GEO DataSets

(Submitter supplied) A long-standing view of development is that transcription is silenced in the oocyte until early divisions in the embryo. The point at which major transcription is reactivated varies in different organisms, but is usually after the 2-cell stage. However, this model may not be universal. We used RNA-seq and exploited the protracted development of the parasitic nematode Ascaris suum, to provide a comprehensive time course of mRNA expression, degradation, and translation during early development. more...

Organism:

Ascaris suum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17050 GPL15654 GPL11672

28 Samples

Download data: TXT

(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) 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) Development of the early embryo is thought to be mainly driven by maternal gene products and post-transcriptional gene regulation. Here, we used metabolic labeling to show that RNA can be transferred by sperm into the embryo. To identify genes with paternal expression in the embryo, we performed crosses of males and females from divergent C. elegans strains. RNA sequencing of mRNAs and small RNAs in the 1-cell hybrid embryo revealed that about two hundred paternal mRNAs are reproducibly expressed in the embryo, and that about half of assayed endogenous siRNAs and piRNAs are also of paternal origin. more...

Organism:

Caenorhabditis elegans

Type:

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

Platforms:

GPL13776 GPL13657

21 Samples

Download data: TXT

(Submitter supplied) The earliest stage of animal development is controlled by maternally deposited mRNA transcripts and proteins. Once the zygote is able to transcribe its own genome, maternal transcripts are degraded, in a tightly regulated process known as the maternal to zygotic transition (MZT). While this process has been well-studied within model species, we have little knowledge of how the pools of maternal and zygotic transcripts evolve. more...

Organism:

Drosophila mauritiana; Drosophila mojavensis; Drosophila pseudoobscura; Drosophila willistoni; Drosophila melanogaster; Drosophila yakuba; Drosophila ananassae; Drosophila erecta; Drosophila miranda; Drosophila sechellia; Drosophila simulans; Drosophila virilis; Drosophila persimilis; Drosophila santomea

Type:

Expression profiling by high throughput sequencing; Third-party reanalysis

14 related Platforms

119 Samples

Download data: TXT

(Submitter supplied) ChIP-chip of Pol II, H3K36me3 and CENP-A in met-1 C. elegans early embryo

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL8647

6 Samples

Download data: GFF, PAIR

(Submitter supplied) Over a billion people are infected by Ascaris spp. intestinal parasites. We investigated gene expression by various tissues of adult A. suum, and used that information to help resolve basic functions of these tissues, basic biology of parasitism and functional aspects of nematode genomes. The A. suum genome was sequenced and assembled to allow generation of microarray elements. Expression of over 40,000 60-mer elements was investigated in a variety of tissues from both male and female adult worms. more...

Organism:

Ascaris suum

Type:

Expression profiling by array

Platform:

GPL15336

10 Samples

Download data: FNA, GPR, TXT

(Submitter supplied) We found that the CSR-1 endoRNAi pathway functions in preventing a premature activation of embryonic transcription in developing Caenorhabditis elegans oocytes. An important component of this pathway is the dicer-related helicase DRH-3. To examine embryonic transcripts in the drh-3(rrr2) mutant on a global scale, we performed RNA sequencing on drh-3(rrr2) mutants and wild type animals. The RNA sequencing data of the wild type animals has been uploaded already under the accession number GSE62858, samples: GSM1534604 RNASeq_N2_1 and GSM1534605 RNASeq_N2_2.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18245

2 Samples

Download data: TXT

(Submitter supplied) Abstract: Cells express distinct sets of genes in a precise spatio-temporal manner during embryonic development. There is a wealth of information about embryonic development in C. elegans, but much less is known about embryonic development at the molecular level in nematodes from other taxa. We are interested in insect pathogenic nematodes from the genus Steinernema as models of parasitism and symbiosis as well as a satellite model for evolution in comparison to C. more...

Organism:

Caenorhabditis angaria; Steinernema carpocapsae; Caenorhabditis elegans; Steinernema feltiae

Type:

Expression profiling by high throughput sequencing

4 related Platforms

175 Samples

Download data: TXT

(Submitter supplied) Spatiotemporal control of gene expression is crucial for development and subject to evolutionary changes. Although proteins are the final product of most genes, the developmental proteome of an animal has not yet been comprehensively defined, and the correlation between RNA and protein abundance during development is largely unknown. Here, we globally measured and compared protein and mRNA expression changes during the life cycle of the nematodes C. more...

Organism:

Caenorhabditis briggsae; Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18072 GPL13776

26 Samples

Download data: TXT

(Submitter supplied) Programmed DNA elimination is a developmentally regulated process leading to the reproducible loss of specific genomic sequences. DNA elimination occurs in unicellular ciliates and a variety of metazoans, including invertebrates and vertebrates. In metazoa, DNA elimination typically occurs in somatic cells during early development, leaving the germline genome intact. Reference genomes for metazoa that undergo DNA elimination are not available. more...

Organism:

Parascaris univalens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23533

7 Samples

Download data: FA, TXT

(Submitter supplied) Programmed DNA elimination is a developmentally regulated process leading to the reproducible loss of specific genomic sequences. DNA elimination occurs in unicellular ciliates and a variety of metazoans, including invertebrates and vertebrates. In metazoa, DNA elimination typically occurs in somatic cells during early development, leaving the germline genome intact. Reference genomes for metazoa that undergo DNA elimination are not available. more...

Organism:

Ascaris suum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15654

12 Samples

Download data: FA, TXT

(Submitter supplied) Chromatin diminution is the programmed elimination of specific DNA sequences during development. It occurs in diverse species, but the function(s) of diminution and the specificity of sequence loss remain largely unknown. Diminution in the nematode Ascaris suum occurs during early embryonic cleavages and leads to the loss of germline genome sequences and the formation of a distinct genome in somatic cells. more...

Organism:

Ascaris suum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11672 GPL15654

10 Samples

Download data: TXT