Saiga mass mortality
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB28184 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2734400_1.fastq.gz | Fastqsanger.gz | |||
| ERR2734400_2.fastq.gz | Fastqsanger.gz | |||
| ERR2734401_1.fastq.gz | Fastqsanger.gz | |||
| ERR2734401_2.fastq.gz | Fastqsanger.gz | |||
| ERR2734402_1.fastq.gz | Fastqsanger.gz |
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Project description:Mass mortality of Saiga antelopes in Kazakhstan, results of NGS investigation
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Project description:The search of the molecular process associated with development and metabolism of muscle mass is still actual, what in humans is related to muscle modification after endurance training exercises. In turn in farm animals, the high meat content in carcasses delivers higher economic benefit. Over a few recent years, scientists using next-generation-sequencing (NGS) methods attempted to indicate proteins/genes engaged in muscle mass development. The aim of the present study was to show mRNA degradome signals that could be characteristic for molecular processes associated with muscle development in pigs and indicate the miRNA regulation controlling this process based using also NGS technology. The preliminary results exhibited that the huge amount of miRNAs regulate gene expression at the different molecular level than mRNA degradation. Moreover, the study found significant differences between investigated pig breeds. The results often were opposite for Pietrain breed that could be related to differences in muscle fibre composition and their microstructure. The present study showed an interesting dependence between miRNA and their targets - the most of transcripts found as being degraded, were associated with controlling muscle mass development such as ENO3, CKM, CRYAB and ADAM19. In turn, performed PAREsnip analysis showed that only a small percentage of identified degraded transcripts was associated with miRNA regulation, what suggested a different mechanism of mRNA degradation. Nevertheless, the complete view of miRNA regulation could be obtained in the more advanced study, which would employ miRNA transfection procedure in muscle tissue cell culture that could be a subject of further research.
2019-04-12 | GSE129681 | GEO
Project description:Many new alternative splice forms have been detected at the transcript level using next generation sequencing (NGS) methods, especially RNA-Seq, but it is not known how many of these transcripts are being translated. Leveraging the unprecedented capabilities of NGS, we collected RNA-Seq and proteomics data from the same cell population (Jurkat cells) and created a bioinformatics pipeline that builds customized databases for the discovery of novel splice-junction peptides. Results: Eighty million paired-end Illumina reads and ~500,000 tandem mass spectra were used to identify 12,873 transcripts (19,320 including isoforms) and 6,810 proteins. We developed a bioinformatics workflow to retrieve high-confidence, novel splice junction sequences from the RNA data, translate these sequences into the analogous polypeptide sequence, and create a customized splice junction database for MS searching. Jurkat T-cell mRNA was analyzed on an Illumina HiSeq2000. ~80 million paired end reads (2x200bp, ~350bp lengths) were collected.
2013-05-17 | E-GEOD-45428 | biostudies-arrayexpress
Project description:Changes in the DNA methylation (DNAm) landscape have been implicated in aging and cellular senescence. To unravel the role of specific DNAm patterns in late-life survival, we performed genome-wide methylation profiling in nonagenarians (n=111) and determined the performance of the methylomic predictors and conventional risk markers in a longitudinal setting. The survival model containing only the methylomic predictors was superior in terms of predictive accuracy compared with the models containing the conventional predictors body mass index and mini-mental state examination. At the 2.55-year follow-up, we identified 19 mortality-associated (false-discovery rate <0.5) CpG sites that mapped to genes functionally clustering around the nuclear factor kappa B (NF-κB) complex. Interestingly, none of the mortality-associated CpG sites overlapped with the established aging-associated DNAm sites. Our results are in line with previous findings on the role of NF-κB in controlling animal life spans and demonstrate the key role of this complex in human longevity.
2017-02-09 | GSE68194 | GEO
Project description:BACKGROUND: Prediction models for old-age mortality have generally relied upon conventional markers such as plasma-based factors and biophysiological characteristics. However, it is unknown whether the existing markers are able to provide the most relevant information in terms of old-age survival or whether predictions could be improved through the integration of whole-genome expression profiles. METHODS: We assessed the predictive abilities of survival models containing only conventional markers, only gene expression data or both types of data together in a Vitality 90+ study cohort consisting of n = 151 nonagenarians. The all-cause death rate was 32.5% (49 of 151 individuals), and the median follow-up time was 2.55 years. RESULTS: Three different feature selection models, the penalized Lasso and Ridge regressions and the C-index boosting algorithm, were used to test the genomic data. The Ridge regression model incorporating both the conventional markers and transcripts outperformed the other models. The multivariate Cox regression model was used to adjust for the conventional mortality prediction markers, i.e., the body mass index, frailty index and cell-free DNA level, revealing that 331 transcripts were independently associated with survival. The final mortality-predicting transcriptomic signature derived from the Ridge regression model was mapped to a network that identified nuclear factor kappa beta (NF-?B) as a central node. CONCLUSIONS: Together with the loss of physiological reserves, the transcriptomic predictors centered around NF-?B underscored the role of immunoinflammatory signaling, the control of the DNA damage response and cell cycle, and mitochondrial functions as the key determinants of old-age mortality. The study consisted of 151 nonagenarians who were analyzed for genome-wide transcriptomic mortality predictors in a longitudinal setting.
2015-01-22 | E-GEOD-65218 | biostudies-arrayexpress