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Small RNA sequencing on affinity capture-purified tRNA-derived small RNAs (tsRNAs)

ABSTRACT: Small RNA sequencing on affinity capture-purified tRNA-derived small RNAs (tsRNAs)

PROVIDER: PRJNA578532 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10314656.fastq.gz	Fastqsanger.gz
	SRR10314657.fastq.gz	Fastqsanger.gz
	SRR10314658.fastq.gz	Fastqsanger.gz
	SRR10314659.fastq.gz	Fastqsanger.gz
	SRR10314660.fastq.gz	Fastqsanger.gz

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Small RNA sequencing on affinity capture-purified tRNA-derived small RNAs (tsRNAs)

Project description:During stress conditions, particular tRNAs are cleaved by stress-induced endonucleases resulting in distinct tRNA-derived small RNAs (tsRNAs). These small RNAs have been implicated in a wide array of mostly stress-related biological processes, however how exactly they exert their functions mechanistically is still largely unknown. Since parental tRNAs carry post-transcriptional modifications, stress-induced tsRNAs are likely modified, too. In order to use endogenously modified tsRNAs, we developed a biochemical pipeline for the production and purification of specific tsRNAs using a human cell culture system. Ectopic expression of Angiogenin combined with chromatography of small RNAs resulted in the production of endogenously modified 5’ tsRNAs on a preparative scale. Small RNA sequencing on purified tsRNAs was used to determine the identity and purity of the 5’ tsRNA preparations.

2020-03-01 | GSE139124 | GEO

Microarray analysis reveals changes in tRNA-derived small RNAs (tsRNAs) expression in mice with septic cardiomyopathy

Project description:Our previous work has focused on the relationship between non-coding RNAs and sepsis, so we chose to use microarray analysis to investigate the relationship between septic cardiomyopathy and a novel class of small non-coding RNA - tRNA-derived small RNAs(tsRNAs). Meanwhile, tRNA-derived small RNA has been studied in many cardiovascular diseases, but the relationship between tsRNAs and septic cardiomyopathy has not been investigated. We sought to analyze changes of tsRNAs expression profile in septic cardiomyopathy and reveal an important role for tsRNAs.

2022-09-29 | GSE214251 | GEO

Circulating tRNA-derived small RNAs (tsRNAs) signature for the diagnosis and prognosis of breast cancer

Project description:Liquid biopsy is noninvasive and convenient to detect cancer-derived materials in blood or other body fluids. The aim of this study was to identify tRNA-derived small RNAs (tsRNAs) in plasma that could distinguish patients with breast cancer (BC) from healthy controls. Basing on high-throughput sequencing, 15 significantly upregulated tsRNAs were selected and assessed in cell supernatants and cell lines. 6 tsRNAs were identified and verified in a large cohort of 120 patients with BC and 112 healthy controls. tRF-Arg-CCT-017, tRF-Gly-CCC-001 and tiRNA-Phe-GAA-003 could serve as novel diagnostic biomarkers. Meanwhile, tRF-Arg-CCT-017 and tiRNA-Phe-GAA-003 could also act as prognostic biomarkers. Target genes of these tsRNAs were related to the development of cancer. These results suggest that specific tsRNAs in plasma might serve as diagnostic and prognostic biomarkers of BC.

2020-10-08 | GSE158945 | GEO

The tRNA-derived small RNAs (tsRNAs) expression profiles in human aortic vascular smooth muscle cells (HAVSMCs)

Project description:Purpose: Next-generation sequencing (NGS) is the main way to mine ncRNA. The purpose of this study is to screen out tRNA-derived small RNAs (tsRNAs) that are differentially expressed in proliferative and quiescent HASMCs Methods: tsRNAs profiles of proliferative and quiescent HASMCs were generated by deep sequencing, in triplicate, using Illumina NextSeq 500. The sequence reads that passed Illumina chastity filter were used for the following analysis. Trimmed reads (with 5ʹ, 3ʹ-adaptor bases removed) were aligned to mature-tRNA and pre-tRNA reference sequences. The alignment statistical analysis was applied to retain the valid sequences for subsequent tsRNAs expression profiles and differential expression analysis. Results: Using an optimized data analysis workflow, we mapped about 8 million sequence reads per sample to mature-tRNA and pre-tRNA sequences from GtRNAdb and identified 3,891 tsRNAs in the proliferative and quiescent HASMCs. According to the standardized TPM, 887 up-regulated and 951 down-regulated tsRNAs were found in the proliferative HASMCs (fold change > 2, P < 0.05).

