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RNA Proximity Ligation to Resolve Intramolecular RNA Structures in situ

ABSTRACT: RNA Proximity Ligation to Resolve Intramolecular RNA Structures in situ

PROVIDER: PRJNA285680 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2048220_1.fastq.gz	Fastqsanger.gz
	SRR2048220_2.fastq.gz	Fastqsanger.gz
	SRR2048230_1.fastq.gz	Fastqsanger.gz
	SRR2048230_2.fastq.gz	Fastqsanger.gz
	SRR2048221_1.fastq.gz	Fastqsanger.gz

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RNA Proximity Ligation to Resolve Intramolecular RNA Structures in situ

Project description:Proof-of-concept of a new method involving the limited digestion and subsequent ligation of intramolecular RNA structures in situ followed by deep sequencing Proof-of-concept of RPL in S. cerevisiae and H. sapiens tissue culture

2015-08-01 | E-GEOD-69472 | biostudies-arrayexpress

RNA Proximity Ligation to Resolve Intramolecular RNA Structures in situ

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Intramolecular ligation method (iLIME) for pre-miRNA quantification and sequencing

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Whole-genome Haplotype Reconstruction using Proximity-ligation and Shotgun Sequencing

Project description:Rapid advances in high-throughput DNA sequencing technologies are accelerating the pace of research into personalized medicine. While methods for variant discovery and genotyping from whole genome sequencing (WGS) datasets have been well established, linking variants together into a single haplotype remains a challenge. An understanding of complete haplotypes of an individual will help clarify the consequences of inheriting multiple alleles in combination, identify novel disease associations, and augment studies of gene regulation. Although numerous methods have been developed to reconstruct haplotypes from WGS data, chromosome-span haplotypes at high resolution have been difficult to obtain. Here we present a novel method to accurately reconstruct chromosome-span haplotypes from proximity-ligation and DNA shotgun sequencing. We demonstrate the utility of this approach in producing high-resolution chromosome-span haplotype phasing in mouse and human. While proximity-ligation based methods were originally designed to investigate spatial organization of the genome, our results lend support for their use as a general tool for haplotyping in the future. Hi-C experiments in two replicates of Human GM12878 Lymphoblastoid cells and two replicates of F123 mouse ES cells (4 total samples)

2013-11-03 | E-GEOD-48592 | biostudies-arrayexpress

Intramolecular ligation method (iLIME) for pre-miRNA quantification and sequencing

Project description:Hairpin-containing pre-miRNAs are precursors of microRNAs (miRNAs) that play important roles in cellular processes and various human diseases. Pre-miRNAs are produced from longer primary transcripts (pri-miRNAs). The falsity in cellular expression and sequences of pre-miRNAs might cause cellular defects or human diseases. However, the current pre-miRNA quantification methods by qPCR cannot discriminate between pre-miRNAs and their parental pri-miRNAs. In addition, the ligation of the sequencing adapter to 5’-end of pre-miRNAs is inefficient, therefore, pre-miRNA sequencing is highly impractical. Here, we developed a method, called the intramolecular ligation method (iLIME) for pre-miRNA quantification and sequencing. This method utilized T4 RNA ligase 1 to convert hairpin-pre-miRNAs into circularized RNAs that do not naturally exist in cells. The resulting circuliarized RNAs allow us to design unique primers to quantify pre-miRNAs by qPCR specicially, and thus this qPCR can distinguish pre-miRNA from pri-miRNAs. In addition, the iLIME also allows us to sequence pre-miRNAs using next-generation sequencing. The iLIME method offers a simple and effective way to quantify and sequence pre-miRNAs. This will be useful in investigating pre-miRNAs for addressing research questions for medical applications. The iLIME can be potentially extended to other hairpin-containing RNAs, such as tRNAs and snRNAs.

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RNA-DNA interactome of a prokaryotic cell uncovered by proximity ligation

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Whole-genome Haplotype Reconstruction using Proximity-ligation and Shotgun Sequencing

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Whole-genome Haplotype Reconstruction using Proximity-ligation and Shotgun Sequencing

Project description:Whole-genome Haplotype Reconstruction using Proximity-ligation and Shotgun Sequencing

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Project description:RNA-DNA interactome of a prokaryotic cell uncovered by proximity ligation

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