GEO DataSets

(Submitter supplied) Here, we adopt a method that combines tRNA-seq and cp-RNA-seq to identify and quantify tRFs and tRNAs in plants. We provide a high-quality expression atlas of tRFs and tRNAs in Arabidopsis and rice, and uncovers complex tRFs repertoire and the dynamic expressions of tRNA genes in plants.

Organism:

Arabidopsis thaliana; Oryza sativa

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL21785 GPL23013

24 Samples

Download data: XLSX

(Submitter supplied) Here, we apply tRNA-seq and YAMAT-seq to profile the expressions of tRFs and tRNAs in plants. We provide a high-quality expression atlas of tRFs and tRNAs in Arabidopsis and rice, and uncover complex tRF population and the dynamic expressions of tRNA genes in plants.

Organism:

Sorghum bicolor; Arabidopsis thaliana; Setaria italica; Zea mays; Glycine max; Hordeum vulgare; Triticum aestivum

Type:

Non-coding RNA profiling by high throughput sequencing

7 related Platforms

13 Samples

Download data: TXT, XLSX

(Submitter supplied) Background: Eukaryotic organisms have evolved a series of mechanisms to regulate transposable element (TE) expression based on RNA silencing. In plants, the initial step in the recognition of TE transcripts relies on microRNAs, but this is unlikely to take place in the pollen grain where natural reactivation of TE transcription occurs but microRNAs accumulate to low levels. We investigated small non-coding RNA accumulation in plants and found conserved tRNA-derived RNA fragment (tRF) accumulation in the pollen grain or analogous reproductive structure in a variety of plant species. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing; Other

Platforms:

GPL13222 GPL17639

11 Samples

Download data: TXT

(Submitter supplied) The human genome encodes hundreds of tRNA genes but their individual contribution to the tRNA pool is not fully understood. Deep sequencing of tRNA transcripts (tRNA-Seq) can estimate tRNA abundance at single gene resolution, but tRNA structures and post-transcriptional modifications impair these analyses. Here we present a bioinformatics strategy to investigate differential tRNA gene expression and use it to compare tRNA-Seq datasets from cultured human cells and human brain. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: XLS

(Submitter supplied) Background: As couples struggle with infertility and livestock producers wish to rapidly improve genetic merit in their herd, assisted reproductive technologies (ART) have become increasingly popular in human medicine as well as the livestock industry. Utilizing ART can cause an increased risk of congenital overgrowth syndromes, such as Large Offspring Syndrome (LOS) in ruminants. A dysregulation of transcripts has been observed in bovine fetuses with LOS, which is suggested to be a cause of the phenotype. more...

Organism:

Bos indicus x Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32674

17 Samples

Download data: TXT

(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) We have performed RNA sequencing after tRNA/tRF overexpression

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

4 Samples

Download data: TXT

(Submitter supplied) We analyzed the small RNA composition of mouse placenta/decidua to determine whether there are specific differences in small RNAs during fetal development and in response to maternal immune activation.

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19057

84 Samples

Download data: CSV

(Submitter supplied) We investigate tRF and tiRNA profiles in lung adenocarcinoma and adjacent tissues using a NextSeq system. Total RNA was extracted from tissues and pretreated to remove the RNA modifications. In patients with lung adenocarcinoma, 338 types of tRFs and tiRNAs were detected via sequencing, 284 of which were not previously reported. Compared with the adjacent tissues, 17 types of tRFs and tiRNAs comprising 34 subtypes were found to be abnormally expressed in lung adenocarcinoma tissues, 20 of which were upregulated and 14 of which were downregulated. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: TXT

(Submitter supplied) MicroRNAs (miRNAs) are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes, namely developmental timing, cell differentiation, cell proliferation, immune response and infection. For this reason, their identification is essential to understand eukaryotic biology. more...

