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Items: 1 to 20 of 78

1.

SMC-mediated dosage compensation in C. elegans evolved in the presence of an ancestral nematode mechanism [Hi-C]

(Submitter supplied) Mechanisms of X chromosome dosage compensation have been studied extensively in a few model species representing clades of shared sex chromosome ancestry. However, the diversity within each clade as a function of sex chromosome evolution is largely unknown. Here, we anchor ourselves to the nematode Caenorhabditis elegans, for which a well-studied mechanism of dosage compensation occurs through a specialized structural maintenance of chromosomes (SMC) complex, and explore the diversity of dosage compensation in the surrounding phylogeny of nematodes. more...
Organism:
Pristionchus pacificus; Oscheius tipulae
Type:
Other
Platforms:
GPL32681 GPL34494
4 Samples
Download data: HIC
Series
Accession:
GSE267963
ID:
200267963
2.

SMC-mediated dosage compensation in C. elegans evolved in the presence of an ancestral nematode mechanism [ChIP-Seq]

(Submitter supplied) Mechanisms of X chromosome dosage compensation have been studied extensively in a few model species representing clades of shared sex chromosome ancestry. However, the diversity within each clade as a function of sex chromosome evolution is largely unknown. Here, we anchor ourselves to the nematode Caenorhabditis elegans, for which a well-studied mechanism of dosage compensation occurs through a specialized structural maintenance of chromosomes (SMC) complex, and explore the diversity of dosage compensation in the surrounding phylogeny of nematodes. more...
Organism:
Oscheius tipulae; Pristionchus pacificus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL34492 GPL34493
16 Samples
Download data: BW
Series
Accession:
GSE267962
ID:
200267962
3.

Small RNA sequencing study of the nematode phylum

(Submitter supplied) Comparison of small RNA profiles across nematode evolution
Organism:
Romanomermis culicivorax; Nippostrongylus brasiliensis; Hypsibius dujardini; Brugia malayi; Globodera pallida; Pristionchus pacificus; Enoplus brevis; Paragordius varius; Caenorhabditis elegans; Trichinella spiralis; Odontophora rectangula
Type:
Non-coding RNA profiling by high throughput sequencing
11 related Platforms
22 Samples
Download data: FA, FASTA
Series
Accession:
GSE56651
ID:
200056651
4.

Male and Female DNA and RNA sequencing in several nematode species

(Submitter supplied) The overall goal of this investigation was to investigate X-content of sex-biased genes in several nematode species. The following species of nematode were investigated: *C. elegans, *N2; *C. brenneri, *PB2801; *C. briggsae, *AF16; *C. remanei*, PB4641; *P. **pacificus, *PS312*.* Genomic DNA sequencing data was used to assign X and autosomal - linkage to unassembled sequencing contigs. Male and female RNA seq data was then generated and used to determine sex-biased expression. more...
Organism:
Caenorhabditis briggsae; Caenorhabditis brenneri; Caenorhabditis elegans; Pristionchus pacificus; Caenorhabditis remanei
Type:
Expression profiling by high throughput sequencing; Other
5 related Platforms
31 Samples
Download data: BEDGRAPH, FPKM_TRACKING
Series
Accession:
GSE53144
ID:
200053144
5.

microRNAs in C. elegans, P. pacificus, and S. ratti: Conserved miRNAs are candidate post-transcriptional regulators of developmental arrest in free-living and parasitic nematodes

(Submitter supplied) Animal development is complex yet surprisingly robust. Animals may develop alternative phenotypes conditional on environmental changes. Under unfavorable conditions C. elegans larvae enter the dauer stage, a developmentally arrested, long-lived, and stress-resistant state. Dauer larvae of free-living nematodes and infective larvae of parasitic nematodes share many traits including a conserved endocrine signaling module (DA/DAF-12), which is essential for the formation of dauer and infective larvae. more...
Organism:
Caenorhabditis elegans; Strongyloides ratti; Pristionchus pacificus
Type:
Non-coding RNA profiling by high throughput sequencing
7 related Platforms
10 Samples
Download data: TXT
Series
Accession:
GSE41402
ID:
200041402
6.

Immune response of germline-ablated P. pacificus exposed to S. marcescens

(Submitter supplied) Transcriptional profiling of germline-ablated P. pacificus worms exposed to S. marcescens for 8 hours versus germline-ablated P. pacificus exposed to the control E. coli OP50. First goal was to identify genes that are involved in immune response of germline-ablated P. pacificus when exposed to S. marcescens. Second, this was compared to longevity-regulating genes in germline-deficient animals (see series GSE37331).
Organism:
Pristionchus pacificus
Type:
Expression profiling by array
Platform:
GPL14372
4 Samples
Download data: GPR
Series
Accession:
GSE37337
ID:
200037337
7.

Effect of germline ablation in the nematode P. pacificus

(Submitter supplied) Transcriptional profiling of germline-ablated P. pacificus worms versus un-ablated wild-type controls. Food source E. coli OP50 for both conditions. The goal was to identify genes that regulate the enhanced longevity observed in germline-deficient animals.
Organism:
Pristionchus pacificus
Type:
Expression profiling by array
Platform:
GPL14372
3 Samples
Download data: GPR
Series
Accession:
GSE37331
ID:
200037331
8.

Pristionchus pacificus and Caenorhabditis elegans: Dauer and Dauer exit versus mix-stage comparisons

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Pristionchus pacificus; Caenorhabditis elegans
Type:
Expression profiling by array
Platforms:
GPL14372 GPL10094
15 Samples
Download data: GPR
Series
Accession:
GSE36644
ID:
200036644
9.

