GEO DataSets

(Submitter supplied) Small RNAs are now known to be major regulatory factors of gene expression. Emerging methods based on deep-sequencing have enabled the analysis of small RNA expression in a high-throughput manner, leading to the identification of large numbers of small RNAs in various species. Moreover, profiling small RNA data together with transcriptome data enables transcriptional and post-transcriptional regulation mediated by small RNAs to be hypothesized. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL16417 GPL17021

4 Samples

Download data: TXT

(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) 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

Platform:

GPL9250

14 Samples

Download data: TXT

(Submitter supplied) Germ cells employ elaborate mechanisms to maintain and protect their genetic material, and also to regulate gene expression during the complex differentiation process of gametogenesis. Piwi proteins, a subclade of the Argonaute family, are expressed mainly in the germline and bind piRNAs, a novel and diverse class of small RNAs whose biogenesis and putative functions are still largely elusive. We employed High Throughput Sequencing after Crosslinking and Immunoprecipitation (HITS-CLIP) coupled with RNA-Seq to characterize the genome-wide target RNA repertoire of Mili and Miwi, two mouse Piwi proteins. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9250

8 Samples

Download data: TXT

(Submitter supplied) Germ cells employ elaborate mechanisms to maintain and protect their genetic material, and also to regulate gene expression during the complex differentiation process of gametogenesis. Piwi proteins, a subclade of the Argonaute family, are expressed mainly in the germline and bind piRNAs, a novel and diverse class of small RNAs whose biogenesis and putative functions are still largely elusive. We employed High Throughput Sequencing after Crosslinking and Immunoprecipitation (HITS-CLIP) coupled with RNA-Seq to characterize the genome-wide target RNA repertoire of Mili and Miwi, two mouse Piwi proteins. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9250

6 Samples

Download data: TXT

(Submitter supplied) Background: Genes, RNAs, and proteins play important roles during germline development. However, the functions of non-coding RNAs (ncRNAs) on germline development remain unclear in avian species. Recent high-throughput techniques have identified several classes of ncRNAs, including micro RNAs (miRNAs), small-interfering RNAs (siRNAs), and PIWI-interacting RNAs (piRNAs). These ncRNAs are functionally important in the genome, however, the identification and annotation of ncRNAs in a genome is challenging. more...

Organism:

Gallus gallus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16133

4 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) The eukaryotic genome has vast intergenic regions containing transposons, pseudogenes and other repetitive sequences. They produce numerous long non-coding RNAs (lncRNAs) and PIWI-interacting RNAs (piRNAs), yet the functions of the vast intergenic regions remain largely unknown. Mammalian piRNAs are abundantly expressed in late spermatocytes and round spermatids. Their expression coincides with the widespread expression of lncRNAs from the genome of these cells. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL13112

12 Samples

Download data: TXT

(Submitter supplied) In animal germline cells, Piwi-interacting RNAs (piRNAs) silence retrotransposons through post-transcriptional and transcriptional mechanisms. However, little is known, especially in mammals, about the functions of piRNAs beyond retrotransposon suppression1-5. In mammalian spermatocytes, piRNAs are known to be abundantly expressed6-10. Here, we show that a subset of coding and noncoding RNAs in mouse spermatocytes is degraded by the piRNA pathway. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: TXT

(Submitter supplied) In animal germline cells, Piwi-interacting RNAs (piRNAs) silence retrotransposons through post-transcriptional and transcriptional mechanisms. However, little is known, especially in mammals, about the functions of piRNAs beyond retrotransposon suppression1-5. In mammalian spermatocytes, piRNAs are known to be abundantly expressed6-10. Here, we show that a subset of coding and noncoding RNAs in mouse spermatocytes is degraded by the piRNA pathway. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

44 Samples

Download data: TXT

(Submitter supplied) In animal germline cells, Piwi-interacting RNAs (piRNAs) silence retrotransposons through post-transcriptional and transcriptional mechanisms. However, little is known, especially in mammals, about the functions of piRNAs beyond retrotransposon suppression1-5. In mammalian spermatocytes, piRNAs are known to be abundantly expressed6-10. Here, we show that a subset of coding and noncoding RNAs in mouse spermatocytes is degraded by the piRNA pathway. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: TXT

