GEO DataSets

(Submitter supplied) We found piRNAs with different lengths represented the predominant small RNA species in oocytes from the 12 explored species, except mouse. We found endo-siRNAs resulted from the truncated Dicer isoform were mouse-specific, and os-piRNAs associating with PIWIL3 in human oocytes are widespread in mammals and are typically with low levels of the 2’-3’-O-methylation. The sequences of many highly expressed piRNA clusters are fast-evolving compared with their syntenic genomic locations, and the TE families distributing in the conserved piRNA clusters are various between species.

Organism:

Macaca fascicularis; Oryctolagus cuniculus; Cricetulus griseus; Mesocricetus auratus; Mus musculus; Capra hircus; Rattus norvegicus; Cavia porcellus; Danio rerio; Homo sapiens; Canis lupus familiaris; Sus scrofa domesticus

Type:

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

12 related Platforms

138 Samples

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(Submitter supplied) We found piRNAs with different lengths represented the predominant small RNA species in oocytes from the 12 explored species, except mouse. We found endo-siRNAs resulted from the truncated Dicer isoform were mouse-specific, and os-piRNAs associating with PIWIL3 in human oocytes are widespread in mammals and are typically with low levels of the 2’-3’-O-methylation. The sequences of many highly expressed piRNA clusters are fast-evolving compared with their syntenic genomic locations, and the TE families distributing in the conserved piRNA clusters are various between species.

Organism:

Canis lupus familiaris

Type:

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

Platform:

GPL25760

8 Samples

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(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:

Macaca fascicularis; Mus musculus; Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

7 related Platforms

111 Samples

Download data: TXT

(Submitter supplied) Small RNAs mediate gene silencing by binding Argonaute/Piwi proteins to regulate target RNAs. Here we describe small RNA profiling of the adult testes of Callithrix jacchus, the common marmoset. The most abundant class of small RNAs in the adult testis was piRNAs, while 353 novel miRNAs but few endo-siRNAs were also identified. MARWI, a marmoset homolog of mouse MIWI and a very abundant PIWI in adult testes, associates with piRNAs that show characteristics of mouse pachytene piRNAs. more...

Organism:

Callithrix jacchus

Type:

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

Platforms:

GPL18020 GPL17712

3 Samples

Download data: TXT

(Submitter supplied) In the male mouse germline, PIWI-interacting RNAs (piRNAs) bound to the PIWI protein MIWI2 guide the DNA methylation of young active transposable elements (TEs) through SPOCD1. We identified loss-of-function variants in the human SPOCD1 gene that cause male infertility and defective TE silencing. One of the SPOCD1 pathogenic alleles encodes a truncated protein that lacks the conserved carboxy-terminus. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL19057 GPL23969

9 Samples

Download data: TXT

(Submitter supplied) The control of transposable element (TE) activity in germ cells provides genome integrity over generations. A distinct small RNA-mediated pathway utilizing Piwi-interacting RNAs (piRNAs) suppresses TE expression in gonads of metazoans. In the fly, primary piRNAs derive from so-called piRNA clusters, which are enriched in damaged repeated sequences. These piRNAs launch a cycle of TE and piRNA cluster transcript cleavages resulting in the amplification of piRNA and TE silencing. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13304

1 Sample

Download data: TXT

(Submitter supplied) We provide a broad overview of sequence diversity in An. gambiae mature microRNAs, including annotation of novel microRNAs identified in this study.

Organism:

Anopheles gambiae

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL17644 GPL15693

8 Samples

Download data: TXT

(Submitter supplied) This study examines the population of transcripts associated with the Xenopus Piwi proteins, Xiwi and Xili, from X.laevis and X.tropicalis. RIP-seq, CLIP-seq, piRNA-seq, and mRNA-seq datasets were integrated to determine how the Xenopus Piwi proteins where using piRNAs and binding interactions to associate with transcripts in gonadal cells.

