GEO DataSets

(Submitter supplied) Small non-coding RNAs (sncRNAs) are generated from different genomic loci and have important roles in biological processes, such as cell proliferation and regulation of gene expression. Next-generation sequencing (NGS) has provided an unprecedented opportunity to discover and quantify diverse kinds of sncRNAs, such as tRFs (tRNA-derived small RNA fragments), phasiRNAs (phased, secondary, small interfering RNAs), piRNAs and plant specific 24-nt short interfering RNAs (siRNAs). more...

Organism:

Populus deltoides

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL20012

11 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL18911 GPL13112

8 Samples

Download data: CSV, GPR

(Submitter supplied) The small non-coding RNAs (sncRNAs) are considered as postranscriptional key regulators of male germ cell development. In addition to microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs), other sncRNAs generated from small nucleolar RNAs (snoRNAs), tRNAs or rRNAs processing may also play important regulatory roles in spermatogenesis. By next generation sequencing (NGS), we characterized the different sncRNA populations detected at three milestone stages in male germ differentiation: primordial germ cells (PGCs) at 13.5 dpc, pubertal spermatogonia cells, and mature spermatozoa. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13112

5 Samples

Download data: CSV

(Submitter supplied) The small non-coding RNAs (sncRNAs) are considered as postranscriptional key regulators of male germ cell development. In addition to microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs), other sncRNAs generated from small nucleolar RNAs (snoRNAs), tRNAs or rRNAs processing may also play important regulatory roles in spermatogenesis. By next generation sequencing (NGS), we characterized the different sncRNA populations detected at three milestone stages in male germ differentiation: primordial germ cells (PGCs) at 13.5 dpc, pubertal spermatogonia cells, and mature spermatozoa. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL18911

3 Samples

Download data: GPR, TXT

(Submitter supplied) We report a novel modular pipeline (iMir) for comprehensive analysis of miRNA-Seq data, from linker removal and sequence quality check to differential expression and biological target prediction, integrating multiple open source modules and resources linker together in an automated flow.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL10999

6 Samples

Download data: TXT

(Submitter supplied) This study annotates the NGS reads in a Sertoli cell sncRNA library. In addition to known sncRNAs, we also identified numerous novel sncRNAs expressed by Sertoli cells. Our data suggest that the Sertoli cell sncRNA transcriptome predominantly consists of miRNAs, piRNA-like RNAs, tRNAs and snoRNAs. This study reports the first comprehensive annotation of the Sertoli cell sncRNA transcriptome.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9522

1 Sample

Download data: GFF

(Submitter supplied) We used deep sequencing to characterize 3 families of sRNAs (piRNAs, miRNAs, and tRFs) present in Sus scrofa gonads and focused on the sRNA fraction present in both male and female gonads. Of the sequences detected in the testes, 2.6% of piRNAs, 9% of miRNAs, and 10% of tRFs were also present in the ovaries. Notably, the majority of the shared piRNAs mapped to the introns of ribosomal RNAs and were derived from clustered loci. more...

Organism:

Sus scrofa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15064

2 Samples

Download data: FA, PDF

(Submitter supplied) Small noncoding RNAs (sncRNAs) are implicated in age-associated pathologies, including sarcopenia and insulin resistance (IR). This study aimed to characterise the wider circulating sncRNA transcriptome of older individuals and associations with sarcopenia and IR. Total RNA was used for sncRNA expression including miRNAs, transfer RNAs (tRNAs), tRNA-associated fragments (tRFs) and piwi-interacting RNAs (piRNAs) was measured in serum from 21 healthy and 21 sarcopenic women matched for age (mean 78.9 years) and HOMA2-IR from the Hertfordshire Sarcopenia Study. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16791

43 Samples

Download data: TXT

(Submitter supplied) Recent results demonstrated that either non-coding or coding genes generate phased secondary small interfering RNAs (phasiRNAs) guided by specific miRNAs. Till now, there is no studies for phasiRNAs in Panax notoginseng (Burk.) F.H. Chen (P. notoginseng), an important traditional Chinese herbal medicinal plant species. Here we performed a genome-wide discovery of phasiRNAs and its host PHAS loci in P. more...

