GEO DataSets

(Submitter supplied) Transfer RNA (tRNA) molecules contain a variety of post-transcriptional modifications which are crucial for tRNA stability, translation efficiency, and fidelity. Besides their canonical roles in translation, tRNAs also originate tRNA-derived small RNAs (tsRNAs), a class of small non-coding RNAs with regulatory functions ranging from translation regulation, to gene expression control and cellular stress response. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL18573 GPL21185

12 Samples

Download data

(Submitter supplied) Transfer RNA (tRNA) molecules contain a variety of post-transcriptional modifications which are crucial for tRNA stability, translation efficiency, and fidelity. Besides their canonical roles in translation, tRNAs also originate tRNA-derived small RNAs (tsRNAs), a class of small non-coding RNAs with regulatory functions ranging from translation regulation, to gene expression control and cellular stress response. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL21185

6 Samples

Download data: XLS

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16791

6 Samples

Download data: TSV

(Submitter supplied) Eukaryotic transfer RNAs (tRNA) contain on average 13 modifications that perform a wide range of roles in translation and in the generation of tRNA fragments that regulate gene expression. Queuosine (Q) modification occurs in the wobble anticodon position of tRNAs for amino acids His, Asn, Tyr, and Asp. In eukaryotes, Q modification is fully dependent on diet or on gut microbiome in multi-cellular organisms. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL15433

4 Samples

Download data: TXT, XLSX, ZIP

(Submitter supplied) To explore which tsRNAs are dysregulated in the tissues of CRC.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

8 Samples

Download data: TXT

(Submitter supplied) Methyl-5-uridine (m5U) is one the most abundant non-canonical bases present in cellular RNAs, and is formed via catalytic conversion of uridines. In yeast, m5U is known to be present at position 54 of tRNAs where modification is catalysed by the methyltransferase Trm2. Although the mammalian enzymes that catalyse m5U formation are yet to be identified via experimental evidence, based on sequence homology to Trm2, two candidates currently exist, TRMT2A and TRMT2B. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL20301

14 Samples

Download data: BED

(Submitter supplied) To identify tRNA fragments regulated by angiogenin (ANG, Rnase 5), we sequenced 15-50nt small RNAs upon ANG overexpression and ANG knockout.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18573

18 Samples

Download data: TXT

(Submitter supplied) 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.

Organism:

Trichomonas vaginalis

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL22655

3 Samples

Download data: FA, TXT

(Submitter supplied) Ischemic injuries will lead to necrotic tissue damage, and post-ischemia angiogenesis plays critical roles in blood flow restoration and tissue recovery. Recently, several types of small RNAs have been reported to be involved in this process. In this study, we first generated a rat brain ischemic model to investigate the involvement of new types of small RNAs in ischemia. We utilized deep sequencing and bioinformatics analyses to demonstrate that the level of small RNA fragments derived from tRNAs was strikingly up-regulated in the ischemic rat brain. more...

Organism:

Rattus norvegicus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL10287

10 Samples

Download data: TXT

(Submitter supplied) Specific environmental insults cause the limited fragmentation of transfer RNAs (tRNAs) into tRNA-derived small RNAs (tsRNAs), which have been implicated in a wide range of biological processes. tRNA fragmentation results from endonucleolytic activities targeting single-stranded tRNA regions. However, how a tRNA with a single hydrolyzed phosphodiester bond in the anticodon loop (‘nicked’ tRNA) gives rise to distinct tsRNAs remains poorly understood. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL15520 GPL24676 GPL21697

6 Samples

Download data: TXT

(Submitter supplied) We used sequencing analyses to identify small RNAs that are generated in a Dicer-dependent manner and the genes that are dysregulated upon Dicer knockdown at the mRNA level, and upon Drosha, Dicer and Ago2 knockdown at the chromatin level in HEK293 cells. We found that levels of tRNA-derived sRNAs decreased alongside microRNAs upon Dicer knockdown. Many genes are dysregulated at the chromatin levels when Dicer and Ago2 levels are reduced, indicating that Dicer and Ago2 can regulate genes directly or indirectly at the transcriptional level. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Other

Platforms:

