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SpyTag-based CLIP (SpyCLIP) sequencing of PQBP1 in ovarian cancer cells

ABSTRACT: SpyTag-based CLIP (SpyCLIP) sequencing of PQBP1 in ovarian cancer cells

PROVIDER: PRJNA925204 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23112944_1.fastq.gz	Fastqsanger.gz
	SRR23112944_2.fastq.gz	Fastqsanger.gz
	SRR23112945_1.fastq.gz	Fastqsanger.gz
	SRR23112945_2.fastq.gz	Fastqsanger.gz

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SpyTag-based CLIP (SpyCLIP) sequencing of PQBP1 in ovarian cancer cells

Project description:Dysregulated expression of splicing factors has important roles in cancer development and progression. However, it remains a major challenge to identify the cancer-specific splicing variants. Here we demonstrated that splicing factor PQBP1 is commonly overexpressed in high-grade serous ovarian carcinoma (HGSOC) and high level of PQBP1 is associated with poor prognosis. To gain global insights into PQBP1-RNA binding property, RNA immunoprecipitation sequencing (RIP-seq) and SpyTag-based CLIP (SpyCLIP) were performed to analysis the interaction between PQBP1 and the target RNA.

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RNA immunoprecipitation sequencing (RIP-seq) of PQBP1 in ovarian cancer cells

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RNA sequencing (RNA-seq) of PQBP1 knockdown in ovarian cancer cells

Project description:To investigate the comprehensive function of PQBP1 in the regulation of RNA splicing, we established Dox-inducible PQBP1 knockdown HEY cell line. We then performed gene expression profiling analysis using data obtained from RNA-seq of PQBP1 knockdown and control HEY cells (three biological replications of each sample).

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Long-read nanopore sequencing (Nanopore-seq) of PQBP1 knockdown in ovarian cancer cells

Project description:To investigate the comprehensive function of PQBP1 in the regulation of RNA splicing, we established Dox-inducible PQBP1 knockdown HEY cell line. We then performed transcript expression profiling analysis using data obtained from long-read nanopore-seq of PQBP1 knockdown and control HEY cells (three biological replications of each sample).

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RNA sequencing (RNA-seq) of PQBP1 knockdown in ovarian cancer cells

Project description:RNA sequencing (RNA-seq) of PQBP1 knockdown in ovarian cancer cells

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RNA immunoprecipitation sequencing (RIP-seq) of PQBP1 in ovarian cancer cells

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Long-read nanopore sequencing (Nanopore-seq) of PQBP1 knockdown in ovarian cancer cells

Project description:Long-read nanopore sequencing (Nanopore-seq) of PQBP1 knockdown in ovarian cancer cells

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Next-generation sequencing identifies mRNAs targets that experience significant changes in alternative splicing upon PQBP1 knockdown in mouse embryonic cortical neurons

Project description:PQBP1 is a highly conserved protein closely related to neurodegenerative disorders. We identified PQBP1 as an important alternative splicing effector necessary for maintaining normal neuron functions in the brain. In order to explore PQBP1's functions in alternative splicing regulation and neuronal activities, we systematically profiled the alternative splicing targets of PQBP1 in mouse embryonic cortical neurons by RNA-seq. The mRNAs whose alternative splicing are affected by PQBP1 showed tissue-specific functional enrichment especially in neurite outgrowth, with strong Gene Ontology (GO) enrichments for neuron projection development/morphogenesis, dendrite development and axonogenesis. PQBP1's alternative splicing targets are also functionally enriched in RNA splicing, chromatin modification, and ARF signal transduction. We applied RNA-seq to compare the transcriptomes of mock and PQBP1 knockdown mouse embryonic cortical neuron samples.

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2023-03-16 | PXD040439 | Pride

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