Ontology highlight
ABSTRACT:
PROVIDER: PRJNA898590 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22198838_1.fastq.gz | Fastqsanger.gz | |||
| SRR22198838_2.fastq.gz | Fastqsanger.gz | |||
| SRR22198839_1.fastq.gz | Fastqsanger.gz | |||
| SRR22198839_2.fastq.gz | Fastqsanger.gz | |||
| SRR22198840_1.fastq.gz | Fastqsanger.gz |
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Project description:Streptococcus agalactiae (Lancefield’s group B Streptococcus, GBS) is a major bacterial species of genus Streptococcus and has medical and veterinary importance by affecting mainly humans (Maione et al., 2005; Johri et al., 2006), cattle (Keefe, 1997) and fish (Mian et al., 2009). The GBS is the most important pathogen for the Nile tilapia, a global commodity of the aquaculture sector, causing outbreaks of septicemia and meningoencephalitis (Hernández et al., 2009; Mian et al., 2009). This study aimed to evaluate the global abundancy of proteins among the main genotypes of GBS isolated from fish identified in Brazil using a label free shotgun liquid chromatography-ultra definition mass spectrometry (LC-UDMSE) approach and to compare the differential expression of proteins identified between isolates from fish and human.
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Project description:Transcriptome analysis of Streptococcus agalactiae (group B Streptococcus) grown under control conditions or coincubated with serine hydroxamate to induce the bacterial stringent response
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Project description:Elongation of very long-chain fatty acids protein 6 (Elovl6) is a crucial enzyme in the synthesis of endogenous fatty acids, which participates in the energy balance and metabolic diseases. The main objective of this study was to explore the molecular characterization of elovl6 and study regulatory mechanism of elovl6 on male Nile tilapia, Oreochromis niloticus. In the present study, the full-length cDNA of Nile tilapia elovl6 was 2255 bp, comprising a 5'-UTR of 193 bp, an ORF of 810 bp, and a 3'-UTR of 1252 bp, encoding 269 amino acids that possesses the characteristic features of Elovl proteins. The transcription expression of elovl6 transcripts showed differential expression in different tissues and fed with different lipid sources diet. Antisense RNA technology was used to knock-down elovl6 in Nile tilapia. Compared with the control treatments (transfected with ultrapure water (control) or the blank expression vector (negative control)), knockdown elovl6 altered hepatic morphology, Long chain fatty acid synthesis, fatty acid oxidation, lead to excess fat deposition in the liver, ultimately cause abnormal glucose/lipid metabolism in male Nile tilapia. Transcriptome analyses (AGPAT2 knock-down vs. negative control) revealed a total of 5877 differentially expressed genes (DEGs). Transcriptome analyses revealed DEGs were greatly involved in some signaling pathways, such as PPAR signaling pathway, fatty acid degradation, glycolysis/gluconeogenesis, and insulin signaling pathway, which were related to lipid and glucose metabolism. We used qRT-PCR to verify the mRNA expression changes of 13 DEGs in related signaling pathways. Our results demonstrate that knock-down of elovl6 in tilapia blocks the synthesis of oleic acid and leads to abnormal glucose/lipid metabolism.
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Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived head kidney leukocytes transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods: The leukocytes of tilapia were treated with PBS(A), heat-killed S.agalactiae(B), sodium nitrite(C) or heat-killed S.agalactiae and sodium nitrite co-treatment(D),respectively. Then the mRNA profiles were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level. qRT–PCR validation was performed using SYBR Green assays Results: Using an optimized data analysis workflow, we mapped about 40 million sequence reads per sample to the tilapia genome in the head kidney leukocytes of tilapia.10 candidate genes were randomly selected to quantify their mRNA expression levels of treatment and control groups by q-PCR. Results showed that the Pearson’s correlation coefficient between q-PCR and RNA-seq was 0.939. Total of 6173 transcripts were differently expressed, with a fold change ≥2 and p value <0.05. Conclusions: Our study represents the first detailed analysis of tilapia head kidney leukocytes transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a fish cell. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
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Project description:We report an association of DNA hydroxymethylation profiling at single nucleotide resolution with gene expression in the fast muscle of Nile tilapia.
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