GPL11154 GPL20301

20 Samples

Download data: BW, TSV

(Submitter supplied) The goals of this study are to screen differential expression profiles of tRNA-Derived small RNAs (tsRNAs) in muscle-invasive bladder cancer (MIBC) in Chinese population using next-generation sequencing and qRT-PCR.As a result, in MIBC tissues, 406 tsRNAs were differentially expressed between in MIBC tissues. Of them, 91 tsRNAs were significantly differentially expressed (fold change>1.5; P<0.05): 65 tsRNAs were significantly up-regulated whereas 26 were significantly down-regulated in MIBC.Taken together,this study explored, for the first time, the significant alteration of tsRNA expression profiles in MIBC in Chinese population and offered deep insights into many possible treatment targets of MIBC by regulating tsRNAs.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: FA

(Submitter supplied) The goals of this study are to screen differential expression profiles of tRNA-Derived small RNAs (tsRNAs) in rats after traumatic spinal cord injury (SCI) using next-generation sequencing and qRT-PCR.As a result, in rat spinal cord 1 day after contusion, totally 297 tsRNAs differentially expressed were identified. 155 tsRNAs were significantly differentially expressed: 91 were significantly up-regulated, while 64 were significantly down-regulated after SCI (folding change>1.5; P<0.05).Next, four tsRNAs were selected to be verified by qRT-PCR. more...

Organism:

Rattus norvegicus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL14844

8 Samples

Download data: FA

(Submitter supplied) Transfer-RNA-Derived Small RNA (tsRNA) is s a novel class of short non-coding RNA including stress-induced tRNA fragments (tiRNA) and tRNA-derived fragments (tRF). Using RNA sequencing, we evaluated the tsRNA expression profiles in the brain of intracerebral hemorrhage (ICH) and sham rats at days 21. Meanwhile, tsRNA levels in ICH treated with the Traditional Chinese Medicine named Buyang Huanwu Decoction (BYHWD) were detected. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20084

9 Samples

Download data: XLSX

(Submitter supplied) Mutations in the cytosine-5 RNA methyltransferase NSun2 can cause Intellectual Disability (ID) and symptoms commonly found in patients with Dubowitz syndrome. By analysing gene expression data with the global cytosine-5 RNA methylome in NSun2-deficient mice, we find that loss of cytosine-5 RNA methylation increases the fragmentation of transfer RNAs (tRNA) leading to an accumulation of 5’ halves. Cleavage of tRNAs by Angiogenin is a common cellular stress response to silence translational programmes, and we show that Angiogenin binds tRNAs lacking site-specific NSun2-methylation with higher affinity. Furthermore, cells lacking functional NSun2 up-regulate stress markers, and deletion of NSun2 compromises cellular survival in response stress stimuli including UV-light and oxidative stress. The decreased tolerance of NSun2 null cells towards oxidative stress can be rescued through inhibition of Angiogenin. In conclusion, cytosine-5 RNA methylation is an essential post-transcriptional mechanism during cellular stress responses and NSun2-mediated tRNA methylation protects from Angiogenin-dependent stress-induced RNA cleavage.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Other

Platform:

GPL9250

21 Samples

Download data: TXT

(Submitter supplied) Microarray detected 816 statistically differentially expressed tsRNAs, of which 243 tsRNAs were upregulated and 573 were downregulated. Eight validated tsRNAs in the results of Real Time-PCR were consistent with the small RNA microarray: four upregulations (tRF3a-AspGTC-9, 5'tiRNA-31-GluCTC-16, i-tRF-31:54-Val-CAC-1 and tRF3b-TyrGTA-4) and four downregulation (5'tiRNA-33-LysTTT-4, i-tRF-8:32-Val-AAC-2, i-tRF-2:30-His-GTG-1, and i-tRF-15:31-Lys-CTT-1).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL31223

6 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL23157

36 Samples

Download data: TXT, XLSX

(Submitter supplied) We applied a tRNA-specific sequencing pipeline to analyze tRNA expression during infection of MC57G fibroblasts with the gammaherpesvirus MHV68. We find that expression of 14% of tRNA genes is significantly upregulated during infection. By mapping reads to either premature tRNA (pre-tRNA) or mature tRNA sequences, we find that increased expression of tRNA genes is manifested at the level of the pre-tRNA only, indicating a homeostatic mechanism to maintain the size and composition of mature tRNA pools.

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21103

8 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18573

9 Samples

Download data: XLSX