GEO DataSets

(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)  While it is now appreciated that certain long noncoding in vivo, particularly with genetic strategies that establish cis versus trans mechanisms.  Pnky is a nuclear-enriched lncRNA that is transcribed divergently from the neighboring proneural transcription factor Pou3f2.  Here we show that conditional deletion of Pnky from the developing cortex regulates the production of projection neurons from neural stem cells (NSCs) in a cell-autonomous manner, altering postnatal cortical lamination.  Surprisingly, Pou3f2 expression is not disrupted by deletion of the entire Pnky gene.  Moreover, expression of Pnky from a BAC transgene rescues the differential gene expression and increased neurogenesis of Pnky-knockout NSCs, as well as the developmental phenotypes of Pnky-deletion in vivo.  Thus, despite being transcribed divergently from a key developmental transcription factor, the lncRNA Pnky regulates development in trans.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

24 Samples

Download data: H5, TXT

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL13112

30 Samples

Download data: BED, TXT

(Submitter supplied) PTBP1 and PTBP2 control alternative splicing programs during neuronal development, but the cellular functions of most PTBP1/2-regulated isoforms remain unknown. We show that PTBP1 guides developmental gene expression by regulating the transcription factor Pbx1. We identify exons that are differentially spliced when mouse embryonic stem cells (ESCs) differentiate into neuronal progenitor cells (NPCs) and neurons, and transition from PTBP1 to PTBP2 expression. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL13112

2 Samples

Download data: BED

(Submitter supplied) PTBP1 and PTBP2 control alternative splicing programs during neuronal development, but the cellular functions of most PTBP1/2-regulated isoforms remain unknown. We show that PTBP1 guides developmental gene expression by regulating the transcription factor Pbx1. We identify exons that are differentially spliced when mouse embryonic stem cells (ESCs) differentiate into neuronal progenitor cells (NPCs) and neurons, and transition from PTBP1 to PTBP2 expression. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL13112

3 Samples

Download data: TXT

(Submitter supplied) PTBP1 and PTBP2 control alternative splicing programs during neuronal development, but the cellular functions of most PTBP1/2-regulated isoforms remain unknown. We show that PTBP1 guides developmental gene expression by regulating the transcription factor Pbx1. We identify exons that are differentially spliced when mouse embryonic stem cells (ESCs) differentiate into neuronal progenitor cells (NPCs) and neurons, and transition from PTBP1 to PTBP2 expression. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL13112

8 Samples

Download data: TXT

(Submitter supplied) PTBP1 and PTBP2 control alternative splicing programs during neuronal development, but the cellular functions of most PTBP1/2-regulated isoforms remain unknown. We show that PTBP1 guides developmental gene expression by regulating the transcription factor Pbx1. We identify exons that are differentially spliced when mouse embryonic stem cells (ESCs) differentiate into neuronal progenitor cells (NPCs) and neurons, and transition from PTBP1 to PTBP2 expression. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

8 Samples

Download data: FPKM_TRACKING

(Submitter supplied) Alternative splicing (AS) generates extensive transcriptomic and proteomic complexity. However, the functions of species- and lineage-specific splice variants are largely unknown. Here, we show that mammalian-specific skipping of exon 9 of PTBP1 alters its splicing regulatory activities and affects the inclusion levels of numerous exons. During neurogenesis, skipping of exon 9 reduces PTBP1 repressive activity so as to facilitate activation of a brain-specific AS program. more...

Organism:

Gallus gallus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL19005

14 Samples

Download data: TAB

(Submitter supplied) Alternative splicing regulates over 90% of multiexon mammlian genes, but its role in specifying neural progenitor cell (NPC) fates has not been explored. Our analyses of purified mouse NPCs and neurons from developing cerebral cortices revealed hundreds of conserved and differentially spliced exons that add or remove key protein domains, especially in genes regulating the cytoskeleton.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: FPKM_TRACKING

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

Organism:

Mus musculus

Type:

Other; Expression profiling by array

Platforms:

GPL11002 GPL6193 GPL8940

22 Samples

Download data: CEL

(Submitter supplied) To assess the requirement of Ptbp2 for alternative processing of RNA in mouse brain

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL8940

6 Samples

Download data: CEL

(Submitter supplied) To assess the requirement of Ptbp2 for alternative mRNA expression in mouse brain

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6193

8 Samples

Download data: CEL

(Submitter supplied) Two polypyrimidine tract RNA-binding proteins (PTBs), one near-ubiquitously expressed (Ptbp1) and another highly tissue-restricted (Ptbp2), regulate RNA in interrelated but incompletely understood ways. Ptbp1, a splicing regulator, is replaced in the brain and differentiated neuronal cell lines by Ptbp2. To define the roles of Ptbp2 in the nervous system, we generated two independent Ptbp2-null strains, unexpectedly revealing that Ptbp2 is expressed in neuronal progenitors and is essential for postnatal survival. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL11002

8 Samples

Download data: BED, WIG

(Submitter supplied) Both microRNAs and alternative pre-mRNA splicing have been implicated in the development of the nervous system (NS), but functional interactions between these two pathways are poorly understood. We demonstrate that the neuron-specific microRNA miR-124a directly targets PTBP1/PTB/hnRNPI mRNA, which encodes a global repressor of alternative pre-mRNA splicing in non-neuronal cells. Among the targets of PTBP1 is a critical cassette exon in the pre-mRNA of PTBP2/nPTB/brPTB, an NS-enriched PTBP1 homolog. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS2846

Platform:

GPL1261

6 Samples

Download data: CEL

Analysis of neuroblastoma CAD cells expressing neuron-specific microRNA miR-124. MicroRNAs have been implicated in the development of the nervous system (NS). Results provide insight into the function of miR-124 in neuronal cells.

Organism:

Mus musculus

Type:

Expression profiling by array, transformed count, 2 protocol sets

Platform:

GPL1261

Series:

GSE8498

6 Samples

Download data: CEL

(Submitter supplied) Purpose: The goals of this study are to determine the differentially expreseed non-coding RNAs during human erythropoiesis Methods:gene expression profiling with cells on days 4,8,11,14 during erythroid differentiation, with two replicated using Illumina Genome Analyzer IIx. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Conclusions: ncRNAs were differentially expressed during erythroid differentiation

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10999

8 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10999

16 Samples

Download data: TXT

(Submitter supplied) Purpose: The goals of this study are to determine possible downstream targets of PTBP1 on day8 of erythroid differentiation with or without PTBP1 knockdown. Methods:gene expression profiling with or without PTBP1 knockdown in differentiated erythroblasts at day8 were generated by deep sequencing, induplicate, using Illumina GAIIx.The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10999

4 Samples

Download data: TXT

(Submitter supplied) Purpose: The goals of this study are to determine possible downstream targets of UCA1 on day8 of erythroid differentiation with or without UCA1 knockdown. Methods:gene expression profiling with or without UCA1 knockdown in differentiated erythroblasts at day8 were generated by deep sequencing, induplicate, using Illumina GAIIx.The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10999

4 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; Expression profiling by array; Non-coding RNA profiling by array

4 related Platforms

32 Samples

Download data: BED, CALLS, PAIR, TSV