Ontology highlight
ABSTRACT:
PROVIDER: PRJNA795284 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17477900_1.fastq.gz | Fastqsanger.gz | |||
| SRR17477900_2.fastq.gz | Fastqsanger.gz | |||
| SRR17477901_1.fastq.gz | Fastqsanger.gz | |||
| SRR17477901_2.fastq.gz | Fastqsanger.gz | |||
| SRR17477902_1.fastq.gz | Fastqsanger.gz |
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Project description:We sequenced mRNA from 9 liver samples of juvenile largemouth bass (Micropterus salmoides) taken from different lead concentration exposure treatment fish and control fish to investigate the transcriptome and comparative expression profiles of largemouth bass liver undergoing lead exposure.
2019-01-12 | GSE124986 | GEO
Project description:In the present study, we used NGST to characterize mRNA-seq of control-, moderate hypoxia-treated and severe hypoxia-treated Micropterus salmoides livers to elucidate the molecular mechanisms of hypoxia adaptation. This is the first report on integrated analysis of the tissue specific and temporal changes in gene expression in largemouth bass (Micropterus salmoides) exposed to hypoxia could reveal mechanisms of hypoxia adaptation. We provide a good case study with which to analyse mRNA expression and profile non-model fish species using NGST.
2020-07-22 | GSE134616 | GEO
Project description:White bass (Morone chrysops) are a popular sportfish throughout the southern United States, and one parent of the commercially successful hybrid striped bass (M. chrysops x M. saxatilis). Currently, white bass are cultured using diets formulated for other carnivorous fish, such as largemouth bass (Micropterus salmoides) or hybrid striped bass and contain a significant percentage of marine fish meal. Since there are no studies regarding the utilization of alternative proteins in this species, we evaluated global gene expression of white bass fed diets in which fish meal was partially or totally replaced by various combinations of soybean meal, poultry by-product meal, canola meal, soy protein concentrate, wheat gluten, or a commercial protein blend (Pro-Cision). Significant differential expressed genes and gene ontology of pairwise comparisons between control diet and each test diet are presented and discussed.
2024-02-14 | GSE220235 | GEO
Project description:Long noncoding RNAs (lncRNAs) are non-protein coding RNAs with a length of more than 200 bp, which play a vital regulatory role in intestinal immunity. Exposure to high temperature leads to death in many fish species, which is implicated in fish enteritis. Our study showed that fish enteritis was induced by acute heat stress. To date, which lncRNAs are participated in this process is still unclear. In the present study, based on the intestinal sequencing data of largemouth bass Micropterus salmoides, a total of 347,351,492 clean reads were generated from six cDNA libraries. Among them, 3399 novel lncRNA transcripts from 2488 lncRNA genes were identified. As expected, these lncRNAs exhibited shorter transcript lengths than protein-coding genes similar to those lncRNAs reported from other fish species. In total, 216 novel lncRNAs were differentially expressed (DE) in largemouth bass intestine (absolute log2 fold change > 2 and p-value < 0.05) and that 210 neighboring genes were cis-regulated by these DE-lncRNAs. An analysis of GO/KEGG enrichment showed that most of these cis-genes seemed to be significantly enriched in immune regulation (p < 0.05) and lncRNA MSTRG.8573 had an important role in regulating jak-stat signaling pathway during this process. Through this study, we showed a catalog of novel DE-lncRNAs involved in the occurrence of enteritis in largemouth bass under acute heat stress, which could provide some useful references by regulating lncRNAs to solve the heat stress-induced fish enteritis for further studies.
2024-07-01 | GSE236409 | GEO
Project description:A novel custom microarray for largemouth bass (Micropterus salmoides) was designed from sequences obtained from a normalized cDNA library using the 454 Life Sciences GS-20 pyrosequencer. The GS-20 yielded in excess of 58 million bases of high-quality sequence. The sequence information was combined with 2,616 reads obtained by traditional suppressive subtractive hybridizations to derive a total of 31,391 unique sequences. Annotation and coding sequences were predicted for these transcripts where possible. 16,350 annotated transcripts were selected as target sequences for the design of the custom largemouth bass oligonucleotide microarray. The microarray was validated by examining the transcriptomic response in male largemouth bass exposed to 17 -oestradiol. Transcriptomic responses were assessed in liver and gonad, and indicated gene expression profiles typical of exposure to oestradiol. The results demonstrate the potential to rapidly create the tools necessary to assess large scale transcriptional responses in non-model species, paving the way for expanded impact of toxicogenomics in ecotoxicology. Keywords: E2 exposure, array validation This experiment tested two organs - liver and gonad from either E2-exposed or control fish, 4 fish (biological replicates) per treament (control and E2).