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Project description:Increasing evidences indicate diet-induced metabolic disorder could be paternally inherited, but the exact sperm epigenetic carrier remains unclear. Here, in a paternal high-fat diet (HFD) mouse model, we revealed that a highly enriched subset of sperm small RNAs (30-34 nt) that derived from the 5â halves of tRNAs (tsRNAs), exhibit changes in both expression profiles and RNA modifications. Injection of sperm tsRNAs from HFD male but not synthetic tsRNAs lacking RNA modifications, into normal zygotes generated metabolic disorders in the F1 offspring. Injection of HFD sperm tsRNAs derails gene expression in both early embryos and islets of F1 offspring, enriched in metabolic pathways, but unrelated to DNA methylation at CpG-enriched region. Collectively, we uncover sperm tsRNAs as a type of âepigenetic carrierâ that mediate intergenerational inheritance of acquired traits. Mature sperm small-RNA profiles between High-fat-diet (HFD) and Normal-diet (ND) males; Transcriptional profiles of 8-cell embryos and balstocysts that developed from zygotes that injected with sperm RNAs from HFD vs ND males. Transcriptional profiles and RRBS profiles of islets of F1 offsrping that generated from zygotes that injected with sperm RNAs from HFD vs ND males.

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Sequencing profiling data of tRNA-derived small RNAs (tsRNAs) in human colorectal cancer.

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Sequencing profiling data of tRNA-derived small RNAs (tsRNAs) in human colorectal cancer.

Project description:Sequencing profiling data of tRNA-derived small RNAs (tsRNAs) in human colorectal cancer.

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Altered expression of transfer-RNA-derived small RNAs (tsRNAs) in human with rheumatic heart disease

Project description:Rheumatic heart disease (RHD) remains a serious public health problem in developing countries. Atrial fibrillation (AF) is a medical complication of RHD. Although the understanding of disease pathogenesis has advanced in recent years, the key questions need to be addressed. Transfer RNA–derived small RNAs (tsRNAs) are a novel type of short non-coding RNAs that have potential regulatory functions in various physiological and pathological processes. The present study used tsRNAs sequencing to investigate the relationship between RHD and atrial fibrillation (AF). Three paired myocardial papilla were taken from six rheumatic RHD patients with AF (3 cases) or without AF (3 cases) from January 2016 to January 2017 in Xiangya Hospital, Central South University. A total of 219 precisely matched tsRNAs were identified, and 77 tsRNAs (fold change > 2.0 and P < 0.05) were differently changed. Three tsRNAs (AS-tDR-001269, AS-tDR-001363, AS-tDR-006049) were randomly selected and verified by qRT-PCR. The results of qRT-PCR were consistent with tsRNAs sequencing, suggesting the tsRNAs sequencing was reliable. Then bioinformatics analysis indicated that the target genes were abundant in regulation of transcription, DNA binding, intracellular. Most of the genes were predicted to interplay with cytokine-cytokine receptor by KEGG analysis. Our findings uncover the pathological process of AF in RHD through tsRNAs sequencing. This study provides new ideas for future research on elucidating the mechanism of AF in RHD and offers potential new candidates for the treatment and diagnosis of RHD.

2021-12-23 | GSE185581 | GEO

Small RNA sequencing Analysis of lung Reveals Novel tRNA-derived Small RNAs with Biomarker Potential for Pulmonary Arterial Hypertension

Project description:Transfer RNA-derived small RNAs (tsRNAs) are important regulators of a variety of biological functions, however, it is yet unclear how tsRNAs work to cause pulmonary arterial hypertension (PAH). The goal of the current study was to gain a better understanding of how tsRNAs contribute to PAH pathogenesis.

2024-07-22 | GSE270791 | GEO

Differential expression profiles of plasma tsRNAs in children with fulminant myocarditis

Project description:We report the application of high-throughput RNA sequencing technology to examine expression profiling of plasma transfer RNA (tRNA)-derived small RNAs (tsRNAs) in children with fulminant myocarditis during acute phase (FM-A group), children with fulminant myocarditis during convalescent phase (FM-C group), and healthy volunteers (Con group). A total of 750 precisely matched tsRNAs were identified in the plasma from the three groups. We find that a total of 13 tsRNAs were differentially expressed in FM-A and CON samples, of which 11 tsRNAs were upregulated and 2 were downregulated, and 694 tsRNAs were excluded ; a total of 8 tsRNAs were differentially expressed in paired FM-C and CON samples, of which 2 tsRNAs were upregulated and 6 were downregulated and 703 tsRNAs were excluded . This study provides new ideas for future research on elucidating the mechanisms of myocarditis through regulating tsRNAs levels.

2020-12-29 | GSE163944 | GEO

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