Ontology highlight
ABSTRACT:
PROVIDER: PRJNA699474 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| JAFFGV01.dat.gz | Other | |||
| JAFFGV01.fasta.gz | Fasta.gz | |||
| JAFFGV01.master.dat | Other | |||
| SRR13632763_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 6 |
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Project description:Thaleichthys pacificus isolate:New Westminster Genome sequencing and assembly
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Project description:Pristionchus pacificus has emerged as a valuable model system for comparative and evolutionary-developmental biology (evo-devo) studies alongside the classic model nematode C. elegans. Previous studies have identified a lack of conservation of genetic networks underlying conserved traits, referred to as developmental systems drift. However, the conservation – or lack thereof – of epigenetic pathways which regulate development have not been investigated. In the manuscript associated with this study, we present an “epigenetic toolkit” for P. pacificus and C. elegans to compare and contrast epigenetic pathways. Assembly of this toolkit was done by identifying orthologous genes, including the “writers” and “erasers” of histone modifications. To complement this evolutionary approach, here we produce a data set of the suite of histone modifications present in P. pacificus.
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Project description:Ixodes pacificus, the vector of Borrelia burgdorferi (Bb) on the west coast, feeds on a variety of hosts including rodents, birds, and lizards. While rodents are reservoirs for Bb and can infect juvenile ticks, lizards are Bb-refractory. Despite the range of bloodmeals for I. pacificus, it is undetermined how larval host bloodmeal identity may affect future nymphal vector competence. Here, we conducted a transcriptome analysis on I. pacificus to determine whether and through what mechanisms host bloodmeal history affects vector competency of I. pacificus for the Lyme disease pathogen.
2021-04-27 | GSE173109 | GEO
Project description: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).
2012-04-18 | GSE37337 | GEO
Project description: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). One-condition experiments. Germline ablated P. pacificus worms exposed to S. marcescens for 8 hours versus germline-ablated P. pacificus exposed to the control E. coli OP50. 4 biological replicates for each condition, including 2 dye-swaps.
2012-04-17 | E-GEOD-37337 | biostudies-arrayexpress
Project description: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. pacificus, and identified in total more than 100 novel expressed miRNA genes, the majority of which belong to P. pacificus. More than half of all identified miRNA genes were found to be conserved at the seed level in all four nematode species, whereas only a few miRNAs appear to be species-specific. In our compendium of miRNAs we observed evidence for known mechanisms of miRNA evolution, including antisense transcription and arm switching, as well as miRNA family expansion through gene duplication. In addition, we identified a novel mode of miRNA evolution, termed ‘hairpin shifting’, in which an alternative hairpin is formed with up- or downstream sequences, leading to shifting of the hairpin and creation of novel miRNA* species. Finally, we identified 21U-RNAs in all four nematodes, including P. pacificus, where the upstream 21U-RNA motif is more diverged. However, the genomic distribution of 21U-RNA clusters in P. pacificus appears more scattered throughout the genome as compared to C. elegans. The identification and systematic analysis of small RNA repertoire in four nematode species described here provides a valuable resource for understanding the evolutionary dynamics of miRNA-mediated gene regulation.
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Project description: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. One-condition experiments. Germline ablated P. pacificus versus un-ablated wild-type P. pacificus. Developmental stage = Young adults. Food source = E. coli OP50 for both conditions. 3 biological replicates for each condition, including 2 dye-swaps.
2012-04-17 | E-GEOD-37331 | biostudies-arrayexpress