improve preclinical biological models. This study aimed to establish and molecularly characterize glioblastoma primary cultures. Additionally, it intended to assess the efficacy of molecular-targeted therapies, in the presence of putative targeting cell lines. Five glioblastoma primary cultures were established exhibiting a diversity of chromosomal alterations by aCGH, with gain of chromosome 7 and loss of chromosome 10, 13 and 17p, the most frequent alterations. Mutation profiling by Ion Torrent and Sanger sequencing showed the present of hotspot mutations in TERT (4/5), TP53 (2/5) and RB, BRAF, PTEN and EGFR (1/5). A similar chromosomal and mutation pattern was observed in the primary cultures and matched frozen tumors. The MTS cell viability assay of the p.Gly598Val EGFR mutated cell line, revealed AST1306 as the most potent EGFR inhibitor, when compared with afatinib, erlotinib, or lapatinib. Herein, glioblastoma primary cultures were successfully established and molecularly characterized. Importantly, we showed that AST1306 inhibits EGFR mutated cells, suggesting that primary cultures are suitable in vitro models for glioblastoma biology and preclinical drugs studies.
2016-07-01 | GSE59967 | GEO
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.
2013-07-11 | GSE43808 | GEO