2010-05-25 | E-GEOD-10693 | biostudies-arrayexpress
Project description:In this study, both male and female sexually regressed largemouth bass (Micropterus salmoides) (LMB) were fed a nominal concentration of 3.0 mg dieldrin/kg in feed for 60 days. A third group of male LMB was fed both 3.0 mg dieldrin/kg dieldrin and 0.7 mg E2/kg in feed. E2 was used as a model compound to elicit estrogenic effects via ER signaling.
2011-04-17 | GSE27963 | GEO
Project description:A novel custom microarray for largemouth bass (Micropterus salmoides) was designed from sequences obtained from a normalized cDNA library using the 454 Life Sciences GS-20 pyrosequencer. The GS-20 yielded in excess of 58 million bases of high-quality sequence. The sequence information was combined with 2,616 reads obtained by traditional suppressive subtractive hybridizations to derive a total of 31,391 unique sequences. Annotation and coding sequences were predicted for these transcripts where possible. 16,350 annotated transcripts were selected as target sequences for the design of the custom largemouth bass oligonucleotide microarray. The microarray was validated by examining the transcriptomic response in male largemouth bass exposed to 17 -oestradiol. Transcriptomic responses were assessed in liver and gonad, and indicated gene expression profiles typical of exposure to oestradiol. The results demonstrate the potential to rapidly create the tools necessary to assess large scale transcriptional responses in non-model species, paving the way for expanded impact of toxicogenomics in ecotoxicology. Keywords: E2 exposure, array validation
2008-08-01 | GSE10693 | GEO
Project description:Largemouth Bass (Micropterus salmoides) Transcriptome
| PRJNA320202 | ENA
Project description:Intensive aquaculture and environmental changes will inevitably lead to hypoxic stress for largemouth bass (Micropterus salmoides). To better understand the hypoxia responds mechanisms of largemouth bass, we compared the miRNA profile in liver under different environmental DO to determine which miRNAs are most affected during hypoxia. A total of 266 miRNAs were identified, and 84 miRNAs were differentially expressed compared with in control group. GO and KEGG analysis indicated that the miRNAs may play important roles in environment information processing. Specifically, we considered the VEGF signaling pathway, Phosphatidylinositol signaling system and MAPK signaling pathway, the results show that, the 13 miRNAs (miR-15b-5p, miR-30a-3p, miR-133a-3p, miR-19d-5p, miR-1288-3p, miR456, miR-96-5p, miR-23a-3p, miR-23b, miR-214, miR-24, miR-20a-3p and miR-2188-5p) involved in these three pathways are significantly down-regulated during hypoxia stress. And 12 target genes of these miRNAs were showed a higher degree of expression. We found the obvious negative correlation between miRNA and their target mRNAs, providing several miRNA-mRNA interaction networks in largemouth bass in response to hypoxia. Although relatively little information is currently available concerning the biological function of miRNAs identified to date, we strongly suggest that miRNAs play an important role in modulating gene expression involved in the physiological response to hypoxic stress in the fish liver.
2021-01-20 | GSE143641 | GEO
Project description:In this study, both male and female sexually regressed largemouth bass (Micropterus salmoides) (LMB) were fed a nominal concentration of 3.0 mg dieldrin/kg in feed for 60 days. A third group of male LMB was fed both 3.0 mg dieldrin/kg dieldrin and 0.7 mg E2/kg in feed. E2 was used as a model compound to elicit estrogenic effects via ER signaling. There were four samples analyzed for 1) control males 2) control females 3) males fed 3 mg/kg dieldrin 4) females fed 3.0 mg/kg dieldrin, and 5) males fed 3.0 mg/kg dieldrin + 0.7 mg/kg E2. There was a total of 20 microarrays and sample processed.
2011-04-17 | E-GEOD-27963 | biostudies-arrayexpress