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PAR-CLIP analysis of neuroblastoma cells in response to amidino-rocaglate treatment

ABSTRACT: PAR-CLIP analysis of neuroblastoma cells in response to amidino-rocaglate treatment

PROVIDER: PRJNA1088607 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28361564_1.fastq.gz	Fastqsanger.gz
	SRR28361564_2.fastq.gz	Fastqsanger.gz
	SRR28361565_1.fastq.gz	Fastqsanger.gz
	SRR28361565_2.fastq.gz	Fastqsanger.gz
	SRR28361566_1.fastq.gz	Fastqsanger.gz

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PAR-CLIP analysis of neuroblastoma cells in response to amidino-rocaglate treatment

Project description:MYCN-amplified neuroblastoma cells exhibit upregulation of translation initiation factors as a result of MYCN-driven transcriptional amplification, including the RNA helicase eIF4A1. Here, we treated MYCN-amplified patient derived xenograft (PDX) neuroblastoma cells with a novel translation initiation inhibitor, amidino-rocaglate CMLD12824, to analyze the impact on the global pattern of eIF4A1 binding to mRNA compared to the naive condition.

2024-06-25 | GSE261761 | GEO

Ribosome profiling analysis of neuroblastoma cells in response to amidino-rocaglate treatment

Project description:MYCN-amplified neuroblastoma cells exhibit upregulation of translation regulation factors and ribosome biogenesis proteins as a result of MYCN-driven transcriptional amplification. Here, we treated MYCN-amplified and non-amplified neuroblastoma cells with a novel translation inhibitor, amidino-rocaglate CMLD12824, to compare the defects in translational efficiency.

2024-06-25 | GSE261760 | GEO

Implementation of PAR-CLIP to characterize RNA-protein interactions in prokaryotes at nucleotide resolution

Project description:The identification of RNAs that are recognized by RNA-binding proteins (RNA-BPs) using techniques such as Crosslinking and Immunoprecipitation (CLIP) has revolutionized the genome-wide discovery of RNA-BP RNA targets. Among the different versions of CLIP that have been developed, the use of photoactivable nucleoside analogs has resulted in high efficiency photoactivable ribonucleoside-enhanced CLIP (PAR-CLIP) in vivo. Nonetheless, PAR-CLIP has not yet been applied in prokaryotes. To determine if PAR-CLIP can be used in prokaryotes, we determined suitable conditions for the incorporation of 4-thiouridine (4SU), a photoactivable nucleoside, into E. coli RNA and for the isolation of RNA crosslinked to RNA-BPs of interest. Applying this technique to Hfq, a well-characterized regulator of small RNA (sRNA)-messenger RNA (mRNA) interactions, we showed that PAR-CLIP identified most of the known sRNA targets of Hfq, as well as functionally relevant sites of Hfq-mRNA interactions at nucleotide resolution. Based on our findings, PAR-CLIP represents an improved method to identify both the RNAs and the specific regulatory sites that are recognized by RNA-BPs in prokaryotes.

2022-10-18 | MSV000090547 | MassIVE

AGO-PAR-CLIP of DG75 and BCBL-1

Project description:AGO-PAR-CLIP was employed to identify microRNA binding sites in BCBL-1, a Kaposi's sarcoma-associated herpesvirus (KSHV) infected B-cell line and DG75, a KSHV negative B-cell line as a control. By using our novel computational method (PARma) and differential analysis of PAR-CLIP data, highly accurate target sites of KSHV microRNAs can be defined. Examination of microRNA target sites in two different cell lines using replicate PAR-CLIP experiments

2013-06-27 | E-GEOD-43909 | biostudies-arrayexpress

AGO-PAR-CLIP of DG75 and BCBL-1

2013-06-27 | GSE43909 | GEO

A fast PAR-CLIP variant using phenolic extractions

Project description:We performed PAR-CLIP in three variants using ELAVL1 (HuR) as example.

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Ribosome profiling analysis of neuroblastoma cells in response to amidino-rocaglate treatment

Project description:Ribosome profiling analysis of neuroblastoma cells in response to amidino-rocaglate treatment

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Genes regulated by Hfq (PAR-CLIP)

Project description:Genes regulated by Hfq (PAR-CLIP)

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Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP

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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Project description:We developed a method for measuring non-specific background in PAR-CLIP data demonstrating that covalently crosslinked background binding is common, reproducible and apparently universal. Furthermore, we show that quantitative determination of background is essential for identifying targets of weakly binding RNA-binding proteins and can substantially improve motif analysis. To define background binding events in PAR-CLIP data we performed the standard PAR-CLIP protocol (Hafner et al., Cell 2010.) on lysates expressing a commonly used non-RBP control, FLAG-GFP. After FLAG-tag immunopurification of UV 365nm irradiated lysates prepared from cells supplemented with 4-thiouridine (4SU), RNA was partially digested with RNase T1, radiolabeled and separated by SDS-PAGE. Reads were sequenced by Illumina HiSeq. PAR-CLIP was also performed for HuR. Included as well is a total from lysates treated like PAR-CLIP, but without immunoprecipitation (see sample description for more detail).

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