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Discovery of DAP3-binding RNA sites by eCLIP

ABSTRACT: Discovery of DAP3-binding RNA sites by eCLIP

PROVIDER: PRJNA603360 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10971802_1.fastq.gz	Fastqsanger.gz
	SRR10971802_2.fastq.gz	Fastqsanger.gz
	SRR10971803_1.fastq.gz	Fastqsanger.gz
	SRR10971803_2.fastq.gz	Fastqsanger.gz
	SRR10971804_1.fastq.gz	Fastqsanger.gz

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Discovery of DAP3-binding RNA sites by eCLIP

Project description:eCLIP paired-end sequencing of DAP3 in EC109 cells with two biological replicates. This analysis revealed the genome-wide RNA binding landscape of DAP3, as the supporting data of the main publication.

2020-06-23 | GSE144318 | GEO

Multiplexed transcriptome discovery of RNA binding protein binding sites by antibody-barcode eCLIP

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Enhanced CLIP (eCLIP) enables robust and scalable transcriptome-wide discovery and characterization of RNA binding protein binding sites

Project description:Enhanced CLIP (eCLIP) enables robust and scalable transcriptome-wide discovery and characterization of RNA binding protein binding sites

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Enhanced CLIP (eCLIP) enables robust and scalable transcriptome-wide discovery and characterization of RNA binding protein binding sites [eCLIP - 293T cells]

Project description:RNA binding proteins (RBPs) play essential roles in cellular physiology by interacting with target RNAs. As defects in protein-RNA recognition lead to human disease, UV-crosslinking and immunoprecipitation (CLIP) of ribonuclear complexes followed by deep sequencing (-seq) is critical in constructing protein-RNA maps to expand our understanding of RBP function. However, current CLIP protocols are technically demanding and involve low complexity libraries that yield squandered sequencing of PCR duplicates and high experimental failure rates. To enable truly large-scale implementation of CLIP-seq, we have developed an enhanced CLIP methodology (eCLIP) that features a decrease of ~10 cycles of requisite amplification with a concomitant >60% decrease in discarded PCR duplicate reads, while maintaining the ability to identify RNA binding with single-nucleotide resolution. By simplifying the generation of paired IgG and size-matched input controls, eCLIP also dramatically improves specificity in discovery of authentic binding sites. To demonstrate that eCLIP enables large-scale and robust profiling of RBPs, 102 eCLIP experiments in biological duplicate for a diverse collection of 74 RBPs in HepG2 and K562 cells were completed (available at https://www.encodeproject.org). We establish that eCLIP is comparable in amplification and sample requirements to ChIP-seq, and enables integrative analysis of diverse RBPs to reveal factor-specific profiles, common artifacts for CLIP experiments and RNA-centric perspectives of RBP activity.

2016-03-28 | GSE77629 | GEO

Enhanced CLIP (eCLIP) enables robust and scalable transcriptome-wide discovery and characterization of RNA binding protein binding sites [eCLIP - HepG2/K562 cells]

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Multiplexed transcriptome discovery of RNA binding protein binding sites by antibody-barcode eCLIP

Project description:UV cross-linking and immunoprecipitation (CLIP) methodologies enable the identification of RNA binding sites of RNA-binding proteins (RBPs). Despite improvements in the library preparation of RNA fragments, the current enhanced CLIP (eCLIP) protocol still requires ~4 days of hands-on time and lacks the ability to scale. We present a new method termed antibody barcode CLIP (ABC) that utilizes DNA-barcoded antibodies to multiplex CLIP detection methods. We demonstrate the scalability and simplicity of ABC by performing CLIP on multiple RBPs simultaneously, minimizing sample-to-sample variation, and maintaining the same material requirement for a single eCLIP experiment.

2022-10-18 | GSE205536 | GEO

Enhanced CLIP (eCLIP) enables robust and scalable transcriptome-wide discovery and characterization of RNA binding protein binding sites [array]

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ENO1's RNA-binding sites in Human HeLa cells using eCLIP

Project description:ENO1's RNA-binding sites in Human HeLa cells using eCLIP

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ENO1's RNA-binding sites in Human HeLa cells using eCLIP

Project description:eCLIP was performed for ENO1 in HeLa cells, following the protocol described by Van Nostrand et al. (2016). Libraries for six immunoprecipitation and size-matched input controls were produced. In addition, libraries were produced for two no-crosslinking controls. The libraries were sequenced using paired-end sequencing (PE125) on an Illumina HiSeq2000 platform.

2020-10-27 | E-MTAB-9031 | biostudies-arrayexpress

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