Ontology highlight
ABSTRACT:
PROVIDER: PRJNA998719 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
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2016-04-30 | E-SYBR-1 | biostudies-arrayexpress
Project description:This research reports genome-wide measurements of genetic and epigenetic patterns of inheritance through an integrative analysis of BS-seq, RNA-seq, and siRNA-seq data in two inbred parents of the Nipponbare (NPB) and Indica (93-11) variety of rice and their hybrid offspring. We generated integrative maps of whole genome cytosine methylation profiles (BS-Seq), transcriptional profiles (RNA-seq), and small RNA profiles (sRNA-seq) to characterize two rice subspecies, Oryza sativa spp japonica (Nipponbare) and Oryza sativa spp indica (93-11) and their two reciprocal hybrid offspring using Illumina's sequencing-by-synthesis (SBS) platform .
2012-07-10 | E-GEOD-38480 | biostudies-arrayexpress
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2020-11-03 | PXD021036 | Pride
Project description:Whole genome sequencing of Bartonella spp. from cultured isolates using Illumina and PacBio.
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Project description:Part of a set of highly integrated epigenome maps for Arabidopsis thaliana. Keywords: Illumina high-throughput bisulfite sequencing Whole genome shotgun bisulfite sequencing of wildtype Arabidopsis plants (Columbia-0), and met1, drm1 drm2 cmt3, and ros1 dml2 dml3 null mutants using the Illumina Genetic Analyzer.
2008-04-21 | E-GEOD-10966 | biostudies-arrayexpress
Project description:Illumina-based whole genome bisulfite sequencing libraries for 4 RNA-directed DNA methylation mutants
2012-05-26 | GSE36143 | GEO
Project description:Dicer sequencing was performed on the Illumina MiSeq System in a total of 16 BCC samples (8 nodular BCCs / 8 sBCCs) and mapped against the human reference genome (hg19). Dicer sequencing was performed in all 16 BCC samples. Whole genome methylation profiling performed with Infinium MethylationEPIC BeadChips as well as RNA and smallRNA sequencing were performed in 5 sBCCs with the Illumina NextSeq500 next generation sequencing system. We identified a variety of Dicer mutations that could play a role in aberrant miRNA expression in BCC. The aforementioned RNA sequences should be further evaluated in functional studies towards their possible pathogenetic role in sBCC.
2019-10-25 | GSE128789 | GEO
Project description:Background & Aims: Environmental toxicants (ETs) associate with various adverse health outcomes. Here, we hypothesized that exposures to ETs are associated with obesity and insulin resistance via a dysbiotic gut microbiota and derived alterations in microbiome-mediated bile acid (BA) synthesis. Methods: Serum BAs, per- and polyfluoroalkyl substances (PFAS) and additional twenty-seven ETs were measured by mass spectrometry in 264 Danes (121 women and 143 men, age 56.6 ± 7.3 years, BMI 29.7 ± 6.0 kg/m2). Bacterial species were identified based on whole-genome shotgun (WGS) sequencing of DNA extracted from purified stool samples. Personalized genome-scale metabolic models (GEMs) of gut microbial communities were developed to elucidate regulation of BA pathways. Subsequently, we compared findings in the human study with metabolic implications of perfluorooctanoic acid (PFOA) exposure in a PPAR-humanized murine model. Results: Fasting serum concentrations of twelve ETs associated directly with measures of obesity and insulin resistance. Several bacterial species including Dorea longicatena, Dorea formicigenerans, Subdoligranulum spp., Veillonella spp., and Roseburia intestinalis associated positively and in a sex-dimorphic manner, particularly in women, with high exposure to ETs. Moreover, high serum concentrations of ETs were linked with higher fasting serum levels of microbiome-synthesized secondary BAs such as lithocholic acid (LCA) and ursodeoxycholic acid (UDCA). These findings were substantiated by the outcome of a murine exposure study. Conclusion: Serum concentrations of ETs, particularly in women, were associated with an altered gut microbiome-mediated secondary BA biosynthesis, linked with obesity and insulin resistance.
2023-02-21 | ST002496 | MetabolomicsWorkbench