(Submitter supplied) In animal germline cells, Piwi-interacting RNAs (piRNAs) silence retrotransposons through post-transcriptional and transcriptional mechanisms. However, little is known, especially in mammals, about the functions of piRNAs beyond retrotransposon suppression1-5. In mammalian spermatocytes, piRNAs are known to be abundantly expressed6-10. Here, we show that a subset of coding and noncoding RNAs in mouse spermatocytes is degraded by the piRNA pathway. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

7 Samples

Download data: CSV

(Submitter supplied) In animal germline cells, Piwi-interacting RNAs (piRNAs) silence retrotransposons through post-transcriptional and transcriptional mechanisms. However, little is known, especially in mammals, about the functions of piRNAs beyond retrotransposon suppression1-5. In mammalian spermatocytes, piRNAs are known to be abundantly expressed6-10. Here, we show that a subset of coding and noncoding RNAs in mouse spermatocytes is degraded by the piRNA pathway. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13112

2 Samples

Download data: TXT

(Submitter supplied) In animal germline cells, Piwi-interacting RNAs (piRNAs) silence retrotransposons through post-transcriptional and transcriptional mechanisms. However, little is known, especially in mammals, about the functions of piRNAs beyond retrotransposon suppression1-5. In mammalian spermatocytes, piRNAs are known to be abundantly expressed6-10. Here, we show that a subset of coding and noncoding RNAs in mouse spermatocytes is degraded by the piRNA pathway. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

5 Samples

Download data: TXT

(Submitter supplied) In animal germline cells, Piwi-interacting RNAs (piRNAs) silence retrotransposons through post-transcriptional and transcriptional mechanisms. However, little is known, especially in mammals, about the functions of piRNAs beyond retrotransposon suppression1-5. In mammalian spermatocytes, piRNAs are known to be abundantly expressed6-10. Here, we show that a subset of coding and noncoding RNAs in mouse spermatocytes is degraded by the piRNA pathway. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: TXT

(Submitter supplied) PIWI-interacting RNAs (piRNAs) function in the nucleus and cytoplasm of animal germ cells to suppress mobile genetic elements. In the mouse male germline, biogenesis of MIWI2-bound nuclear piRNAs depends on endonuclease activity of cytosolic MILI, but the process is poorly understood. Here we use a mouse model expressing an artificial piRNA precursor to show that MILI slicing of the precursor generates a 16-nt by-product and a pre-piRNA intermediate that requires 3ʹ end processing to mature as a new piRNA. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13112

40 Samples

Download data: CSV, TXT

(Submitter supplied) PIWI-interacting RNAs (piRNAs) guide PIWI proteins to suppress transposable elements in animal gonads. Here we demonstrate that in the mouse embryonic male germline, endonucleolytic cleavage (slicing) of a transcript by cytosolic MILI acts as a trigger to initiate its further 5??3? processing into non-overlapping fragments. These fragments accumulate as new piRNAs within the nuclear PIWI protein MIWI2. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

13 Samples

Download data: CSV, TXT

(Submitter supplied) RNAs that are enriched in AGO2 Immunoprecipitated (IP) products or PIWIL1 IP products were identified from mouse(BALB/C) adult testes by examine the ratio of total RNA signal intensity to AGO2 IP RNA or PIWIL1 IP RNA signal intensity.

Organism:

Mus musculus

Type:

Other

Platform:

GPL5642

2 Samples

Download data: GPR

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

Organism:

Ascaris suum

Type:

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

Platforms:

GPL11671 GPL11672

76 Samples

Download data: FA

(Submitter supplied) Eukaryotic cells express several classes of small RNAs that regulate gene expression and ensure genome maintenance. Endogenous siRNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs) mainly control gene and transposon expression in the germline, while microRNAs (miRNAs) generally function in post-transcriptional gene silencing in both somatic and germline cells. To provide an evolutionary and developmental perspective on small RNA pathways in nematodes, we identified and characterized known and novel small RNA classes through gametogenesis and embryo development in the parasitic nematode Ascaris suum and compared them with known small RNAs of Caenorhabditis elegans. more...

Organism:

Ascaris suum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11672

25 Samples

Download data: FA