Minke whale gut metagenome
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ABSTRACT:
PROVIDER: PRJEB23480 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Metagenomic analysis of the minke whale (Balaenoptera acutorostrata) gut microbiome
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Project description:Balaenoptera acutorostrata (minke whale) genome assembly, mBalAcu1
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Project description:Balaenoptera acutorostrata (minke whale), genomic and transcriptomic data
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Project description:Balaenoptera acutorostrata (minke whale) genome assembly, mBalAcu1, alternate haplotype
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Project description:Balaenoptera musculus (Blue Whale) and Balaenoptera physalus (Fin Whale) Genome sequencing and assembly
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Project description:The present study examines the effects of whale meat extract (WME) supplementation on the senescence-accelerated mouse prone 8 (SAMP8) model at the level of learning memory formation and gene expression profiles genome-wide. Our present study builds up on these previous studies by focusing on two sets of experiments examining WME-supplemented diet, on SAMP8 and SAMR1 (senescence-accelerated mouse resistant 1) learning and memory deficits (experiment 1) and whole-genome DNA microarray-based transcriptomics profiling in conjunction with Ingenuity Pathway Analysis (IPA) (experiment 2). We also examined the SAMP8 and SAMR1 mice fed with the regular (control; low-safflower oil, LSO) diets specifically to know the gene profiles in the brain of the SAMP8 mouse. Results revealed that WME supplementation on SAMP8 mouse resulted in an increase in the level of learning memory formation and positive changes in the transcriptome of the brain, suggested through the observation of recovery of gene expressions in the SAMP8 model over the not-supplemented mouse. 6-week-old mice (SAMP8 and SAMR1; CLEA, Tokyo, Japan) were housed at the Animal Institution Facility in Showa University, and maintained in individual cages in a ventilated animal room with controlled temperature and relative humidity under a 12-h light: 12-h dark regime (8:00 AM, lights turned on). Mice were fed chow (CE-2, CLEA Japan) and tap water ad libitum until 24-weeks-old. Then, 24-week-old SAMs mice were given experimental diet, LSO diet as a control diet and WME-supplemented diet, both in a powder form. The WME was made from red meat of Antarctic minke whale (Balaenoptera bonaerensis), taken from the Japanese Whale Research Program under Special Permit in the Antarctic-Phase II in 2009/2010 by heat, enzyme and drying treatments. The quality standard of WE were measured by Marugei Co. Ltd. (Hyogo, Japan). SAMP8 mice were randomly given LSO or WME diet, respectively. SAMR1 mice were given LSO diet only until 50-weeks-old. The behavioral tests were performed at the timing of 49-weeks-old for 8 days. At the end of the experiment (50 weeks of age) following the behavioral analysis (open field test, Y-maze test, new object recognition test (NOR), and water-filled multiple T-maze) and the last day of the feeding, the mice were removed from their cages, decapitated and their brains carefully removed on ice. The whole brains were quickly frozen in liquid nitrogen in a sterile freeze tube and stored at -80ºC till extraction of total RNA followed by DNA microarray analysis using a whole-genome mouse chip (Agilent-014868, 4 x 44K (G4122F)) with two-color dye-swap approach in conjunction with IPA bioinformatic analysis. All animal studies were conducted in accordance with the Standards Relating to the Care Management of Experimental Animalsâ (Notice No. 6 of the Office of Prime Minister dated March 27, 1980) and with approval from the Animal Use Committee of Showa University (Approval Number: #04093).
2016-07-03 | E-GEOD-76459 | biostudies-arrayexpress
Project description:Gut microbiome of stranded whale calves Targeted loci environmental
| PRJNA421279 | ENA
Project description:This series includes 3 microarrays used to detect SWCoV1, a novel group III coronavirus in Delphinapterus leucas (Beluga whale) liver. The series includes 2 control whale livers and 1 whale liver containing SWCoV1.
2008-04-15 | E-GEOD-9238 | biostudies-arrayexpress
Project description:The gut microbiome is significantly altered in inflammatory bowel diseases, but the basis of these changes is not well understood. We have combined metagenomic and metatranscriptomic profiling of the gut microbiome to assess changes to both bacterial community structure and transcriptional activity in a mouse model of colitis. Gene families involved in microbial resistance to oxidative stress, including Dps/ferritin, Fe-dependent peroxidase and glutathione S-transferase, were transcriptionally up-regulated in colitis, implicating a role for increased oxygen tension in gut microbiota modulation. Transcriptional profiling of the host gut tissue and host RNA in the gut lumen revealed a marked increase in the transcription of genes with an activated macrophage and granulocyte signature, suggesting the involvement of these cell types in influencing microbial gene expression. Down-regulation of host glycosylation genes further supports a role for inflammation-driven changes to the gut niche that may impact the microbiome. We propose that members of the bacterial community react to inflammation-associated increased oxygen tension by inducing genes involved in oxidative stress resistance. Furthermore, correlated transcriptional responses between host glycosylation and bacterial glycan utilisation support a role for altered usage of host-derived carbohydrates in colitis. Complementary RNA-seq and DNA-seq data sets of the microbiome from this study have also been deposited at ArrayExpress under accession number E-MTAB-3562 ( http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3562/ ).
2015-05-22 | E-MTAB-3590 | biostudies-arrayexpress