29 research outputs found
Resolving the complete genome of Kuenenia stuttgartiensis from a membrane bioreactor enrichment using Single-Molecule Real-Time sequencing
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190074.pdf (publisher's version ) (Open Access)10 p
Determining the quality and complexity of next-generation sequencing data without a reference genome
Genomics, epigenetics, population genetics and bioinformatic
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Full-length mRNA sequencing uncovers a widespread coupling between transcription initiation and mRNA processing
Background: The multifaceted control of gene expression requires tight coordination of regulatory mechanisms at transcriptional and post-transcriptional level. Here, we studied the interdependence of transcription initiation, splicing and polyadenylation events on single mRNA molecules by full-length mRNA sequencing. Results: In MCF-7 breast cancer cells, we find 2700 genes with interdependent alternative transcription initiation, splicing and polyadenylation events, both in proximal and distant parts of mRNA molecules, including examples of coupling between transcription start sites and polyadenylation sites. The analysis of three human primary tissues (brain, heart and liver) reveals similar patterns of interdependency between transcription initiation and mRNA processing events. We predict thousands of novel open reading frames from full-length mRNA sequences and obtained evidence for their translation by shotgun proteomics. The mapping database rescues 358 previously unassigned peptides and improves the assignment of others. By recognizing sample-specific amino-acid changes and novel splicing patterns, full-length mRNA sequencing improves proteogenomics analysis of MCF-7 cells. Conclusions: Our findings demonstrate that our understanding of transcriptome complexity is far from complete and provides a basis to reveal largely unresolved mechanisms that coordinate transcription initiation and mRNA processing. Electronic supplementary material The online version of this article (10.1186/s13059-018-1418-0) contains supplementary material, which is available to authorized users
Aging as Accelerated Accumulation of Somatic Variants: Whole-Genome Sequencing of Centenarian and Middle-Aged Monozygotic Twin Pairs
Mapping 123 million neonatal, infant and child deaths between 2000 and 2017
Since 2000, many countries have achieved considerable success in improving child survival, but localized progress remains unclear. To inform efforts towards United Nations Sustainable Development Goal 3.2—to end preventable child deaths by 2030—we need consistently estimated data at the subnational level regarding child mortality rates and trends. Here we quantified, for the period 2000–2017, the subnational variation in mortality rates and number of deaths of neonates, infants and children under 5 years of age within 99 low- and middle-income countries using a geostatistical survival model. We estimated that 32% of children under 5 in these countries lived in districts that had attained rates of 25 or fewer child deaths per 1,000 live births by 2017, and that 58% of child deaths between 2000 and 2017 in these countries could have been averted in the absence of geographical inequality. This study enables the identification of high-mortality clusters, patterns of progress and geographical inequalities to inform appropriate investments and implementations that will help to improve the health of all populations
Characterizing IonTorrent PGM Error Profiles using TSSV
<p>This dataset contains sequencing reads used to characterize systematic errors of IonTorrent PGM sequencer as well as all of the analysis results in separate files.</p
Allele-specific Characterization of STR Structures in Pure and Mixed Forensic Samples using TSSV
<p>This dataset contains sequencing reads used to characterize allelic STR structures in pure and mixed forensic samples as well as all of the analysis results in separate files.</p
Resolving the complete genome of Kuenenia stuttgartiensis from a membrane bioreactor enrichment using Single-Molecule Real-Time sequencing
Contains fulltext :
190074.pdf (publisher's version ) (Open Access)10 p