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

ABSTRACT: 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).

ORGANISM(S): Homo sapiens

PROVIDER: GSE223091 | GEO | 2024/05/01

REPOSITORIES: GEO

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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

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RNA immunoprecipitation sequencing (RIP-seq) 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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SpyTag-based CLIP (SpyCLIP) sequencing of PQBP1 in ovarian cancer cells

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

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Project description:Our study shows that deletion of the alternative splicing regulator PQBP1 in striatal progenitors resulted in defective striatal development due to impaired neurogenesis of spiny projection neurons (SPNs). Therefore, we further reveal that PQBP1 associated with components in splicing machinery by LC-MS/MS. These findings identify PQBP1 as a novel regulator in balancing striatal progenitor proliferation and differentiation.

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