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Omics score: 1000

SRNA sequencing of HDL from human donors

ABSTRACT: sRNA sequencing of HDL from human donors

PROVIDER: PRJNA512494 | ENA |

REPOSITORIES: ENA

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Dataset's files

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primary

			Action	DRS
	SRR8383430.fastq.gz	Fastqsanger.gz
	SRR8383431.fastq.gz	Fastqsanger.gz
	SRR8383432.fastq.gz	Fastqsanger.gz
	SRR8383433.fastq.gz	Fastqsanger.gz
	SRR8383434.fastq.gz	Fastqsanger.gz

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Publications

Beta cell secretion of miR-375 to HDL is inversely associated with insulin secretion.

Sedgeman Leslie R LR Beysen Carine C Ramirez Solano Marisol A MA Michell Danielle L DL Sheng Quanhu Q Zhao Shilin S Turner Scott S Linton MacRae F MF Vickers Kasey C KC

Scientific reports 20190307 1

Extracellular microRNAs (miRNAs) are a new class of biomarkers for cellular phenotypes and disease, and are bioactive signals within intercellular communication networks. Previously, we reported that miRNAs are secreted from macrophage to high-density lipoproteins (HDL) and delivered to recipient cells to regulate gene expression. Despite the potential importance of HDL-miRNAs, regulation of HDL-miRNA export from cells has not been fully studied. Here, we report that pancreatic islets and beta c ...[more]

PMID: 30846744

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sRNA sequencing of HDL from human donors

Project description:miRNAs and other small RNAs have been found associated with high-density lipoproteins (HDL). The aim of this study was to investigate the miRNA signature on human HDL from 10 donors. Overall design: Examination of miRNAs on human HDL

2019-01-03 | GSE124559 | GEO

sRNA sequencing of miRNAs exported to HDL from primary human islets

Project description:sRNA sequencing of miRNAs exported to HDL from primary human islets

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sRNA sequencing of miRNAs exported to HDL from primary human islets

Project description:miRNAs are exported to high density lipoproteins (HDL). This study aimed to understand what miRNAs are exported from primary islets to HDL in vitro. Overall design: Examination of miRNAs exported from primary islets to HDL

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Physico-chemical principles of HDL-small RNA binding interactions

Project description:Profiling the host and non-host human HDL-tDR profile in those with atherosclerosis Overall design: sRNA sequencing of human high density lipoproteins (HDL) from healthy controls and those with a coronary artery calcium score > 0

2021-12-24 | GSE191337 | GEO

MS2-affinity purification coupled with RNA sequencing (MAPS) reveals RyhB sRNA targetome

Project description:Despite the overwhelming information about sRNAs, one of the biggest challenges in the sRNA field is characterizing sRNA targetomes. Thus, we develop a novel method to identify RNAs that interact with a specific sRNA, regardless of the type of regulation (positive or negative) or targets (mRNA, tRNA, sRNA). This method is called MAPS: MS2 affinity purification coupled with RNA sequencing. As proof of principle, we identified RNAs bound to RyhB, a well-characterized E. coli sRNA. Identification of RNAs co-purified with MS2-RyhB in a rne131 ?ryhB strain. RyhB (without MS2) was used as control

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MS2-affinity purification coupled with RNA sequencing (MAPS) reveals RybB sRNA targetome

Project description:Despite the overwhelming information about sRNAs, one of the biggest challenges in the sRNA field is characterizing sRNA targetomes. Thus, we develop a novel method to identify RNAs that interact with a specific sRNA, regardless of the type of regulation (positive or negative) or targets (mRNA, tRNA, sRNA). This method is called MAPS: MS2 affinity purification coupled with RNA sequencing. As proof of principle, we identified RNAs bound to RybB, a well-characterized E. coli sRNA. Identification of RNAs co-purified with MS2-RybB in a rne131 ΔrybB strain. RybB (without MS2) was used as control

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sRNA sequencing of miRNAs exported to HDL from INS-1 rat insulinoma cells

Project description:miRNAs are exported to high density lipoproteins (HDL). This study aimed to understand what miRNAs are exported from INS-1 cells to HDL in vitro. Overall design: Examination of miRNAs exported from INS1 cells to HDL

2019-01-16 | GSE125135 | GEO

sRNA sequencing of miRNAs exported to HDL from INS-1 rat insulinoma cells

Project description:sRNA sequencing of miRNAs exported to HDL from INS-1 rat insulinoma cells

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Targeted next-generation sequencing to diagnose disorders of HDL cholesterol.

Project description:A low level of HDL cholesterol (HDL-C) is a common clinical scenario and an important marker for increased cardiovascular risk. Many patients with very low or very high HDL-C have a rare mutation in one of several genes, but identification of the molecular abnormality in patients with extreme HDL-C is rarely performed in clinical practice. We investigated the accuracy and diagnostic yield of a targeted next-generation sequencing (NGS) assay for extreme levels of HDL-C. We developed a targeted NGS panel to capture the exons, intron/exon boundaries, and untranslated regions of 26 genes with highly penetrant effects on plasma lipid levels. We sequenced 141 patients with extreme HDL-C levels and prioritized variants in accordance with medical genetics guidelines. We identified 35 pathogenic and probably pathogenic variants in HDL genes, including 21 novel variants, and performed functional validation on a subset of these. Overall, a molecular diagnosis was established in 35.9% of patients with low HDL-C and 5.2% with high HDL-C, and all prioritized variants identified by NGS were confirmed by Sanger sequencing. Our results suggest that a molecular diagnosis can be identified in a substantial proportion of patients with low HDL-C using targeted NGS.

| S-EPMC4583092 | BioStudies

5´XP sRNA-seq: efficient identification of transcripts with and without 5´ phosphorylation reveals evolutionary conserved small RNA.

Project description:Small RNA (sRNA) sequencing has been critical for our understanding of many cellular processes, including gene regulation. Nonetheless, the varying biochemical properties of sRNA, such as 5´ nucleotide modifications, make many sRNA subspecies incompatible with common protocols for sRNA sequencing. Here we describe 5XP-seq that outlines a novel strategy that captures a more complete picture of sRNA. By tagging 5´P sRNA during library preparation, 5XP-seq combines an open approach that includes all types of 5'-terminal modifications (5´X), with a selective approach for 5-phosphorylated sRNA (5´P). We show that 5XP-seq not only enriches phosphorylated miRNA and piRNA but successfully discriminates these sRNA from all other sRNA species. We further demonstrate the importance of this strategy by successful inter-species validation of sRNAs that would have otherwise failed, including human to insect translation of several tRNA (tRFs) and rRNA (rRFs) fragments. By combining 5´ insensitive library strategies with 5´ sensitive tagging, we have successfully tackled an intrinsic bias in modern sRNA sequencing that will help us reveal the true complexity and the evolutionary significance of the sRNA world.

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