Organism:

Panax notoginseng

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL23359

7 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) Although mitochondria are widely studied organelles, the recent interest in the role of mitochondrial small non-coding RNAs (sncRNA) is providing new functional perspectives in germ cell development and differentiation. PIWI-interacting RNAs (piRNAs) are single-stranded sncRNAs of 20-35 nt generated from the processing of pre-piRNAs longer molecules to be functionally bound to PIWI proteins. Initially ascribed to germ cells, as protectors against transposons, we now know that they are also expressed in somatic cells. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19057

12 Samples

Download data: TXT

(Submitter supplied) We have characterized by small-RNAseq the miRNA expression pattern of mouse male and female Primordial Germ Cells (PGCs) and somatic stromal cells from gonads at E11.5, E12.5 and E13.5. MiRNA accumulation was higher in somatic cells than in PGCs and more stable across the different developmental stages analyzed. Differential expression analyses showed differences in the regulation of key miRNA clusters such as miR-199-214, miR-182-183-96 and miR-34c-5p whose targets have defined roles in both germ and somatic cells in gonadal sexual determination. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16417

12 Samples

Download data: TXT

(Submitter supplied) The ongoing pandemic of coronavirus disease 2019 (COVID-19), which results from the rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a significant global public health threat, with molecular mechanisms underlying its pathogenesis largely unknown. Small non-coding RNAs (sncRNAs) are known to play important roles in almost all biological processes. In the context of viral infections, sncRNAs have been shown to regulate the host responses, viral replication, and host-virus interaction. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21697

8 Samples

Download data: TXT

(Submitter supplied) Anaphylaxis is the most severe manifestation of allergic disorders. Currently, an increasing number of cells, pathways and molecules involved in the etiopathogenesis of anaphylaxis are being discovered. However, there are no conclusive biomarkers to confirm its diagnosis. Small non-coding RNAs (sncRNAs) are 18-200 nucleotide molecules that can be divided into: microRNAs (miRNAs), Piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), small nuclear RNAs (snRNAs), transference RNA derived fragments (tRFs) and YRNA derived fragments (YRFs). more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18573

20 Samples

Download data: XLS

(Submitter supplied) Our aims in this study were: 1) to identify the miRNAs of the bumble bees Bombus terrestris and B. impatiens; 2) to compare the total numbers of miRNAs between both bumble bee species and between them and the honey bee, Apis mellifera; and 3) to test whether the sequences and expression patterns of miRNAs were conserved between species. To investigate each of these aims we used miRNA-seq (deep sequencing of miRNA-enriched libraries) in B. more...

Organism:

Bombus terrestris

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19585

8 Samples

Download data: CSV

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL24247 GPL21103

28 Samples

Download data: TXT

(Submitter supplied) Purpose: To reveal the small RNA profiles in the intima using traditional and PANDORA-seq methods. Methods: 3-week-old LDLR-/- male mice were fed a high cholesterol or low cholesterol diet for 9 weeks. Intimal RNA was extracted by injecting Trizol into the aorta and collecting the flow through for further processing. Results: PANDORA-seq revealed an abundant amount of tsRNA and rsRNA that were undetected by traditional-seq. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21103

18 Samples

Download data: TXT

(Submitter supplied) Purpose: To investigate the effects of high cholesterol diet on the intimal transcriptome related to atherosclerosis. Methods: 3-week-old LDLR-/- male mice were fed a high cholesterol or low cholesterol diet for 9 weeks. Intimal RNA was extracted by injecting Trizol into the aorta and collecting the flow through for further processing. Results: Mice fed a high cholesterol revealed upregulation in atherosclerosis and immune/inflammatory related genes.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

10 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