RNA-seq of astrocytes isolated from parental isolated mice
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PROVIDER: PRJNA707540 | ENA |
REPOSITORIES: ENA
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Project description:To understand the transcriptome change in astrocytes after parental isolation
2021-09-08 | GSE168479 | GEO
Project description:Isolated astrocytes from young BMAL1aKO and wildtype mice
| PRJNA945943 | ENA
Project description:Isolated astrocytes from aged BMAL1aKO and wildtype mice
| PRJNA947531 | ENA
Project description:Purpose: The core clock protein BMAL1 serves as the primary positive circadian transcriptional regulator and its depletion in astrocytes not only disrupts circadian function, but also leads to a unique cell-autonomous activation phenotype. We have undertaken RNAsequencing of isolated astrocytes from young wildtype and BMAL1 astrocyte-specific knockout mice (Bmal1fl/fl, ALDH1L1-CreERT2, termed BMAL1 aKO) to uncover changes to gene expression as a result of BMAL1 disruption in astrocytes. Methods: BMAL1 aKO mice and wildtype littermates were given tamoxifen at 2 months of age and harvested around 7 months of age and brains were collected. After collagenase digestion and debris removal, astrocytes were isolated from the rest of the brain cells (termed "flowthrough") using Miltenyi MACS Anti-ACSA-2 magnetic beads. RNA was extracted in Trizol reagent and sent for sequencing. Samples from BMAL1 aKO and wildtype astrocytes were compared and flowthrough samples were compared to astrocytes to confirm cell-type purity. Results: BMAL1 aKO results in both up- and down-regulation of many astrocyte genes. GO pathway analysis points to lysosomal pathways as dysregulated by knockout of BMAL1 in astrocytes. While astrocytes are enriched by our isolation methods, there is some degree of contamination from neurons and oligodendrocytes. Conclusions: While our astrocyte isolation method has some caveats in terms of purity, BMAL1 aKO appears to dysregulate lysosomal pathways, which will be investigated by further experiments.
2023-04-26 | GSE227633 | GEO
Project description:Purpose: The core clock protein BMAL1 serves as the primary positive circadian transcriptional regulator and its depletion in astrocytes not only disrupts circadian function, but also leads to a unique cell-autonomous activation phenotype. We have undertaken RNAsequencing of isolated astrocytes from aged wildtype and BMAL1 astrocyte-specific knockout mice (Bmal1fl/fl, ALDH1L1-CreERT2, termed BMAL1 aKO) to uncover changes to gene expression as a result of BMAL1 disruption in astrocytes and to confirm those changes persist during aging. Methods: BMAL1 aKO mice and wildtype littermates were given tamoxifen at 2 months of age and harvested around 20 months of age and brains were collected. After collagenase digestion and debris removal, astrocytes were isolated from the rest of the brain cells (termed "flowthrough") using Miltenyi MACS Anti-ACSA-2 magnetic beads. RNA was extracted in Trizol reagent and sent for sequencing. Samples from BMAL1 aKO and wildtype astrocytes were compared and flowthrough samples were compared to astrocytes to confirm cell-type purity. Results: BMAL1 aKO results in both up- and down-regulation of many astrocyte genes. GO pathway analysis points to lysosomal pathways as dysregulated by knockout of BMAL1 in astrocytes. While astrocytes are enriched by our isolation methods, there is some degree of contamination from neurons and oligodendrocytes. Conclusions: While our astrocyte isolation method has some caveats in terms of purity, BMAL1 aKO appears to dysregulate lysosomal pathways, which will be investigated by further experiments.
2023-04-26 | GSE227932 | GEO
Project description:Comparison of expression data of rat forebrain astrocytes from P1, P7 acutely isolated by immunopanning or cultured with astrocytes prepared by McCarthy and de Vellis' (1980) method. Elucidating the genes induced by serum in immunopannedrat astrocytes.
2011-09-06 | GSE26066 | GEO
Project description:Comparison of expression data of rat forebrain astrocytes from P1, P7 acutely isolated by immunopanning or cultured with astrocytes prepared by McCarthy and de Vellis' (1980) method. Elucidating the genes induced by serum in immunopannedrat astrocytes. Three biological replicates for each sample were done. MD-astrocytes were prepared as described in McCarthy and de Vellis 1980 and harvested for mRNA after 7DIV. IP-astrocytes were isolated from P1 or P7 Sprague Dawley rats and processed for RNA immediately (IP-astrocytes P1/P7), or cultured for 7 days in HBEGF before harvesting (Cult. IP-astrocytes P1/P7). For the serum studies, we plated IP-astrocytes P7 in MD-astrocyte media containing 10% fetal calf serum immediately after isolation and cultured them for 7 days. After 7 days, the cultures were either processed for total RNA or washed 3x with dPBS and astrocyte base media with HBEGF was added. The cells were cultured for an additional 7 days and then processed for RNA. We isolated total RNA with the QIAshredder and Qiagen RNeasy Mini Kit. We used the 3’IVT Express kit for preparation of the RNA and the Rat Genome 230 2.0 Array chip (Affymetrix, Santa Clara). RT-PCR was used to elucidate the level of contamination in each cell sample.
2011-09-05 | E-GEOD-26066 | biostudies-arrayexpress
Project description:Isolation of glia from Alzheimer's mice reveals inflammation and dysfunction. Reactive astrocytes and microglia are associated with amyloid plaques in Alzheimer's disease (AD). Yet, not much is known about the molecular alterations underlying this reactive phenotype. To get an insight into the molecular changes underlying AD induced astrocyte and microglia reactivity, we performed a transcriptional analysis on acutely isolated astrocytes and microglia from the cortex of aged controls and APPswe/PS1dE9 AD mice. As expected, both cell types acquired a proinflammatory phenotype, which confirms the validity of our approach. Interestingly, we observed that the immune alteration in astrocytes was relatively more pronounced than in microglia. Concurrently, our data reveal that astrocytes display a reduced expression of neuronal support genes and genes involved in neuronal communication. The microglia showed a reduced expression of phagocytosis and/or endocytosis genes. Co-expression analysis of a human AD expression data set and the astrocyte and microglia data sets revealed that the inflammatory changes in astrocytes were remarkably comparable in mouse and human AD, whereas the microglia changes showed less similarity. Based on these findings we argue that chronically proinflammatory astrocyte and microglia phenotypes, showing a reduction of genes involved in neuronal support and neuronal signaling, are likely to contribute to the neuronal dysfunction and cognitive decline in AD. 2 cell types from 2 conditions: cortical microglia and cortical astrocytes from 15-18 month old APPswe/PS1dE9 mice compared to wildtype littermates. Biological replicates: microglia from APPswe/PS1dE9, N=7, microglia from WT, N=7, astrocytes from APPswe/PS1dE9, N=4, microglia from WT, N=4
2015-11-04 | E-GEOD-74615 | biostudies-arrayexpress
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
Project description:To investigate the mechansims that underly astrocyte dedifferentiation, we performed single cell RNA sequencing analysis of primary astrocytes after p53 loss and exposure to mitogens, EGF and and FGF. Primary astrocytes were isolated from postnatal day 3 inducible p53 knockout mice (GFAP-CreERT2;p53flox/flox;LSL-tdTomato), whereby treatment with 4-hydroxytamoxifen (4OHT) induces p53 loss and tdTomato labelling in GFAP+ astrocytes. Astrocytes were treated with 4OHT in media supplemented with EGF and FGF to induce recombination and astrocyte dedifferentiation in vitro.
2023-02-23 | GSE196408 | GEO