Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1102420 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28746533_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR28746534_1.fastq.gz | Fastqsanger.gz | |||
| SRR28746534_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 3 of 3 |
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Project description:Eubalaena glacialis (North Atlantic right whale) genome, mEubGla1, haplotype 1
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Project description:An 8X15k oligonucleotide microarray was developed consisting of 2334 E. glacialis probes and 2166 Tursiops truncatus probes and used to measure the transcriptome level effects of right whale kidney fibroblast cells exposed to cadmium. Cells were exposed to three concentrations of cadmium chloride (CdCl2) for three exposure times. Cells exposed to 10-6M CdCl2 for 4 hours and 24 hours showed upregulated genes involved in protection from metal toxicity, oxidative stress, protein renaturation, apoptosis inhibition, and several regulators of cellular processes. Downregulated genes represented a suite of functions including cell proliferation, transcription regulation, actin polymerization, and stress fiber synthesis. The collection of differentially expressed genes in this study support proposed mechanisms of cadmium-induced apoptosis such as mitochondrial membrane potential collapse, reactive oxygen species (ROS) influx, and cell cycle arrest. The results confirm the right whale microarray as a reproducible tool in measuring differentiated gene expression and should be a valuable asset for transcriptome analysis of other baleen whales and potential health assessment protocols.
2009-08-03 | GSE17457 | GEO
Project description:An 8X15k oligonucleotide microarray was developed consisting of 2334 E. glacialis probes and 2166 Tursiops truncatus probes and used to measure the transcriptome level effects of right whale kidney fibroblast cells exposed to cadmium. Cells were exposed to three concentrations of cadmium chloride (CdCl2) for three exposure times. Cells exposed to 10-6M CdCl2 for 4 hours and 24 hours showed upregulated genes involved in protection from metal toxicity, oxidative stress, protein renaturation, apoptosis inhibition, and several regulators of cellular processes. Downregulated genes represented a suite of functions including cell proliferation, transcription regulation, actin polymerization, and stress fiber synthesis. The collection of differentially expressed genes in this study support proposed mechanisms of cadmium-induced apoptosis such as mitochondrial membrane potential collapse, reactive oxygen species (ROS) influx, and cell cycle arrest. The results confirm the right whale microarray as a reproducible tool in measuring differentiated gene expression and should be a valuable asset for transcriptome analysis of other baleen whales and potential health assessment protocols. 35 Samples were analyzed representing 3 biological replicates for each treatment and corresponding controls except treatment 4hour_0.01uMCdCl2 had only two biological replicates due to spot intensity values. There are 3 spot replicates/probe on the array, along with Agilent control grid specific for 8X15K arrays, and 4 Karenia brevis sequences used as a negative control (K.brevis.chlorophyllA/Bbindingprotein, K.brevis.flavodoxin,K.brevis.photolyase,K.brevis.photosystemcoreprotein).
2009-08-03 | E-GEOD-17457 | biostudies-arrayexpress
Project description:Transcriptome Analysis of North Atlantic Right Whale Kidney Fibroblast Cell line exposed to cadmium
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Project description:Basque whalers were active in the North Atlantic between the 11th and 18th. In the 16th and 17th c., they focused their attention to the coasts of Labrador and the Gulf of St. Lawrence, establishing shore stations from where they launched boats for chasing whales. On shore, they proceeded to render the blubber into oil by boiling it in large trypots. The residual blubber and remaining tissues were then used as fuel to boil more blubber. When the fire pit was full, the cinders were shoveled out, and the process began anew with new materials. Fist-sized lumps of cinder found at Bonne Espérance-4 (EiBk-61), a 16th Basque whaling site on the Quebec Lower North Shore, were sampled for proteomics analysis, to detect potential remains of whale tissues in the cinder. A simple protocol was employed for rapidly processing samples for nanoLC-MS/MS analysis. Out of 10 spots sampled on two lumps, materials recovered from one successfully yielded whale proteins. The study confirmed the presence of blubber and muscle remains (42 protein groups, including proteins such as myosin, myoglobin and hemoglobin) as well as baleen remains identified by cuticular keratins (12 protein groups, and up to 46 % protein coverage on type I keratin). Baleen, abundantly found at the site, was likely also used as fuel; based on keratin markers, the baleen belonged to a Balaenidae species. The processing of bowhead whale tissue was substantiated by specific peptides from myoglobin and obscurin, a result consistent with the targeting of bowhead whale by Basque whalers.
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Project description:Pygmy right whale Evolutionary Genomics
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