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Homo sapiens

ABSTRACT: Identification of RNA target of Matrin3 and PTBP1 in neuroblastoma cell line SH-SY5Y by PAR-CLIP

PROVIDER: PRJDB5171 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR071072.fastq.gz	Fastqsanger.gz
	DRR071073.fastq.gz	Fastqsanger.gz
	DRR093363.fastq.gz	Fastqsanger.gz
	DRR093364.fastq.gz	Fastqsanger.gz

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

Project description: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.

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Genome-wide chromatin binding of ERRα and ERRγ in SH-SY5Y cells

Project description:The SH-SY5Y Human neuroblastoma cell line was subcloned from the SK-N-SH cell line, which has been isolated from a bone marrow biopsy of a 4 year-old female patient. To examine the transcriptional regulation by ERRα and ERRγ in human neuronal cells, we investigated chromatin binding regions of ERRαlpha and ERRγ genome-wide in the SH-SY5Y cells. We detected thier target genes, which were largely overlap.

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TRPM7 maintains progenitor-like features of neuroblastoma cells

Project description:Analysis of the effect of shRNA-mediated knockdown of TRPM7 on gene expression levels in SH-SY5Y and SH-EP2 human neuroblastoma cells. Results were used for the identification of neural-crest-associated transcription factors that were affected by TRPM7 knockdown. Total RNA isolated from SH-EP2 and SH-SY5Y human neuroblastoma cells transduced with a scrambled shRNA (control) or TRPM7 shRNA, experiment performed in duplicate.

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Project description:This SuperSeries is composed of the following subset Series: GSE21574: Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: QKI data GSE21575: Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: IGF2BP data GSE21577: Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: miRNA inhibition data GSE21918: Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: sequencing data Refer to individual Series

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