Ontology highlight
ABSTRACT:
PROVIDER: PRJNA996530 | ENA |
REPOSITORIES: ENA
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Project description:Physiological changes in response to environmental cues are not easily documented in pelagic copepods using traditional methods. Molecular biological tools provide new approaches to the investigation of difficult to sample organisms such as oceanic zooplankton. Here, we describe the development of a species-specific microarray for high-throughput studies of the physiological ecology of the North Atlantic copepod Calanus finmarchicus. An EST database was generated for this species using a normalized cDNA library derived from adult and sub-adult individuals from the Gulf of Maine. Sequence data were clustered into contigs and annotated using Blastx. Target transcripts were selected, and unique, 50 base-pair long, oligomer probes were designed and synthesized for 995 genes. Bioinformatic processing using Blast2GO software provided detailed information on gene function. The selected targets include a broad representation of biological processes, cellular components, and molecular functions. The microarray was tested on both experimental and ecological samples, i.e. food abundance and two morphotypes exhibiting distinct lipid stores, respectively. Differentially regulated transcripts were identified for both comparisons. Two comparisons were performed: 1) Lipid-rich (fat) and Lipid-poor (thin) morphotypes 2) Copepods kept under high food and low food experimental conditions
2012-03-23 | E-GEOD-34322 | biostudies-arrayexpress
Project description:Our data demonstrate the suitability of target capture technology for purifying very low quantities of Leptospira DNA from biological samples where the human genome is in vast excess. This enables deep sequencing of partial Leptospira genomes directly from clinical samples using next generation technologies and genotyping.
2022-05-23 | E-MTAB-11667 | biostudies-arrayexpress
Project description:The copepod, Calanus finmarchicus is a keystone species for the North Atlantic. Because of recent changes in the geographic distribution of this species, there are questions as to how this organism responds physiologically to environmental cues. Molecular techniques allow for examination and new understanding of these physiological changes. Here, we describe the development of a microarray for high-throughput studies of the physiological ecology of C. finmarchicus. An EST database was generated for this species using a normalized cDNA library derived from adult and sub-adult individuals. Sequence data were clustered into contigs and annotated using Blastx. Target transcripts were selected, and unique, 50 base-pair, oligomer probes were generated for 995 genes. Blast2GO processing provided detailed information on gene function. The selected targets included broad representation of biological processes, cellular components, and molecular functions. The microarray was tested in two sets of comparisons: adult females maintained at different food concentrations and field-caught sub-adults showing differences in lipid storage. Up-regulated and down-regulated transcripts were identified for both comparisons. Only a small subset of the genes up-regulated in low food individuals were also up-regulated in lipid-poor animals; no overlap was seen between the genes down-regulated in the two comparisons.
2012-03-23 | GSE34322 | GEO
Project description:In order to illustrate the epigenetic heterogeneity, versatile tools of single-cell ChIP-seq(scChIP-seq) are necessary to meet the convenience and accuracy. Here, we develop MobiChIP, a compatible ChIP-seq library construction method based current sequencing platform with single cell level. As a novel capture strategy, MobiChIP is efficient to capture the fragments from tagmented nuclei of numerous species and execute the mixing of samples from different tissues or species. Especially, this strategy enables the flexible sequencing manipulation and sufficient nucleosome amplification without customized sequencing primers. MobiChIP reveals the landscape of chromatin regulation regions with active(H3K27ac) and repressive(H3K27me3) histone modification markers in peripheral blood mononuclear cells (PBMCs), and accurately unveiled the epigenetic repression of hox gene cluster in PBMCs than ATAC-seq. Meanwhile, we complete the bioinformatics pipeline to integrate the scChIP-seq and scRNA-seq data to illustrate the cellular epigenetic and genetic heterogeneity.
2024-10-27 | GSE273350 | GEO