GEO DataSets

(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) 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 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) 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) Small RNAs were deep sequenced from the liver and spleen of adult mice in an effort to identify somatic piRNAs. Following sequencing of all small RNAs, known non-coding RNAs were computationally removed from the dataset. The remaining RNAs were then mapped to the genome and analyzed for sequence characteristics (5' base, length) typical of known piRNAs. To determine if any of the identified small RNAs were MIWI2 dependent, we deep sequenced small RNAs from liver and spleen of MIWI2 KO mice and analyzed them as above.

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: BED, TXT

(Submitter supplied) Piwi-interacting small RNAs (piRNAs) of fetal prospermatogonia of mice have been strongly implicated in transposon control. In contrast, little is known about biogenesis and function of abundant piRNAs from adult testes expressed in late spermatocytes and round spermatids. These so-called "pachytene" piRNAs are processed from long non-coding piRNA precursors and have no defined RNA targets in the transcriptome even though their binding partner Piwi, MIWI, is essential for spermiogenesis and fertility. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

17 Samples

Download data: BW, TXT

(Submitter supplied) In the male germ cells of eutherian animals, 26–30-nt-long PIWI-interacting RNAs (piRNAs) emerge when spermatocytes enter the pachytene phase of meiosis. These pachytene piRNAs derive from ~100 discrete autosomal loci resemble canonical protein-coding genes and long non-coding RNA-producing genes—they are transcribed by RNA polymerase II, bearing 5´ caps and 3´ poly(A) tails, and their transcripts often contain introns that are removed before nuclear export and processing into piRNAs. more...

Organism:

Mus musculus; Macaca mulatta

Type:

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

Platforms:

GPL19057 GPL21120

19 Samples

Download data: BW

(Submitter supplied) piRNAs can derive from transposable elements (TEs), long non-coding RNAs, or the 3'UTR of mRNAs, the last being the least characterized out of the three piRNA classes. In this study, we systematically defined the regulation, biogenesis and function of the 3'UTR piRNAs that are expressed throughout mouse spermatogenesis. These piRNAs are regulated by A-MYB transcription factors, and their precursors are bifunctional mRNAs which are processed into piRNAs after pioneer rounds of translation. more...

Organism:

Gallus gallus; Mus musculus

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL13112 GPL16133

27 Samples

Download data: BIGWIG, 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) In order to monitor the changes in small RNAs expression during mouse spermatogenesis. Type A spermatogonia, pachytene spermatocytes and round spermatids were isolated following collagenase treatment of testes and trypsin digestion of isolated seminiferous tubules using unit gravity sedimentation in a bovine serum albumin gradient. The small RNA fraction (18-36nt) was cloned and sequenced from total RNA of each cell type.

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9185

3 Samples

Download data

(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

Download data

(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

Download data

(Submitter supplied) Piwi-interacting RNAs (piRNAs) are ~24-30 nucleotide regulatory RNAs that are abundantly expressed in gonads. The most well-understood piRNAs mediate post-transcriptional defense against transposable elements (TEs), and derive from sense or antisense strands as a consequence of "ping-pong" amplification of complementary sequences of active TEs and piRNA master control transcripts. Another class of piRNAs, such as those expressed in pachytene testis, derive from large intergenic clusters that are strictly single-stranded. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platform:

GPL1322

3 Samples

Download data: CEL