GEO DataSets

(Submitter supplied) Transcriptome analysis of somatic stem cells and their progeny is fundamental to identify new factors controlling proliferation versus differentiation during tissue formation. Here we generated a combinatorial, fluorescent reporter mouse line to isolate proliferating neural stem cells, differentiating progenitors and newborn neurons that coexist as intermingled cell populations during brain development. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

9 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

8 Samples

Download data

(Submitter supplied) To quantitative analysis of transcriptome changes caused by lnc-OPC knockdown during OPC differentiation from NSC, lentivirus-based short hairpin RNAs were used to knockdown the lnc-OPC expression in a neural stem cell culture . Subsequently, puromycin-selected NSCs were differentiated to OPC in culture for three days.RNA-Seq was performed on the polyadenylated fraction of RNA isolated from cell samples. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: XLSX

(Submitter supplied) To better understand the OLIG2 binding site in the whole-genome of mouse neural stem cells, ChIP was performed using 107 mouse neural stem cells. The ChIP-Seq library was constructed by using DNA SMART ChIP-Seq Kit according to the manufacturer's instructions (Clontech) and was sequenced on the Illumina HiSeq 2000 Sequencer.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

2 Samples

Download data: XLSX

(Submitter supplied) To better understand the transcriptome of mouse neural stem cells (including known genes and novel long non coding RNA genes), RNA-Seq was performed on the polyadenylated fraction of RNA isolated from cell samples. Read mapping and transcriptome construction were done by using optimized pipeline which integrate Tophat followed by Cufflinks.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

2 Samples

Download data: XLSX

(Submitter supplied) While thousands of long noncoding RNAs (lncRNAs) have been identified, few lncRNAs that control neural stem cell (NSC) behavior are known. Here, we identify Pinky (Pnky) as a novel, neural-specific lncRNA that regulates neurogenesis from NSCs in the embryonic and postnatal brain. In postnatal NSCs, Pnky knockdown potentiates neuronal lineage commitment and expands the transit-amplifying cell population, increasing neuron production several-fold. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: DIFF, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by array; Non-coding RNA profiling by array

4 related Platforms

32 Samples

Download data: BED, CALLS, PAIR, TSV

(Submitter supplied) 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. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by array

Platform:

GPL16745

12 Samples

Download data: CALLS, PAIR

(Submitter supplied) 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. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL15887

11 Samples

Download data: CALLS, PAIR

(Submitter supplied) 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. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11002

3 Samples

Download data: BED

(Submitter supplied) 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. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11002

5 Samples

Download data: BED, TXT

(Submitter supplied) 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. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16815

1 Sample

Download data: BED, TSV

(Submitter supplied) Purpose: In this study we investigated the molecular role of cytosine modification in the developing cortex of mice. To this aim we isolated thee linage related cell populations of the developing cortex and mapped both, 5mC as well as 5hmC on a genome-wide scale. Furthermore we established a system to site-specifcally demethylate DNA by using a dCas9-Tet1 fusion protein. Methods: Neuronal stem cells (Btg2-/Tubb3-), neurogenic progenitors (Btg2+/Tubb3-) and neurons (Tubb3+) were isolated from E14.5 Btg2-RFP/Tubb3-GFP double heterozygous mouse embryos (Aprea et al. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17021

12 Samples

Download data: BW, TXT

(Submitter supplied) MicroRNAs (miRNAs) are short (~22 nt) single-stranded non-coding RNAs that regulate gene expression at the post-transcriptional level. Over the past years, many studies have extensively characterized the involvement of miRNA-mediated regulation in neurogenesis and brain development. However, a comprehensive catalog of cortical miRNAs cell-specifically expressed in progenitor types of the developing mammalian cortex is still missing. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17021

9 Samples

Download data: TXT

(Submitter supplied) Regulation of neuronal commitment in mouse embryonic stem cells by the Reno/Bahcc1 locus

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19057 GPL24247

77 Samples

Download data: BW, NARROWPEAK, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL21103

34 Samples

Download data: TXT

(Submitter supplied) Cardiac maturation during perinatal transition of heart is critical for functional adaptation to hemodynamic load and nutrient environment. Perturbation in this process has major implications in congenital heart defects (CHDs). Transcriptome programming during perinatal stages is important information but incomplete in current literature, particularly, the expression profiles of the long noncoding RNAs (lncRNAs) are not fully elucidated

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

17 Samples

Download data: TXT

(Submitter supplied) Cardiac maturation during perinatal transition of heart is critical for functional adaptation to hemodynamic load and nutrient environment. Perturbation in this process has major implications in congenital heart defects (CHDs). Transcriptome programming during perinatal stages is important information but incomplete in current literature, particularly, the expression profiles of the long noncoding RNAs (lncRNAs) are not fully elucidated

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21103

17 Samples

Download data: TXT

(Submitter supplied) In order to get a better understanding of the gene signature of aneuploid cells, we applied single cell RNA sequencing on human bone marrow cells from healthy donors and patients with bone marrow failure and cytogenetic abnormalities. We chacterized normal hemaopoiesis as binary differentiation and identified aneuploid cells from patient samples.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21290 GPL16791

1202 Samples

Download data: CSV, GTF

(Submitter supplied) The human cerebral cortex depends for its normal development and size on a precisely controlled balance between self-renewal and differentiation of diverse neural progenitor cells. Specialized progenitors that are common in humans, but virtually absent in rodents, called ‘outer radial glia’ (ORG), have been suggested to be crucial to the evolutionary expansion of the human cortex. We combined cell type-specific sorting with transcriptome-wide RNA-sequencing to identify genes enriched in human ORG, including targets of the transcription factor Neurogenin, and previously uncharacterized, evolutionarily dynamic, long noncoding RNAs. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

9 Samples

Download data: FPKM_TRACKING