Ontology highlight
ABSTRACT:
PROVIDER: PRJNA601124 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10898215.fastq.gz | Fastqsanger.gz | |||
| SRR10898216.fastq.gz | Fastqsanger.gz | |||
| SRR10898217.fastq.gz | Fastqsanger.gz | |||
| SRR10898218.fastq.gz | Fastqsanger.gz | |||
| SRR10898219.fastq.gz | Fastqsanger.gz |
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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.
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Project description:This study examines the genomic effects of dieldrin in the hypothalamus of largemouth bass. Dieldrin is an insectide and organic pollutant.
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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).
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