Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA286209 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We performed deep-sequencing analysis of small RNA extracted from neuronal progenitors at different developmental stages. The RNA samples were extracted from microdissected tissues of dorsal or lateral sub-ventricular zone (SVZ) (to analyze the immature progenitor pools), of rostral migration stream (RMS) (to analyze the migrating neuroblasts) or of olfactory bulbs (OB) (to analyze both immature and mature neurons). These tissues were dissected from animals at variable ages: P1 and P6 for SVZ samples, P15 and P28 for RMS and OB samples. Expression profile of microRNA in time and space along post-natal neurogenesis
2014-08-28 | E-GEOD-60817 | biostudies-arrayexpress
Project description:We performed deep-sequencing analysis of small RNA extracted from neuronal progenitors at different developmental stages. The RNA samples were extracted from microdissected tissues of dorsal or lateral sub-ventricular zone (SVZ) (to analyze the immature progenitor pools), of rostral migration stream (RMS) (to analyze the migrating neuroblasts) or of olfactory bulbs (OB) (to analyze both immature and mature neurons). These tissues were dissected from animals at variable ages: P1 and P6 for SVZ samples, P15 and P28 for RMS and OB samples.
2014-08-28 | GSE60817 | GEO
Project description:Sonic hedgehog (Shh) signals via Gli transcription factors to promote maintenance and proliferation of neural stem cells in the adult mouse forebrain. We have analyzed the gene expression pattern in neurogenic Shh-responding astroglia (= neural stem cells ) in the subventicular zone of the lateral ventricle and dentate gyrus of the hippocampus in comparison to the non-neurogenic Shh-responding glia (=Bergman glia) in the cerebellum to identify the genes specifically involved in neurogenic function downstream of Shh signaling. In this dataset, we include the expression data obtained from FACS-sorted Gli1+ GFAP+ cells from microdissected SVZ, hippocampus and cerebellum. GFAP expression is based on hGFAP-GFP reporter line and Gli1 expression is lineage marked using Gli1-CreER;ROSA26-tdTomato mice. 15 Total samples were analyzed. We compared expression levels of SVZ vs. Cerebellum, Hippocampus vs. Cerebelllum to identify genes which had more than 4 fold change in expression levels with p < 0.01. From this narrowed list, we compared between SVZ and Hippocampus to identify the common genes up and down regulated. In addition, we also identified commonly expressed genes in hippocampus and SVZ at high level.
2013-09-18 | E-GEOD-50950 | biostudies-arrayexpress
Project description:The subependymal zone (SEZ), also known as the subventricular zone (SVZ), constitutes a neurogenic niche that persists during post-natal life. To investigate the cellular diversity of this brain region during human adulthood, we characterized the complete cellular niche of the adult human SEZ by single-nucleus RNA sequencing (snRNAseq), in youth and middle-aged adults.
2024-02-19 | GSE234790 | GEO
Project description:Long noncoding RNAs (lncRNAs) have been described in cell lines and various whole tissues, but lncRNA analysis of development in vivo is limited. Here, we comprehensively analyze lncRNA expression for the adult mouse subventricular zone neural stem cell lineage. We utilize complementary genome-wide techniques including RNA-seq, RNA CaptureSeq, and ChIP-seq to associate specific lncRNAs with neural cell types, developmental processes, and human disease states. By integrating data from chromatin state maps, custom microarrays, and FACS purification of the subventricular zone lineage, we stringently identify lncRNAs with potential roles in adult neurogenesis. shRNA-mediated knockdown of two such lncRNAs, Six3os and Dlx1as, indicate roles for lncRNAs in the glial-neuronal lineage specification of multipotent adult stem cells. Our data and workflow thus provide a uniquely coherent in vivo lncRNA analysis and form the foundation of a user-friendly online resource for the study of lncRNAs in development and disease. RNA-seq (both paired end and single) from the adult neurogenic niches- subventricular zone (SVZ), olfactory bulb (OB), dentate gyrus (DG) and control non-neurogenic tissue, striatum (STR). Reads were used to assemble a lncRNA catalogue and determine expression values for both protein-coding and noncoding genes
2013-04-11 | E-GEOD-45278 | biostudies-arrayexpress
Project description:Purpose: While great progress has been made in understanding the differences in regional stem cell potential using viral and genetic lineage tracing strategies, the core molecular heterogeneity that underlies these regional differences is largely unknown. Methods: Here we present a single nucleus sequencing dataset of four microdissected regions of adult CD1 wild type mouse ventricular-subventricular zones (V-SVZ). Four samples (anterior-ventral, AV; anterior dorsal, AD; posterior ventral, PV; posterior dorsal, PD) were generated at the same time from the same mice, and each sample was run on its own lane of a 10x Chromium Single Cell Controller chip for single nucleus barcoding. Results: Here we present single nucleus and single whole cell sequencing datasets of microdissected adult mouse V-SVZ, and evidence for the existence of two broad subtypes of adult neural stem cells. By using spatially resolved microdissections in the single nucleus sequencing dataset as a reference, and mapping marker gene expression in the V-SVZ, we find that these two populations reside in largely non-overlapping domains in either the dorsal or ventral V-SVZ. Furthermore, we identified two subpopulations of newly born neurons that have gene expression consistent with dorsal or ventral origins. Finally, we identify genes expressed by both stem cells and the neurons they generate that specifically mark either the dorsal or ventral adult neurogenic lineage. These datasets, methods and findings will enable future study of region-specific regulation of adult neurogenesis.
