GEO DataSets

(Submitter supplied) small RNA libraries from wild-type and Hen1 mutant testes were made with either polyA tailing (VASAGFPHen1minus/plus) or adapter ligation (Hen1Testis and WTTestis) and sequenced on an Illumina GAII platform.

Organism:

Danio rerio

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9319

4 Samples

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(Submitter supplied) Piwi proteins specify an animal-specific subclass of the Argonaute family, that in vertebrates are specifically expressed in germ cells. We demonstrate that zebrafish Piwi (Ziwi) is expressed in both the male and the female gonad, and is a component of a germline specifying structure, called nuage. Loss of Ziwi function results in a progressive loss of germ cells due to apoptosis during larval development. more...

Organism:

Danio rerio

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11102

2 Samples

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(Submitter supplied) RNA libraries from immunoprecipitates of Tdrd1, Ziwi and Zili, total testis RNA, total RNA from 3 week old wild-type and tdrd1 mutant gonads.

Organism:

Danio rerio

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9319

7 Samples

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(Submitter supplied) Murine Adult Stomach Small RNA

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16331

2 Samples

Download data: TXT

(Submitter supplied) This study annotates the NGS reads in ICC and Sm Int sncRNA libraries. In addition to known sncRNAs, we identified numerous somatic piRNA-like RNAs. This study confirms the expression of pilRNAs in somatic tissues and outlines their major characteristics.

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9522

2 Samples

Download data: GFF

(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) HUA ENHANCER 1 (Hen1) is a RNA 2'-O-methyltransferase that modifies small non-coding RNAs (sncRNAs) by adding a methyl group to the 2'-OH of 3'-terminal nucleotides, thereby protecting them from other modifications and degradation. The molecular mechanism underlying the methylation of small RNA duplexes has been revealed by the crystal structure of Hen1 in Arabidopsis (AtHen1). However, the molecular basis of single-stranded RNA methylation by mammalian Hen1 homologues, especially p-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs), remains elusive. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: TXT

(Submitter supplied) Small RNAs have important functions. However, small RNAs in primate oocytes remain unexplored. Herein, we develop CAS-seq, a single-cell small RNA sequencing method, and profiled the small RNAs in human oocytes and embryos. We discover a class of ~20-nt small RNAs that are predominantly expressed in human and monkey oocytes, but not in mouse oocytes. They are specifically associated with HIWI3 (PIWIL3), whereas significantly shorter than the commonly known PIWI-interacting RNAs (piRNAs), designated as oocyte short piRNAs (os-piRNAs). more...

Organism:

Homo sapiens; Mus musculus; Macaca fascicularis

Type:

Non-coding RNA profiling by high throughput sequencing

7 related Platforms

111 Samples

Download data: TXT

(Submitter supplied) Germ cells of most animals critically depend on piRNAs and Piwi proteins. Surprisingly, piRNAs in mouse oocytes are relatively rare and dispensable. We present compelling evidence for strong Piwi-piRNA expression in oocytes of other mammals. Human fetal oocytes express PIWIL2 and transposon-enriched piRNAs. Oocytes in adult human ovary express PIWIL1 and PIWIL2, while those in bovine ovary just express PIWIL1. more...

Organism:

Bos taurus; Macaca fascicularis; Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL19647 GPL15520 GPL19646

41 Samples

Download data: FASTA

(Submitter supplied) The piRNA machinery is known for its role in mediating epigenetic silencing of transposons. Recent studies suggest that this function also involves piRNA-guided cleavage of transposon-derived transcripts. As many piRNAs also appear to have the capacity to target diverse mRNAs, this raises the intriguing possibility that piRNAs may act extensively as siRNAs to degrade specific mRNAs. To directly test this hypothesis, we compared mouse PIWI (MIWI)-associated piRNAs with experimentally identified cleaved mRNA fragments from mouse testes, and observed cleavage sites that predominantly occur at position 10 from the 5' end of putative targeting piRNAs. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL9185

2 Samples

Download data: FA

(Submitter supplied) Piwi-interacting RNAs (piRNAs) are essential for silencing of transposable elements in the germline but their biogenesis is poorly understood. Here we demonstrate that MOV10L1, a germ cell-specific putative RNA helicase, is associated with Piwi proteins. Genetic disruption of the MOV10L1 RNA helicase domain in mice renders both MILI and MIWI2 devoid of piRNAs. Absence of a functional piRNA pathway in Mov10l1 mutant testes causes loss of DNA methylation and subsequent de-repression of retrotransposons in germ cells. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9185

3 Samples

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(Submitter supplied) Small RNAs exert an effect through diverse RNA interference pathways to transcriptionally or post-transcriptionally silence their targets. The Piwi-interacting RNAs (piRNAs) represent a germline-specific small RNA pathway where Piwi proteins themselves are thought to mediate piRNA biosynthesis. Here, we provide strong evidence for a piRNA amplification loop in zebrafish, in which Ziwi and Zili bind piRNAs of opposite polarity. more...