Organism:

Xenopus tropicalis; Xenopus laevis

Type:

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

Platforms:

GPL15472 GPL17682

11 Samples

Download data: TXT

(Submitter supplied) The piRNA pathway controls transposon expression in animal germ cells, thereby ensuring genome stability over generations. piRNAs are maternally deposited and required for proper transposon silencing in adult offspring. However, a long-standing question in the field is the precise function of maternally deposited piRNAs and its associated factors during embryogenesis. Here, we probe the spatio-temporal expression patterns of several piRNA pathway components during early stages of development. more...

Organism:

Drosophila melanogaster

Type:

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

Platform:

GPL21306

62 Samples

Download data: BED, BW

(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) 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:

Homo sapiens; Macaca fascicularis; Bos taurus

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL19647 GPL15520 GPL19646

41 Samples

Download data: FASTA

(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) The nematode Caenorhabditis elegans contains each of the broad classes of eukaryotic small RNAs, including microRNAs (miRNAs), endogenous small-interfering RNAs (endo-siRNAs) and piwi-interacting RNAs (piRNAs). To better understand the evolution of these regulatory RNAs, we deep sequenced small RNAs from C. elegans and three closely related nematodes: C. briggsae, C. remanei and C. brenneri. The results reveal a fluid landscape of small RNA pathways with essentially no conservation of individual sequences aside from a subset of miRNAs. more...

Organism:

Caenorhabditis briggsae; Caenorhabditis elegans; Caenorhabditis brenneri; Caenorhabditis remanei

Type:

Non-coding RNA profiling by high throughput sequencing

4 related Platforms

12 Samples

Download data: TXT

(Submitter supplied) Transposable elements (TEs) are widely represented in eukaryotic genomes. Recently, a set of small RNAs known as rasRNAs (repeat-associated small RNAs) have been related to the down-regulation of TEs conferring a means to safeguard genome integrity. Two key members of the rasRNAs group are piRNAs and endo-siRNAs. In this study, we have performed a comparative analysis of piRNAs and endo-siRNAs present in mouse oocytes, spermatozoa and zygotes, identified by deep sequencing and bioinformatic analysis. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13112

3 Samples

Download data: CSV, TXT

(Submitter supplied) In order to control transposable element (TE) activity, PIWI-interacting RNAs (piRNAs) have been evolved to silence TE transcriptionally and post-transcriptionally, and produced from heterochromatic genomic loci, called piRNA cluster. Maternal inherited piRNAs transmission is considered as the key step of piRNA cluster maintenance and induction of de nove piRNA cluster formation, however, how the original piRNAs were produced without maternal piRNAs deposition remains unclear. more...

Organism:

Drosophila melanogaster

Type:

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

Platform:

GPL13304

104 Samples

Download data: TXT

(Submitter supplied) Here we show that MIWI is a small RNA-guided ribonuclease (Slicer) that requires extensive complementarity for target cleavage in vitro. Disruption of its catalytic activity in mice by a single point mutation results in male infertility and displays increased accumulation of LINE1 transposon transcripts.

Organism:

Mus musculus

Type:

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

Platforms:

GPL11002 GPL9250

12 Samples

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL9250 GPL11002 GPL6246

20 Samples

Download data: CEL

(Submitter supplied) Here we show that MIWI is a small RNA-guided ribonuclease (Slicer) that requires extensive complementarity for target cleavage in vitro. Disruption of its catalytic activity in mice by a single point mutation results in male infertility and displays increased accumulation of LINE1 transposon transcripts.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

8 Samples

Download data: CEL

(Submitter supplied) We aim to comprehensively characterize the small RNA population in oocytes Pseudogenes populate the mammalian genome as remnants of artifactual incorporation of coding mRNAs into transposon pathways 1. Here, we show that a subset of pseudogenes generates endogenous small interfering RNAs (endo-siRNAs) in mouse oocytes. In these cases, endo-siRNAs are often processed from double-stranded RNAs formed by hybridization of spliced transcripts from protein coding genes to antisense transcripts from homologous pseudogenes. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9185

3 Samples

Download data: TXT

(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