2021-02-10 | GSE165551 | GEO
Project description:Histone 3 Lysine 9 (H3K9) methylation is known to be associated with pericentric heterochromatin and important in genomic stability. In this study, we show that trimethylation at H3K9 (H3K9me3) is enriched in an adult neural stem cell niche- the subventricular zone (SVZ) on the walls of the lateral ventricle in both rodent and non-human primate baboon brain. Previous studies have shown that there is significant correlation between baboon and human regarding genomic similarity and brain structure, suggesting that findings in baboon are relevant to human. To understand the function of H3K9me3 in this adult neurogenic niche, we performed genome-wide analyses using ChIP-Seq (chromatin immunoprecipitation and deep-sequencing) and RNA-Seq for in vivo SVZ cells purified from baboon brain. Through integrated analyses of ChIP-Seq and RNA-Seq, we found that H3K9me3-enriched genes associated with cellular maintenance, post-transcriptional and translational modifications, signaling pathways, and DNA replication are expressed, while genes involved in axon/neuron, hepatic stellate cell, or immune-response activation are not expressed. As neurogenesis progresses in the adult SVZ, cell fate restriction is essential to direct proper lineage commitment. Our findings highlight that H3K9me3 repression in undifferentiated SVZ cells is engaged in the maintenance of cell type integrity, implicating a role for H3K9me3 as an epigenetic mechanism to control cell fate transition within this adult germinal niche. SVZ H3K9me3 ChIP-seq profile of an adult baboon subventricular zone was generated by deep sequencing with Illumina HiSeq2000
2014-10-01 | E-GEOD-59074 | biostudies-arrayexpress
Project description:Sonic hedgehog (Shh) signals via Gli transcription factors to promote maintenance and proliferation of neural stem cells in the adult mouse forebrain. We have analyzed the gene expression pattern in neurogenic Shh-responding astroglia (= neural stem cells ) in the subventicular zone of the lateral ventricle and dentate gyrus of the hippocampus in comparison to the non-neurogenic Shh-responding glia (=Bergman glia) in the cerebellum to identify the genes specifically involved in neurogenic function downstream of Shh signaling. In this dataset, we include the expression data obtained from FACS-sorted Gli1+ GFAP+ cells from microdissected SVZ, hippocampus and cerebellum. GFAP expression is based on hGFAP-GFP reporter line and Gli1 expression is lineage marked using Gli1-CreER;ROSA26-tdTomato mice.
2013-09-18 | GSE50950 | GEO
Project description:In the adult murine brain, neural stem cells (NSCs) reside in two main niches, the dentate gyrus (DG), and the subventricular zone (SVZ). In the DG, NSCs give rise to intermediate progenitors that differentiate into excitatory neurons, while progenitors in the SVZ migrate to the olfactory bulb (OB) where they mainly differentiate into inhibitory interneurons. Neurogenesis, the production of new neurons, persists throughout life but decrease dramatically during aging, concomitantly with increased inflammation. Many cell types, including microglia, undergo dramatic transcriptional changes but few such changes have been detected in neural progenitors. Furthermore, transcriptional profiles in progenitors from different neurogenic regions have not been compared at single cell level, and little is known about how they are affected by age-related inflammation. We have generated a single cell RNA sequencing dataset enriched for intermediate progenitors, which revealed that most aged neural progenitors only acquire minor transcriptional changes. However, progenitors set to become excitatory neurons decrease faster than others. In addition, a population in the aged SVZ, not detected in the OB, acquired major transcriptional activation related to immune responses. This suggests that differences in age related neurogenic decline between regions is not due to tissue differences but rather cell type specific intrinsic transcriptional programs, and that subset of neuroblasts in the SVZ react strongly to age related inflammatory cues.
2024-07-29 | GSE261458 | GEO
Project description:In the adult murine brain, neural stem cells (NSCs) reside in two main niches, the dentate gyrus (DG), and the subventricular zone (SVZ). In the DG, NSCs give rise to intermediate progenitors that differentiate into excitatory neurons, while progenitors in the SVZ migrate to the olfactory bulb (OB) where they mainly differentiate into inhibitory interneurons. Neurogenesis, the production of new neurons, persists throughout life but decrease dramatically during aging, concomitantly with increased inflammation. Many cell types, including microglia, undergo dramatic transcriptional changes but few such changes have been detected in neural progenitors. Furthermore, transcriptional profiles in progenitors from different neurogenic regions have not been compared at single cell level, and little is known about how they are affected by age-related inflammation. We have generated a single cell RNA sequencing dataset enriched for intermediate progenitors, which revealed that most aged neural progenitors only acquire minor transcriptional changes. However, progenitors set to become excitatory neurons decrease faster than others. In addition, a population in the aged SVZ, not detected in the OB, acquired major transcriptional activation related to immune responses. This suggests that differences in age related neurogenic decline between regions is not due to tissue differences but rather cell type specific intrinsic transcriptional programs, and that subset of neuroblasts in the SVZ react strongly to age related inflammatory cues.
2024-07-29 | GSE261457 | GEO