Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

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

PROVIDER: PRJNA924816 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR23101441_1.fastq.gz	Fastqsanger.gz
	SRR23101442_1.fastq.gz	Fastqsanger.gz
	SRR23101443_1.fastq.gz	Fastqsanger.gz
	SRR23101444_1.fastq.gz	Fastqsanger.gz
	SRR23101445_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

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).

2024-05-01 | GSE223088 | GEO

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).

2024-05-01 | GSE223091 | GEO

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.

2024-05-01 | GSE223196 | GEO

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

2024-05-01 | GSE223090 | GEO

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

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

| PRJNA924813 | ENA

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.

2013-03-15 | E-GEOD-44402 | biostudies-arrayexpress

Assembly of the Arabidopsis (Col-0) centromeres using Oxford Nanopore Technology long-read DNA sequencing.

Project description:Nanopore long-read sequencing was used to generate a complete assembly of the Arabidopsis centromeres.

2021-04-02 | E-MTAB-10272 | biostudies-arrayexpress

Xdrop - Oxford Nanopore long read seqeuncing of HepG2 genetic modified clones

Project description:This dataset contains Xdrop followed by oxford nanopore long read sequencing performed in target tRNA gene deletion (t8) and intergenic region deletion (i50) clones in HepG2 . By applying de novo assembly based approach to Xdrop-LRS data, we identified Cas9-induced on-target genomic alteration.

2022-09-16 | E-MTAB-11327 | biostudies-arrayexpress

Transcriptome analysis of TSC1 and TSC2 using Nanopore long-read sequencer

Project description:Tuberous sclerosis complex (TSC) is a relatively common autosomal dominant disorder characterized by multiple dysplastic organ lesions and neuropsychiatric symptoms, caused by loss-of-function mutation of either TSC1 or TSC2. Target-capture full-length double-stranded cDNA sequencing using long-read sequencer Nanopore (Nanopore Long-read Target Sequencing) revealed that the various kinds of the TSC1 and TSC2 full-length transcripts and the novel intron retention transcripts of TSC2 in TSC patient. Our results indicate that the Nanopore Long-read Target Sequencing is useful for the detection of mutations and confers information on the full-length alternative splicing transcripts for the genetic diagnosis.

2023-09-04 | GSE241410 | GEO

Nanopore long-read sequencing from Nutlin-3a-treated MCF-7 cells

Project description:Nanopore long-read sequencing from MCF-7 cells treated with Nutlin-3a or DMSO control

2024-09-18 | GSE226080 | GEO