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Items: 1 to 20 of 357

1.

Small RNA pathways in the nematode Ascaris in the absence of piRNAs

(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
Series
Accession:
GSE189061
ID:
200189061
2.

Comparative Genome Analysis of Programmed DNA Elimination in Nematodes (Ascaris)

(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
Series
Accession:
GSE99523
ID:
200099523
3.

Differential Chromosomal Localization of Centromeric Histone CENP-A Contributes to Nematode Programmed DNA Elimination

(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
Series
Accession:
GSE76914
ID:
200076914
4.

Transcription in Pronuclei and One- to Four-Cell Embryos Drives Early Development in a Nematode

(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
Series
Accession:
GSE46277
ID:
200046277
5.

Silencing of Germline-Expressed Genes by DNA Elimination in Somatic Cells

(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
Series
Accession:
GSE38470
ID:
200038470
6.

Gene expression analysis distinguishes tissue specific and gender related functions among adult Ascaris suum tissues.

(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
Series
Accession:
GSE36690
ID:
200036690
7.

Deep Small RNA Sequencing from the Nematode Ascaris Reveals Conservation, Functional Diversification, and Novel Developmental Profiles

(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
Series
Accession:
GSE26957
ID:
200026957
8.

Ascaris suum transcriptome (RNA-Seq) data

(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
Series
Accession:
GSE26956
ID:
200026956
9.

Ascaris suum Small RNA-Seq data

(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
Series
Accession:
GSE26955
ID:
200026955
10.

Illumina NovaSeq 6000 (Ascaris suum)

Organism:
Ascaris suum
1 Series
138 Samples
Download data
Platform
Accession:
GPL31097
ID:
100031097
11.

Illumina HiSeq 2500 (Ascaris suum)

Organism:
Ascaris suum
1 Series
5 Samples
Download data
Platform
Accession:
GPL31096
ID:
100031096
12.

Illumina MiSeq (Ascaris suum)

Organism:
Ascaris suum
1 Series
1 Sample
Download data
Platform
Accession:
GPL17050
ID:
100017050
13.

Agilent-018257 NematodeNet_Ascaris suum_42K_v1.0

(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
Platform
Accession:
GPL15336
ID:
100015336
14.

Illumina HiSeq 2000 (Ascaris suum)

Organism:
Ascaris suum
4 Series
92 Samples
Download data
Platform
Accession:
GPL15654
ID:
100015654
15.

Illumina Genome Analyzer II (Ascaris suum)

Organism:
Ascaris suum
4 Series
44 Samples
Download data
Platform
Accession:
GPL11672
ID:
100011672
16.

Illumina Genome Analyzer (Ascaris suum)

Organism:
Ascaris suum
2 Series
51 Samples
Download data
Platform
Accession:
GPL11671
ID:
100011671
17.

4cell embryo - INPUT_rep2

Organism:
Ascaris suum
Source name:
4 cells embryos
Platform:
GPL31096
Series:
GSE189061
Download data: FA
Sample
Accession:
GSM5735990
ID:
305735990
18.

4cell embryo - INPUT_rep1

Organism:
Ascaris suum
Source name:
4 cells embryos
Platform:
GPL31096
Series:
GSE189061
Download data: FA
Sample
Accession:
GSM5735989
ID:
305735989
19.

4cell embryo - WAGO1_rep2

Organism:
Ascaris suum
Source name:
4 cells embryos
Platform:
GPL31096
Series:
GSE189061
Download data
Sample
Accession:
GSM5735912
ID:
305735912
20.

4cell embryo - WAGO1_rep1

Organism:
Ascaris suum
Source name:
4 cells embryos
Platform:
GPL31096
Series:
GSE189061
Download data
Sample
Accession:
GSM5735911
ID:
305735911
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