P. pacificus young adults: Exposed to Xenorhabdus nematophila versus exposed to E. coli OP50 : 4 hours

(Submitter supplied) Transcriptional profiling of P. pacificus young adult worms exposed to pathogen Xenorhabdus nematophila for 4 hours versus age-matched worms exposed to control lab food E. coli OP50. The goal was to identify genes regulated in response to pathogen. The broader goal of study was to study evolution of pathogen response by comparing this expression profile to that obtained by exposing the nematode C. elegans to the same pathogen. more...
Organism:
Pristionchus pacificus
Type:
Expression profiling by array
Platform:
GPL14372
4 Samples
Download data: GPR
Series
Accession:
GSE36523
ID:
200036523
10.

P. pacificus young adults: Exposed to Serratia marcescens versus exposed to E. coli OP50 : 4 hours

(Submitter supplied) Transcriptional profiling of P. pacificus young adult worms exposed to pathogen Serratia marcescens for 4 hours versus age-matched worms exposed to control lab food E. coli OP50. The goal was to identify genes regulated in response to pathogen. The broader goal of study was to study evolution of pathogen response by comparing this expression profile to that obtained by exposing the nematode C. elegans to the same pathogen. more...
Organism:
Pristionchus pacificus
Type:
Expression profiling by array
Platform:
GPL14372
4 Samples
Download data: GPR
Series
Accession:
GSE36521
ID:
200036521
11.

P. pacificus young adults: Exposed to Staphylococcus aureus versus exposed to E. coli OP50 : 4 hours

(Submitter supplied) Transcriptional profiling of P. pacificus young adult worms exposed to pathogen Staphylococcus aureus for 4 hours versus age-matched worms exposed to control lab food E. coli OP50. The goal was to identify genes regulated in response to pathogen. The broader goal of study was to study evolution of pathogen response by comparing this expression profile to that obtained by exposing the nematode C. elegans to the same pathogen. more...
Organism:
Pristionchus pacificus
Type:
Expression profiling by array
Platform:
GPL14372
3 Samples
Download data: GPR
Series
Accession:
GSE36519
ID:
200036519
12.

P. pacificus young adults: Exposed to Bacillus thuringiensis DB27 versus exposed to E. coli OP50 : 4 hours

(Submitter supplied) Transcriptional profiling of P. pacificus young adult worms exposed to pathogen Xenorhabdus nematophila for 4 hours versus age-matched worms exposed to control lab food E. coli OP50. The goal was to identify genes regulated in response to pathogen. The broader goal of study was to study evolution of pathogen response by comparing this expression profile to that obtained by exposing the nematode C. elegans to the same pathogen. more...
Organism:
Pristionchus pacificus
Type:
Expression profiling by array
Platform:
GPL14372
4 Samples
Download data: GPR
Series
Accession:
GSE36517
ID:
200036517
13.

P. pacificus and C. elegans exposed to various pathogens

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Pristionchus pacificus; Caenorhabditis elegans
Type:
Expression profiling by array
Platforms:
GPL10094 GPL14372
30 Samples
Download data: GPR
Series
Accession:
GSE36636
ID:
200036636
14.

P. pacificus : Dauers and Dauer-Exit at 12 hour time-point vs. Mix-stage worms

(Submitter supplied) Transcriptional profiling of P. pacificus worms from (1) dauer stage, or (2) dauer-exit at 12 hours stage, compared to mix-stage worms as a common reference. The goal was to determine genes regulated during dauer development and recovery or exit from dauer stage. This data was then compared to data generated for corresponding developmental stages in the C. elegans (see NCBI GEO series GSE30977) , to study evolution of developmental pathways regulating dauer development.
Organism:
Pristionchus pacificus
Type:
Expression profiling by array
Platform:
GPL14372
7 Samples
Download data: GPR
Series
Accession:
GSE31861
ID:
200031861
15.

Repertoire and evolution of miRNA genes in four divergent nematode species

(Submitter supplied) We have performed small RNA sequencing in the nematodes Caenorhabditis elegans, C. briggsae, C. remanei and Pristionchus pacificus, which have diverged up to 400 million years ago, to establish the repertoire and evolutionary dynamics of miRNAs in these species. In addition to previously known miRNA genes from C. elegans and C. briggsae we demonstrate expression of many of their homologs in C. remanei and P. more...
Organism:
Caenorhabditis remanei; Pristionchus pacificus; Caenorhabditis briggsae; Caenorhabditis elegans
Type:
Non-coding RNA profiling by high throughput sequencing
4 related Platforms
4 Samples
Download data: FA, QUAL
Series
Accession:
GSE15169
ID:
200015169
16.

Illumina NovaSeq 6000 (Pristionchus pacificus)

Organism:
Pristionchus pacificus
1 Series
2 Samples
Download data
Platform
Accession:
GPL34494
ID:
100034494
17.

Illumina NextSeq 500 (Pristionchus pacificus)

Organism:
Pristionchus pacificus
1 Series
8 Samples
Download data
Platform
Accession:
GPL34493
ID:
100034493
18.

Illumina HiSeq 2000 (Pristionchus pacificus)

Organism:
Pristionchus pacificus
3 Series
14 Samples
Download data
Platform
Accession:
GPL16154
ID:
100016154
19.

AB SOLiD System 3.0 (Pristionchus pacificus)

Organism:
Pristionchus pacificus
1 Series
1 Sample
Download data
Platform
Accession:
GPL16153
ID:
100016153
20.

Illumina Genome Analyzer II (Pristionchus pacificus)

Organism:
Pristionchus pacificus
1 Series
1 Sample
Download data
Platform
Accession:
GPL16152
ID:
100016152
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