GEO DataSets

(Submitter supplied) Most DNA double-strand breaks (DSBs) are harmful to genome integrity. However, some forms of DSBs are essential to biological processes, such as meiotic recombination and V(D)J recombination. DSBs are also required for programmed DNA elimination (PDE) in ciliates and nematodes. In nematodes, the DSBs are healed with telomere addition. While telomere addition sites have been well-characterized, little is known regarding the DSBs that fragment nematode chromosomes. more...

Organism:

Parascaris univalens; Ascaris suum

Type:

Other

Platforms:

GPL31096 GPL31097 GPL34158

42 Samples

Download data: BW

(Submitter supplied) A cocktail of five bioinformatically and experimentally prioritized recombinant proteins was used immunize pigs and test for active antibody responses.

Organism:

Sus scrofa; Ascaris suum

Type:

Protein profiling by protein array

Platform:

GPL33467

111 Samples

Download data: TXT, XLSX

(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:

GPL31097 GPL31096

143 Samples

Download data: FA

(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) The stability of the genome is paramount to organisms. However, diverse eukaryotes carry out programmed DNA elimination in which portions or entire chromsomes are lost in early development or during sex determination. During early development of the parasitic nematode, Ascaris suum, 13% of the genome is eliminated. How different genomic segments are reproducibly retained or discarded is unknown. Here, we show that centromeric histone CENP-A localization plays a key role in this process. more...

Organism:

Ascaris suum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL15654

62 Samples

Download data: XLSX

(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:

GPL15654 GPL11672 GPL17050

28 Samples

Download data: 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

(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) 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) Cloning and expression was performed using standard techniques. All sequences were PCR amplified from cDNA using sequence specific forward and reverse primers that encompassed the mature protein and contained Sac I (forward) and Xho I (reverse) restriction sites for downstream subcloning. Translation stop sites were incorporated into all reverse primers. Amplified sequences were first cloned into pCR2.1-TOPO by TA cloning then transformed into DH5α cells for sequence verification. more...

Organism:

Ascaris suum

1 Series

111 Samples

Download data

(Submitter supplied) Agilent 4x44K format chips were used for this genome-wide expression array. The Agilent gene expression custom array for A. suum was designed in Agilent eArray: 4x44K Design ID 018257 The final array contains 42,212 customized probes, each derived from a single predicted A. suum gene. We also included 1,591 spike control spots of ten probes, each targeting a different Arabidopsis thaliana gene that did not have homology to known non-plant sequences currently in public databases (SpotReport@-10 Array Validation System, Stratagene).

Organism:

Ascaris suum

1 Series

10 Samples

Download data