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Gene expression and alternative splicing profiles of N2a siEwsr1 cells

ABSTRACT: Gene expression and alternative splicing profiles of N2a siEwsr1 cells

PROVIDER: PRJNA725528 | ENA |

REPOSITORIES: ENA

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Gene expression and alternative splicing profiles of N2a siEwsr1 cells

Project description:N2a cells treated with either control or siEwsr1 oligonucleotides

2022-04-13 | GSE173439 | GEO

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

Project description: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). In this study, we analyzed exon and gene expression changes followed by Ptbp1 knock down. Methods : The knockdown experiment was performed in mouse neuroblastoma (N2A) cells. Total RNA was collected from cells and further treated with DNase I to avoid DNA contamination. RNA-seq libraries were constructed in a strand specific way using dUTP and Uracil-Specific Excision Reagent enzyme. The libraries were subjected to 100bp paired-end sequencing (Illumina HiSeq2000 platform). Poly(A)-mRNA and exon profiles of N2A mouse blastoma cells in two samples: shRNA transfection control, single knock down of ptbp1. RNA-seq libraries were generated in strand specific way using dUTP and USER enzyme and sequenced using Illumina HiSeq2000.

2013-12-01 | E-GEOD-45119 | biostudies-arrayexpress

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

2013-12-01 | GSE45119 | GEO

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

Project description: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). In this study, we analyzed exon and gene expression changes followed by Ptbp1, Ptbp2, and both Ptbp1 & Ptbp2 knock down. Methods: The knockdown experiment was performed in mouse neuroblastoma (N2A) cells. Total RNA was collected from cells and further treated with DNase I to avoid DNA contamination. RNA-seq libraries were constructed in a strand specific way using dUTP and Uracil-Specific Excision Reagent enzyme. The libraries were subjected to 100bp paired-end sequencing (Illumina HiSeq2000 platform).

2014-12-02 | GSE52856 | GEO

Brd2 regulates gene expression and alternative splicing.

Project description:We analyzed a role of Brd2 protein in transcription and alternative splicing. 289 genes change alternative splicing after Brd2 knockdown and 1459 genes alter gene expression compared to cells treated with negative control siRNA. 6 samples (3 independent samples of cells treated with Brd2 siRNA, 3 samples of cells treated with negative control siRNA)

2013-12-03 | E-GEOD-39937 | biostudies-arrayexpress

Brd2 regulates gene expression and alternative splicing.

2013-12-03 | GSE39937 | GEO

miRNA sequencing of exosomes derived from N2A and APP-N2A cells

Project description:APP misexpression plays a crucial role in triggering a complex pathological cascade, leading to Alzheimer’s disease (AD). The aim of this study is for determine the influence of APP ectopic expression on the miRNA profiles of neuronal exosomes. In study, miRNA sequencing was done using the exosomes derived from N2A (control) and APP-N2A (N2A with APP overexpression).

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Gene Array Analyzer (GAA): Alternative usage of gene arrays to study alternative splicing events

Project description:This SuperSeries is composed of the following subset Series: GSE30429: Gene Array Analyzer (GAA): Alternative usage of gene arrays to study alternative splicing events (MoGene array) GSE32998: Gene Array Analyzer (GAA): Alternative usage of gene arrays to study alternative splicing events (MoEx array) Refer to individual Series

2011-11-28 | E-GEOD-33183 | biostudies-arrayexpress

Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB

Project description:This SuperSeries is composed of the following subset Series: GSE23513: Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB (HJAY) GSE23514: Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB (Exon array) Refer to individual Series

2010-09-01 | E-GEOD-23522 | biostudies-arrayexpress

Profiles of gene expression and alternative splicing in K562 cells exposed to 2 mM sodium valproate for 12 hours assessed using exon array

Project description:To investigate the effect of valproate (VPA) treatment on K562 cell line, the growth and survival of the K562 cell line were investigated using the Annexin V/PI dual staining method, and global profiles of gene expression and alternative splicing in K562 cells were assessed using exon microarray. A significant increase in cell apoptosis was observed in valproate exposed K562 cells using flow cytometry. A total of 628 transcripts were identified as being significantly differentially expressed. The number of genes demonstrating increased expression levels was greater than the number of genes demonstrating decreased expression levels (445 genes vs. 183 genes, respectively). The significant enrichment analysis of GO terms for the differentially expressed genes revealed that these genes are involved in many important biological processes such as apoptosis. Six of observed differentially expressed genes that might be involved in apoptosis were selected to undergo qRT-PCR validation. In total, 198 candidates of alternative splicing variants were identified. Among them, three alternative splicing events were selected for validation, and CBLC and TBX1 were confirmed as alternative splicing by semi-nested PCR. In conclusion, valproate exposure facilitated cell apoptosis, altered mRNA expression and alternative splicing events in the K562 cell line. Gene expression/alternative splicing in K562 cell line were measured after exposure to 2 mM valproate for 12 hours or left untreated as a control using exon array.

2011-11-11 | E-GEOD-32047 | biostudies-arrayexpress

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