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Calanus sinicus

ABSTRACT: Identification of molecular markers associated with starvation or diapause in copepods

PROVIDER: PRJDB7229 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR144873_1.fastq.gz	Fastqsanger.gz
	DRR144873_2.fastq.gz	Fastqsanger.gz
	DRR144874_1.fastq.gz	Fastqsanger.gz
	DRR144874_2.fastq.gz	Fastqsanger.gz
	DRR144875_1.fastq.gz	Fastqsanger.gz

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Calanus sinicus

Project description:Calanus sinicus Transcriptome or Gene expression

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Calanus sinicus

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Testing of the physiological microarray for Calanus finmarchicus by using experimental and field collected samples

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

RNA-seq of the diatom Skeletonema marinoi grown in the presence or absence of the copepod Calanus finmarchicus

Project description:The experiment was designed to study the transcriptomic response of the centric diatom Skeletonema marinoi to the presence of cues from the grazer Calanus finmarchicus. Samples were collected in triplicate after 65 and 89 hours of exposure of diatom cells to the copepods. Control samples with no copepods were collected at the same time points.

2018-03-29 | E-MTAB-6076 | biostudies-arrayexpress

Transcriptome sequencing and de novo analysis of the copepod Calanus sinicus using 454 GS FLX.

Project description:BackgroundDespite their species abundance and primary economic importance, genomic information about copepods is still limited. In particular, genomic resources are lacking for the copepod Calanus sinicus, which is a dominant species in the coastal waters of East Asia. In this study, we performed de novo transcriptome sequencing to produce a large number of expressed sequence tags for the copepod C. sinicus.ResultsCopepodid larvae and adults were used as the basic material for transcriptome sequencing. Using 454 pyrosequencing, a total of 1,470,799 reads were obtained, which were assembled into 56,809 high quality expressed sequence tags. Based on their sequence similarity to known proteins, about 14,000 different genes were identified, including members of all major conserved signaling pathways. Transcripts that were putatively involved with growth, lipid metabolism, molting, and diapause were also identified among these genes. Differentially expressed genes related to several processes were found in C. sinicus copepodid larvae and adults. We detected 284,154 single nucleotide polymorphisms (SNPs) that provide a resource for gene function studies.ConclusionOur data provide the most comprehensive transcriptome resource available for C. sinicus. This resource allowed us to identify genes associated with primary physiological processes and SNPs in coding regions, which facilitated the quantitative analysis of differential gene expression. These data should provide foundation for future genetic and genomic studies of this and related species.

| S-EPMC3646036 | biostudies-literature

Transcriptome responses in copepods Calanus glacialis exposed to phenanthrene and benzo[a]pyrene

Project description:The arctic ecosystems are increasingly exposed to pollution particularly from offshore petroleum extraction-related activities. The objective of the study is to map transcriptome responses in copepods of the arctic region in response to PAHs phenanthrene (Phe) and benzo[a]pyrene (BaP) found in crude-oil contaminants.

2021-10-01 | E-MTAB-10911 | biostudies-arrayexpress

Transcriptome responses in copepods Calanus finmarchicus exposed to phenanthrene and benzo[a]pyrene

2021-10-01 | E-MTAB-10917 | biostudies-arrayexpress

Transcriptome responses in copepods Calanus hyperboreus exposed to phenanthrene and benzo[a]pyrene

2021-10-01 | E-MTAB-10918 | biostudies-arrayexpress