Similar studies for GEO DataSets (Select 200037933) - GEO DataSets

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Items: 20

Select item 2000379331.

Coordinated regulation of neuronal mRNA steady-state levels through developmentally controlled intron retention

(Submitter supplied) Differentiated cells acquire unique structural and functional traits through coordinated expression of lineage-specific genes. An extensive battery of genes encoding components of the synaptic transmission machinery and specialized cytoskeletal proteins is activated during neurogenesis, but the underlying regulation is not well understood. Here we show that genes encoding critical presynaptic proteins are transcribed at a detectable level in both neurons and non-neuronal cells. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11002
3 Samples

Download data: TSV

Series

Accession:: GSE37933

ID:: 200037933

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000084982.

The MicroRNA miR-124 Promotes Neuronal Differentiation by Triggering Brain-Specific Alternative Pre-mRNA Splicing

(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

Series

Accession:: GSE8498

ID:: 200008498

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 28463.

MicroRNA miR-124 expression effect on neuronal cell line

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

DataSet

Accession:: GDS2846

ID:: 2846

PubMed Full text in PMC Similar studies GEO Profiles Analyze DataSet

Select item 2000851654.

Identification of PTBPs RNA binding sites in mouse brain

(Submitter supplied) PTBP1 and PTBP2 are RNA-binding proteins that control RNA processings, including alternative pre-mRNA splicing. The sequential down-regulation of the two proteins is necessary for neuronal maturation. However, their binding substrates in neural tissues have not been examined.

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL13112
6 Samples

Download data: GFF

Series

Accession:: GSE85165

ID:: 200085165

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000848035.

Transcriptome of the mouse neocortices

(Submitter supplied) Derive alternative splicing regulatory networks of PTBP1 and PTBP2

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL13112
7 Samples

Download data: XLSX

Series

Accession:: GSE84803

ID:: 200084803

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000715696.

Interactions of aCPs with Cytosine-rich Polypyrimidine Tracts Enhance Splicing of Cassette Exons

(Submitter supplied) Alternative splicing comprises a robust generator of mammalian transcriptome complexity. Splice site specification and activity are controlled by interactions of cis-acting determinants on a transcript with specific RNA binding proteins. A major subset of these interactions comprises interactions localized to the intronic U-rich polypyrimidine tract located immediately 5’ to the majority of splice acceptors. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
6 Samples

Download data: TXT, XLSX

Series

Accession:: GSE71569

ID:: 200071569

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Select item 2000696567.

An Alternative Splicing Event Amplifies Evolutionary Differences Between Vertebrates

(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

Series

Accession:: GSE69656

ID:: 200069656

PubMed Similar studies SRA Run Selector

Select item 2000598848.

PTBP1 excludes UPF1 to protect long 3'UTRs from nonsense-mediated mRNA decay

(Submitter supplied) RNA-seq analysis of human 293 Tet-off cells depleted of PTBP1 and UPF1 alone and in tandem with specific siRNAs.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
8 Samples

Download data: TXT

Series

Accession:: GSE59884

ID:: 200059884

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Select item 2000869679.

Analysis of splicing pattern and gene expression level of Matrin3 knockdown.

(Submitter supplied) We identified RNA targets of Matrin3 using SH-SY5Y by PAR-CLIP analysis. Because Matrin3 mainly bound to intron of pre-mRNA, in order to find the effect of Matrin3 on splicing pattern and expression, we knocked down Matrin3 using SH-SY5Y cells by electroporation and extracted total RNAs from those cells. The total RNAs were subjected to whole transcripts microarray GeneChip® Affymetrix Human Transcriptome array 2.0.

Organism:: Homo sapiens

Type:: Expression profiling by array

Platforms:: GPL17585 GPL17586
12 Samples

Download data: CEL

Series

Accession:: GSE86967

ID:: 200086967

Select item 20021058110.

Capture RIC-seq reveals positional rules of PTBP1-associated RNA loops in splicing regulation [SELEX]

(Submitter supplied) RNA-binding proteins (RBPs) bind at different positions of pre-mRNA molecules to promote or reduce the usage of a particular exon. Seeking to understand the working principle of these positional effects, we develop a capture RIC-seq (CRIC-seq) method to enrich specific RBP-associated in situ proximal RNA-RNA fragments for deep sequencing. We determine hnRNPA1-, SRSF1-, and PTBP1-associated proximal RNA-RNA contacts and regulatory mechanisms in HeLa cells. more...

Organism:: synthetic construct

Type:: Other

Platform:: GPL26697
2 Samples

Download data: TXT

Series

Accession:: GSE210581

ID:: 200210581

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Select item 20004511911.

Gene Expression and Exon Splicing Change Analysis of Mouse N2A Cell Transcriptome upon Polypyrimidine tract-binding protein depletion.

(Submitter supplied) Purpose : Splicing factors regulate splice site choices in pre-mRNA and determine final exon set in mRNA. To understand mechanisms of splicing regulation, it is important to identify and characterize exon targets of splicing factors. Recently, development of RNA-seq technology enables researchers to investigate exon splicing profiles as well as gene expression profiles in transcriptome-wide. The goal of this study is to investigate transcriptome changes by splicing factors, Polypyrimidine Tract Binding proteins (PTB). more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL13112
2 Samples

Download data: BW, GTF, TXT

Series

Accession:: GSE45119

ID:: 200045119

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Select item 20007619812.

Cell type-specific alternative splicing of cytoskeletal domains governs cell fate in the developing cerebral cortex

(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

Series

Accession:: GSE76198

ID:: 200076198

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20020666113.

human iPSC-neurons and human cortex

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

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24676
21 Samples

Download data: BW, TAR

Series

Accession:: GSE206661

ID:: 200206661

PubMed Full text in PMC Similar studies

Select item 20020666014.

PTBP2 knock-down RNA-seq from human iPSC-neurons

(Submitter supplied) To determine targets of PTBP2-dependent alternative splicing, we depleted PTBP2 in human neurons derived from induced-pluripotent stem cells (iPSC-neurons) using an LNA gapmer and performed RNA-seq on untreated, negative control-treated, and knock-down samples.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24676
9 Samples

Download data: TAR, TXT

Series

Accession:: GSE206660

ID:: 200206660

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Select item 20020665015.

PTBP2 eCLIP from human iPSC-neurons and human cortex (Brodmann area 4) [CLIP-seq]

(Submitter supplied) To determine direct targets of PTBP2-dependent alternative splicing, we performed CLIP-seq analysis of PTBP2 binding in both human cortical tissue and human neurons derived from induced-pluripotent stem cells (iPSC-neurons), and we combine this with splicing analysis following PTBP2 depletion in iPSC-neurons.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24676
12 Samples

Download data: BB, BW

Series

Accession:: GSE206650

ID:: 200206650

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Select item 20024137916.

Alternative splicing of a chromatin modifier alters the transcriptional regulatory programs of embryonic stem cell maintenance and neuronal differentiation [ChIP-seq]

(Submitter supplied) Maintenance of embryonic stem cells (ESCs) and their differentiation to neuronal lineages requires complex genetic regulation of transcription, splicing, and translation, but the interconnections of these processes is not well understood. We found that the splicing regulator polypyrimidine tract binding protein 1 (PTBP1) alters the neuronal transcriptional program. Transcripts for DPF2, a subunit of the BRG1/BRM-associated factor (BAF) chromatin remodeling complex, contain an additional exon (exon 7) in brain. more...