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Monosome and disome profiling of Flag-STAU1 Flp-In 293 T-REx cells

ABSTRACT: Monosome and disome profiling of Flag-STAU1 Flp-In 293 T-REx cells

PROVIDER: PRJEB40792 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR4677230.fastq.gz	Fastqsanger.gz
	ERR4677231.fastq.gz	Fastqsanger.gz
	ERR4677232.fastq.gz	Fastqsanger.gz
	ERR4677233.fastq.gz	Fastqsanger.gz
	ERR4677234.fastq.gz	Fastqsanger.gz

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Monosome and disome profiling of Flag-STAU1 Flp-In 293 T-REx cells

Project description:Monosome and disome profiling was performed on Flag-STAU1 Flp-In 293 T-REx to study the causes of ribosomal collisions, and whether this may be modulated by the presence/absence of Staufen-1. Cells were treated with either an siRNA targeting STAU1 transcript (4x samples) or a control siRNA (2x samples). Two of the four samples treated with the STAU1 siRNA had siRNA-resistant STAU1 mRNA expression induced by doxycycline (rescue). Sequencing libraries from monosome and disome fractions were generated in parallel from the same samples. Note that unique molecular identifiers/random barcodes (UMIs/RBCs) were included in the sequencing experiment. Each UMI has been moved to the fastq read name of each read. For example \\"xxxxxxrbc:AGCCAAT\\" in the read name signifies that the given read had a UMI of \\"AGCCAAT\\". Using these UMIs, PCR duplicates can be removed with UMI-Tools following read alignment.

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Project description:RNPS1 is a splicing regulatory protein and a component of the ASAP/PSAP complex, which is associated with the exon junction complex and modulates alternative splicing. It was previously postulated that the isolated RRM domain of RNPS1 in complex with ASAP/PSAP is able to regulate certain alternative splicing events. We aimed to investigate in Flp-In T-REx 293 cells which alternative splicing events are rescued by the expression of the wild type RNPS1 or the isolated RRM domain of RNPS1 in a RNPS1 knockdown background by using RNA-Seq analyses. The rescue construct was stably integrated into the genome using the PiggyBac transposon system. As controls, either Luciferase (Luc) siRNA was used or RNPS1 was knocked down without rescue.

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