Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

E-GEOD-45278

ABSTRACT: Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo [RNA-seq]

OTHER RELATED OMICS DATASETS IN: PRJNA193408PRJNA193410PRJNA193406PRJNA193412PRJNA193411PRJNA193409

TISSUE(S): Striatum, Dentate Gyrus Of Hippocampal Formation, Olfactory Bulb, Subventricular Zone

PROVIDER: E-GEOD-45278 | ExpressionAtlas | 2016-05-13

REPOSITORIES: ExpressionAtlas

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	E-GEOD-45278-analysis-methods.tsv	Tabular
	E-GEOD-45278-atlasExperimentSummary.Rdata	Rdata
	E-GEOD-45278-coexpressions.tsv.gz	Tabular
	E-GEOD-45278-configuration.xml	Xml
	E-GEOD-45278-factors.xml	Xml

Items per page:

1 - 5 of 32

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

E-GEOD-52564
E-GEOD-27843
E-MTAB-3725
E-GEOD-44366
E-MTAB-599
E-GEOD-73175
E-MTAB-3718
E-ERAD-169
E-GEOD-74747
E-GEOD-43721

Similar Datasets

FOXO3 shares common targets with ASCL1 genome-wide and inhibits ASCL1-dependent neurogenesis

Project description:FOXO transcription factors are central regulators of longevity from worms to humans. FOXO3 – the FOXO isoform associated with exceptional human longevity – preserves adult neural stem cell pools. Here we identify FOXO3 direct targets genome-wide in primary cultures of adult neural progenitor cells (NPCs). Interestingly, FOXO3-bound sites are enriched for motifs for bHLH transcription factors and FOXO3 shares common targets with the pro-neuronal bHLH transcription factor ASCL1/MASH1 in NPCs. Analysis of the chromatin landscape reveals that FOXO3 and ASCL1 are particularly enriched at the enhancers of genes involved in neurogenic pathways. Intriguingly, FOXO3 inhibits ASCL1-dependent neurogenesis in NPCs and direct neuronal conversion in fibroblasts. FOXO3 also restrains neurogenesis in vivo. Our study identifies a genome-wide interaction between the pro-longevity transcription factor FOXO3 and the cell fate determinant ASCL1, and raises the possibility that FOXO3’s ability to restrain ASCL1-dependent neurogenesis may help preserve the neural stem cell pool. ChIP-seq profiles of two transcription factors (FOXO3 and ASCL1) and three histone marks (H3K4me1, H3K4me3 and H3K27me3) in adult mouse neural progenitor cells.

2013-08-13 | E-GEOD-48336 | biostudies-arrayexpress

Mus musculus

Project description:Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo [RNA-seq]

| PRJNA193409 | ENA

Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo [ChIP-seq]

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. CHIP-seq was performed on SVZ-derived neurospheres to determine the chromatin state of lncRNA promoters in adult neural stem cells

2013-04-11 | E-GEOD-45279 | biostudies-arrayexpress

Mus musculus

Project description:Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo [RNA CaptureSeq]

| PRJNA193408 | ENA

Mus musculus

Project description:Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo [ChIP-seq]

| PRJNA193410 | ENA

Project description:Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo

| PRJNA193406 | ENA

Mus musculus

Project description:Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo [expression]

| PRJNA193411 | ENA

Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo [RNA CaptureSeq]

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 CaptureSeq was perfomed on RNA extracted from adult mouse subventricular zone to better characterize rare lncRNA isoforms. Genomic regions used to design capture array are included in the raw file target_regions.bed.

2013-04-11 | E-GEOD-45277 | biostudies-arrayexpress

Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo [RNA-seq]

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

FOXO3 shares common targets with ASCL1 genome-wide and inhibits ASCL1-dependent neurogenesis

2013-08-13 | GSE48336 | GEO