Organism:

Danio rerio

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19872

12 Samples

Download data: TXT

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

Organism:

Phytophthora infestans

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL19416 GPL19354

16 Samples

Download data

(Submitter supplied) Background: The oomycete Phytophthora infestans possesses active RNA silencing pathways, which presumably enable this plant pathogen to control the large numbers of transposable elements present in its 240 Mb genome. Small RNAs (sRNAs), central molecules in RNA silencing, are known to also play key roles in this organism, notably in regulation of critical effector genes needed for infection of its potato host. more...

Organism:

Phytophthora infestans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19416

8 Samples

Download data: FA, TXT

(Submitter supplied) Background: The oomycete Phytophthora infestans possesses active RNA silencing pathways, which presumably enable this plant pathogen to control the large numbers of transposable elements present in its 240 Mb genome. Small RNAs (sRNAs), central molecules in RNA silencing, are known to also play key roles in this organism, notably in regulation of critical effector genes needed for infection of its potato host. more...

Organism:

Phytophthora infestans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19354

8 Samples

Download data: TSV

(Submitter supplied) We analyzed small RNA sequencing data from CD5+/CD19+ B cells of a cohort of indolent and aggressive CLL patients compared with CD19+ B-cells of healthy donors. We identified tsRNA signatures in indolent and aggressive CLL vs. normal B-cells; we also found a drastic dysregulation of the expression of mature tRFs in CLL.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16791

28 Samples

Download data: TXT

(Submitter supplied) tRNA-derived fragments (tRFs) have served as new class of non-coding RNA and played important role in regulating cellular RNA processing and protein translation, which was also proved have function on the intergenerational effects of paternal disease. However, there was no study reported the influence of tRFs on myocardial hypertrophy. In the current study, we explore the hypothesis that tRFs in response to myocardial hypertrophy and contribute to intergenerational inheritance.We used isoproterenol induced myocardial hypertrophy rat model. more...

Organism:

Rattus norvegicus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL14844

6 Samples

Download data: FA

(Submitter supplied) Transfer RNA-derived fragments (tRFs) and transfer RNA halves (tiRNAs) have been shown to play crucial roles in gene regulation. This study targets to reveal the expression profile of tRFs and tiRNAs and their possible biological roles in lung adenocarcinoma (LUAD). Five paired clinical lung adenocarcinoma tissues (LAT) and adjacent normal lung tissues (ANLT) were selected to conduct the expression of tRFs and tiRNAs. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18573

10 Samples

Download data: TXT

(Submitter supplied) We sequenced the small RNA transcriptome of prostate cancer at different stages and generated a quantified catalogue of 3927 small non-coding RNAs (sncRNAs) detected in normal and malignant prostate tissue. From these sncRNAs less than half are microRNAs. The remaining sncRNAs represent stable sncRNAs species that originate from snoRNA, tRNA and other sncRNAs.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9052

11 Samples

Download data: TXT

(Submitter supplied) MicroRNAs (miRNAs) are a well-characterized class of small RNAs (sRNAs) that regulate gene expression post-transcriptionally. miRNAs function within a complex milieu of other sRNAs of similar size and abundance, with the best characterized being tRNA fragments or tRFs. The mechanism by which the RNA-induced silencing complex (RISC) selects for specific sRNAs over others is not entirely understood in human cells. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing; Other

Platform:

GPL18573

12 Samples

Download data: XLSX

(Submitter supplied) In this study, we performed deep sequencing and bioinformatics analyses of short RNAs from Plasmodium falciparum parasites to identify and characterize novel type of small RNAs. A total of 14,828,877 raw reads were produced from small RNA libraries. We detected a new type of small RNA from tranfer RNA known as tRFs.

Organism:

Plasmodium falciparum 3D7

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17634

1 Sample

Download data: FA

(Submitter supplied) tRNA related fragments(tRF) and tRNA halves(tiRNA) are novel class of short non-coding RNA derived from tRNAs. Using RNA sequencing, we evaluated the tRFs/tiRNAs expression profiles in relapsed/refractory multiple myeloma and multiple myeloma patients. Bioinformatics analyses indicated that tRFs/tiRNAs may be involved in the progression and drug-resistance of multiple myeloma.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

10 Samples

Download data: XLSX