Organism:

Danio rerio

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL7207

6 Samples

Download data: FA, FNA, QUAL

(Submitter supplied) Small silencing RNAs are key regulators of gene expression in both plants and animals. HEN1-mediated 3’ terminal 2’-O-methylation plays a crucial role in small RNA stability control. In the absence of HEN1, small RNAs are frequently uridylated (untemplated uridine addition) and trimmed, a phenomenon that is conserved across species. However, the underlying molecular mechanism is largely unknown. In this study, we have discovered UTP: RNA uridylyltransferase (URT1) acts redundantly with HESO1 in the uridylation of miRNAs, in addition to its role in oligo-adenylated mRNA uridylation. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13222

12 Samples

Download data: TXT

(Submitter supplied) Small RNA and mRNA high-throughput sequencing was done to explore the roles of henn-1 and small RNA methylation in regulating gene expression and small RNA stability in C. elegans. Our results point to a requirement for henn-1 in methylating piRNAs, primary siRNAs, and a subset of miRNAs. In the absence of henn-1, modest changes in gene expression were observed in animals grown under optimal condition.

Organism:

Caenorhabditis elegans

Type:

Other

Platforms:

GPL19757 GPL18245 GPL13657

60 Samples

Download data: XLSX

(Submitter supplied) Many animals have a conserved adaptive genome defense system known as the Piwi-interacting RNA (piRNA) pathway which is essential for germ cell development and function. Disruption of individual mouse Piwi genes results in male but not female sterility, leading to the assumption that PIWI genes do not play a role in mammalian oocytes. Contrary to this, PIWIL1- and PIWIL3-defective golden hamsters we have produced show defects in production of functional oocytes. more...

Organism:

Mesocricetus auratus

Type:

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

Platforms:

GPL28997 GPL29575

36 Samples

Download data: CSV, TSV, TXT

(Submitter supplied) piRNAs function in silencing retrotransposons by associating with the PIWI proteins, AGO3, Aub, and Piwi, in Drosophila germlines. Bioinformatics analyses of piRNAs in Drosophila ovaries suggested that piRNAs are produced by two systems, the primary processing pathway and the amplification loop, from repetitive genes and piRNA clusters in the genome. The amplification loop occurs in a Dicer-independent, PIWI-Slicer-dependent manner. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9333

1 Sample

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(Submitter supplied) Transposable elements can drive genome evolution, but their enhanced activity is detrimental to the host and therefore must be tightly regulated. The piwi-interacting small RNAs (piRNAs) pathway is critically important for transposable element regulation, by inducing transcriptional silencing or post-transcriptional decay of mRNAs. We show that piRNAs and piRNA biogenesis components regulate pre-mRNA splicing of P transposable element transcripts in vivo, leading to the production of the non-transposase-encoding mature mRNA isoform in germ cells. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL17275

20 Samples

Download data: BEDGRAPH, BIGWIG

(Submitter supplied) Piwi-interacting RNAs (piRNAs) are small RNAs predominantly expressed in germ cells that function in gametogenesis in various species. Notably, PIWI-deficient female mice are fertile and mouse oocytes express a panel of small RNAs that do not appear widely representative of mammals. Thus, the function of piRNAs in mammalian oogenesis remains largely elusive. Here, we generated PIWIL1- and MOV10L1-deficient golden hamsters and found that all female and male mutants were sterile, with severe defects in embryogenesis and spermatogenesis, respectively. more...

Organism:

Mesocricetus auratus

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL28882

128 Samples

Download data: TXT

(Submitter supplied) We examined in Xenopus tropicalis eggs piRNAs that are associated with Y12 antibody, which binds symmetrically methylated arginines that are present on diverse Piwi proteins. The goal of this experiment is to more deeply characterize the piRNA pool from adult Xenopus extracts, using the Illumina platform.

Organism:

Xenopus tropicalis

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9320

1 Sample

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(Submitter supplied) We deep-sequenced small RNAs after immunoprecipitation of Mili or Miwi, as well as total small RNA from adult mouse testis. The goal of this experiment is to more deeply characterize the piRNA pool from adult mouse testes, using the Illumina platform.

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9250

3 Samples

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