GEO DataSets

(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:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11671

51 Samples

Download data: FA

(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

(Submitter supplied) Small RNA pathways play diverse regulatory roles in the nematode C. elegans. However, our understanding of small RNA pathways, their conservation, and their roles in other nematodes is limited. Here, we analyzed small RNA pathways in the parasitic nematode Ascaris. Ascaris has ten Argonautes with five worm-specific Argonautes (WAGOs) that are associated with secondary 5’-triphosphate small RNAs (22-24G-RNAs). more...

Organism:

Ascaris suum

Type:

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

Platforms:

GPL31096 GPL31097

143 Samples

Download data: FA

(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 remanei; Caenorhabditis briggsae; Caenorhabditis elegans; Caenorhabditis brenneri

Type:

Non-coding RNA profiling by high throughput sequencing

4 related Platforms

12 Samples

Download data: TXT

(Submitter supplied) To explore the roles of piRNAs and WAGO-class 22G-RNAs in regulating gene expression and transposon silencing in Caenorhabditis elegans, we used RNA-seq to assess changes in small RNA and mRNA levels in prg-1 and mut-16 mutants, which disable the piRNA and WAGO-class 22G-RNA pathways respectively. We identified numerous roles for piRNAs and WAGO-class 22G-RNAs in regulating germline genes, including transposons, histones, and spermatogenic and oogenic transcripts.

Organism:

Caenorhabditis elegans

Type:

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

Platform:

GPL19757

39 Samples

Download data: XLSX

(Submitter supplied) Illumina sequencing of small RNAs from Brugia pahangi and Haemonchus contortus

Organism:

Brugia pahangi; Haemonchus contortus

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL15031 GPL15032

4 Samples

Download data: TXT

(Submitter supplied) Analysis of small RNAs with 5'p, 3'OH Raw data files are available on our FTP site: ftp://ftp.ncbi.nlm.nih.gov/pub/geosup/Series/GSE20341

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL9309 GPL9085

11 Samples

Download data: TXT

(Submitter supplied) Small RNAs, including piRNAs, miRNAs and endogenous siRNAs, bind Argonaute proteins to form RNA-silencing complexes that target coding genes, transposons and aberrant RNAs. To assess the requirements for endogenous siRNA formation and activity in C. elegans, we developed a GFP-based sensor for the endogenous siRNA 22G siR-1, one of a set of abundant siRNAs processed from a precursor RNA mapping to the X chromosome, the X-cluster. more...

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL9269 GPL13657

5 Samples

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(Submitter supplied) Argonaute-associated siRNAs and Piwi-associated piRNAs have overlapping roles in silencing mobile genetic elements in animals. In C. elegans, mutator-class (mut) genes mediate siRNA-guided repression of transposons as well as exogenous RNA-directed gene silencing (RNAi), but their roles in endogenous RNA silencing pathways are not well understood. To characterize the endogenous small RNAs dependent on mutator-class genes, small RNA populations from a null allele of mut-16, as well as a regulatory mut-16(mg461) allele that disables only somatic RNAi, were subjected to deep sequencing.

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9269

5 Samples

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(Submitter supplied) High-throughput sequencing of small RNAs from Xenopus tropicalis (adult liver, adult skin, oocytes stage I, II, III, IV, V, VI). total RNA, ~18-42 nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

Organism:

Xenopus tropicalis

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9320

5 Samples

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(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare small non-coding RNA profiling (snRNA-seq) in WT oocyte, sperm and 2PN stage embryos to those sperm and 2PN stage embryos derived from WT, Dicer cKO and Drosha cKO. We further study the roles of sperm-borne small RNA on fertilization and pre-implantation embryonic development. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18635

11 Samples

Download data: TXT

(Submitter supplied) To genome-widely investigate functions of C. elegans argonautes (AGOs), we applied CRISPR/Cas9 technology to introduce an in-frame GFP::FLAG multiplex tag into the endogenous locus of C. elegans AGOs and performed RNA immunoprecipitation (IP) with anti-GFP or anti-FLAG antibody, followed by unique molecular identifier (UMI)-mediated cDNA library constructions and subjected to high-throughput sequencing. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26672

20 Samples

Download data: BW

(Submitter supplied) The piRNA pathway is studied in great detail in Drosophila female germline. In this study we show that unlike the female germline where all Piwi proteins are expressed throughout oogenesis, Ago3 - a Piwi family protein shows a spatial expression male germline. To understand dynamics of piRNA pathway during spermatogonia and primary spermatocyte stages of male germline development, we used arrest mutants. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13304

9 Samples

Download data: XLSX

(Submitter supplied) During early vertebrate development, a large number of noncoding RNAs are maternally inherited or expressed upon activation of zygotic transcription. The exact identity, expression levels, and function during early vertebrate development for most of these noncoding RNAs remains largely unknown. miRNAs (microRNAs) and piRNAs (piwi-interacting RNAs) are two classes of small non-coding RNAs that play important roles in gene regulation during early embryonic development. more...

Organism:

Danio rerio

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9319

5 Samples

Download data: FA, TXT

(Submitter supplied) Small RNAs play important roles in early embryonic development. However, their expression dynamics and modifications are poorly understood because of the scarcity of RNA that is obtainable for sequencing analysis. Using an improved deep sequencing method that requires as little as 10 ng of total RNA or 50 oocytes, we profile small RNAs in mouse oocytes and early embryos. We find that microRNA (miRNA) expression starts soon after fertilization, and the mature miRNAs carried into the zygote by sperm during fertilization are relatively rare compared to the oocyte miRNAs. more...

Organism:

Homo sapiens; Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL13112 GPL11154

26 Samples

Download data: TXT

(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

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(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) There have been substantial researches focused on the roles of microRNAs (miRNA) and Piwi-interacting RNAs (piRNA) delivered from mammalian spermatozoa, comparatively little is known about the role of sperm-delivered miRNAs and piRNAs within cockerels’ (breeding cock) sperm. A small RNA library of cockerels’ sperm was constructed using Illumine high-throughput sequencing technology.

Organism:

Gallus gallus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19005

1 Sample

Download data: XLSX

(Submitter supplied) Comparison of small RNA profiles across nematode evolution

Organism:

Brugia malayi; Globodera pallida; Pristionchus pacificus; Enoplus brevis; Paragordius varius; Romanomermis culicivorax; Nippostrongylus brasiliensis; Hypsibius dujardini; Caenorhabditis elegans; Trichinella spiralis; Odontophora rectangula

Type:

Non-coding RNA profiling by high throughput sequencing

11 related Platforms

22 Samples

Download data: FA, FASTA