Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA349062 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:5' tRNA halves are abundantly present in small RNA libraries prepared from serum samples, thereby limiting the detection of other small RNA species. In this study, we developed and compared two protocols for the selective depletion of 5' tRNA halves in RNA isolated from murine serum samples. To evaluate the efficacy of both protocols on small RNA sequencing, we performed the two 5' tRNA halves depletion protocols on total RNA isolated from a serum pool collected from healthy mice. Each RNA sample was divided into three and the resulting fractions were either depleted using beads or RNase H, or used as a control. The experiment was performed in triplicate. Upon depletion, libraries were prepared using TruSeq Small RNA Library Preparation kit. For both protocols, very high depletion efficiencies were observed, with more than 99% of the targeted tRNA-types being depleted. This resulted in a more than 6-fold increase in mapped miRNA reads and 60% more detected mature miRNAs when performing small RNA sequencing on murine serum samples. Importantly, we observed no considerable effects on the relative expression values of miRNAs.
2017-02-22 | GSE88913 | GEO
Project description:To investigate the effectiveness of performing 5' tRNA half depletion, we evaluated the association of tumor burden on circulating miRNAs present in mouse serum. Three nude mice (NCr) were orthotopically injected with SH-SY5Y human neuroblastoma cells. Serum samples were collected one week before cell injection and two weeks after injection, when mice had palpable tumors. We performed 5' tRNA half depletion using biotinylated probes and streptavidin beads and prepared small RNA libraries using the TruSeq Small RNA Library Prep kit. By depleting the 5' tRNA halves in the serum-derived RNA samples, we were able to detect 3 times more differentially expressed miRNAs when comparing serum from mice carrying orthotopically engrafted tumors with serum from healthy control mice. We detected 34 differentially expressed miRNAs, of which six are unique to humans, 13 unique to mice and 15 have complete conservation between the two species.
2017-02-22 | GSE88728 | GEO
Project description:Depletion of tRNA-halves enables effective small RNA sequencing of low-input murine serum samples
| PRJNA349073 | ENA
Project description:We evaluated the effect of the small RNA library preparation method on 5' tRNA-halves and miRNA abundance in libraries prepared from serum RNA using three commercially available small RNA library preparation kits (TruSeq small RNA library preparation kit v2 (Illumina), TailorMix miRNA sample preparation kit v2 (Seqmatic) and the NEBNext Multiplex Small RNA library prep kit (New England Biolabs)). RNA isolated from 100 µl of serum collected from healthy mice was used as input for the preparation of a small RNA library in duplicate and libraries were single end sequenced.
2017-02-22 | GSE88914 | GEO
Project description:Evaluation of three small RNA library preparation kits on serum-derived RNA
| PRJNA349074 | ENA
Project description:Apart from their primordial role in protein synthesis, tRNAs can be cleaved to produce tRNA-derived small RNAs (tsRNAs). The biological functions of tsRNAs in plants remain largely unknown. In this study, we developed RtcB-based RNA sequencing, a method that captures and distinguishes between 2’,3’-cyclic-phosphate (cP)-terminated RNAs and 3’-OH-terminated RNAs, and profiled 5’ tsRNAs and 5’ tRNA halves in Arabidopsis thaliana. We found that Arabidopsis 5’ tsRNAs and 5’ tRNA halves predominantly contain a cP at the 3’ end and require S-like RNase 1 (RNS1) and RNS3 for their production. One of the most abundant 5’ tsRNA, 5’ tsR-Ala, likely by associating with AGO1, negatively regulates Cytochrome P450 71A13 (CYP71A13) expression and camalexin biosynthesis to repress anti-fungal defense. 5’ tsR-Ala is downregulated upon fungal infection. Our study provides a global view of 5’ tsRNAs and 5’ tRNA halves in Arabidopsis and unravels an important role of a 5’ tsRNA in regulating anti-fungal defense.
2022-02-16 | GSE183560 | GEO
Project description:Recent evidence demonstrates that serum levels of specific small noncoding RNAs (sncRNAs) including miRNAs and 5’ tRNA halves significantly change with age. The ability of circulating sncRNAs to act as signaling molecules and regulate a broad spectrum of cellular functions implicates them as key players in the aging process. To discover circulating sncRNAs that impact aging in the long-lived Ames dwarf mice, we conducted deep sequencing of small RNAs extracted from serum of young and old mice. Our analysis showed genotype-specific changes in the circulating levels of 43 miRNAs and 19 5’ tRNA halves during aging [Genotype-by-Age interaction (GbA)]. GbA miRNAs showed four distinct expression patterns and significant over-targeting of transcripts involved in age-related processes. Functional enrichment analysis of putative miRNA targets highlighted cellular processes such as tumor suppression, anti-inflammatory response, and modulation of Wnt, insulin, mTOR, and MAPK signaling pathways, among others. The comparative analysis of circulating GbA miRNAs in Ames mice with circulating miRNAs modulated by calorie restriction (CR) in another long-lived mouse suggests CR-like and CR-independent mechanisms contributing to longevity in the Ames mouse. In conclusion, we showed for the first time a signature of circulating miRNAs and 5’-tRNA halves modulated by age in the long-lived Ames mouse.
2018-05-27 | GSE69274 | GEO
Project description:In this study, we performed deep sequencing and bioinformatics analyses of short RNAs from three strains of Trichomonas vaginalisto identify and characterize novel type of small RNAs. We detected a new type of small RNA from tranfer RNA known as tRFs and tRNA-halves.
2021-02-03 | GSE160464 | GEO
Project description:Argonaute/Piwi proteins associate with small RNAs that typically provide sequence specificity for RNP function in gene and genome regulation. Here we show that Twi12, a Tetrahymena Piwi protein essential for growth, is loaded with mature tRNA fragments. The tightly bound ~18-22 nt tRNA 3’ fragments are biochemically distinct from the tRNA halves produced transiently in response to stress. Notably, the end positions of Twi12-bound tRNA 3' fragments precisely match RNAs detected in total small RNA of mouse embryonic stem cells and human cancer cells. Our studies demonstrate unanticipated evolutionary conservation of mature tRNA processing to tRNA-fragment small RNAs.
2010-10-26 | GSE24916 | GEO
Project description:tRNA-derived small RNAs (tsRNA) are a new type of noncoding RNAs that can be mainly classified into two groups: tRFs (tRNA-derived fragments) and tiRNAs (tRNA halves). The abnormal expression of tsRNAs is known to play an important role in the biological progression of breast cancer. However, it's still unclear about the mechanism of tsRNAs in cancer. tRF-1-Ser is a tRF that is high expression in breast cancer and negatively regulated by 25(OH)D. Our study aims to find out the effect of tRF-1-Ser on breast cancer and explore the change of RNA in tRF-1-Ser knock-down breast cancer cells.
2024-05-15 | GSE249937 | GEO