Ontology highlight
ABSTRACT:
PROVIDER: PRJNA949242 | 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).
| 2533916 | ecrin-mdr-crc
Project description:UCE phylogenomics and biogeography of the agriculturally important mason bee subgenus Osmia (Osmia)
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Project description:Sorghum is a C4 cereal important not only as food, but also as forage and a bioenergy resource. Its resistance to harsh environments has made it an agriculturally important research subject. Recent accumulation of genomic and transcriptomic information has facilitated genetic studies. Yet genome-wide translational profiles in sorghum are still missing, although increasing evidence has demonstrated that translation is an important regulatory step, and the transcriptome does not necessarily reflect the profile of functional protein production in some organisms. Deep sequencing of ribosome-protected mRNA fragments (ribosome profiling, or Ribo-seq) has enabled genome-wide analysis of translation. In this study, we took advantage of Ribo-seq and identified actively translated reading frames throughout the genome. We detected translation of 7,304 main ORFs annotated in the sorghum reference genome version 3.1 and revealed a number of unannotated translational events. A comparison of the transcriptome and translatome between sorghums grown under normal and sulfur-deficient conditions revealed that gene expression is modulated independently at transcript levels and translation levels. Our study revealed the translational landscape of sorghum’s response to sulfur and provides datasets that could serve as a fundamental resource to extend research on sorghum, including translational studies.
2022-11-16 | GSE184725 | GEO
Project description:Understanding how DNA sequence variation is translated into variation for complex phenotypes has remained elusive, but is essential for predicting adaptive evolution, selecting agriculturally important animals and crops, and personalized medicine. Here, we quantified genome-wide genetic variation in gene expression in the sequenced inbred lines of the Drosophila melanogaster Genetic Reference Panel. We found that a substantial fraction of the Drosophila transcriptome is genetically variable and organized into modules of genetically correlated transcripts, which provide functional context for newly identified novel transcribed regions. We identified regulatory variants for the mean and variance of gene expression, both of which showed oligogenic genetic architecture. Expression quantitative trait loci the mean, but not the variance, of gene expression were concentrated near genes. This comprehensive characterization of transcriptomic diversity and its genetic basis in the DGRP is critically important for a systems understanding of quantitative trait variation.
2015-10-05 | E-MTAB-3216 | biostudies-arrayexpress
Project description:The turkey, an agriculturally important avian species, has a karyotype that is similar to the chicken's
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Project description:Small RNAs have variety of important roles in plant development, stress responses, and other processes. They exert their influence by guiding mRNA cleavage, translational repression, and chromatin modification. To identify novel and regulated rice miRNAs, 62 small RNA libraries were constructed from rice plants and deeply sequenced with Illumina technology. The libraries represent several tissues from control plants and plants subjected to different environmental stress treatments. More than 94 million genome-matched reads were obtained resulting in more than 16 million distinct small RNA sequences. This allowed an evaluation with current criteria of about 400 annotated miRNAs and the finding that among these, about 150 had siRNA-like characteristics. Seventy nine new miRNAs were identified and miRNAs were distinguished that are regulated in response to water stress, nutrient stress, or temperature stress. Among the new examples of miRNA regulation were members of the same miRNA family that were differentially regulated in different organs and had distinct sequences Some of these distinct family members result in differential target cleavage and provide new insight about how an agriculturally important rice phenotype could be controlled in the panicle. This high resolution analysis of rice miRNAs should be relevant to plant miRNAs in general, particularly in the Poaceae. Examination of different tissue types and tissues treated with various environmental and nutrient stresses in rice by high throughput sequencing for small RNA profiling
2011-12-12 | E-GEOD-32973 | biostudies-arrayexpress
Project description:Our overarching goal is to understand how microbes along a glacier forefield chronosequence and productivity gradient interact with their environment, how this influences carbon and nitrogen cycling, and how the microbes respond to temperature increases. Specifically, using the novel approach of quantitative SIP paired with metagenomic sequencing, we will calculate growth rates for targeted functional genes and metagenome assembled genomes, quantifying their ecophysiology, in situ. And when paired with gene expression using metatranscriptomic libraries and metabolite production, we will gain a clearer understanding of how microbes grow, how they cycle carbon and nitrogen and how their metabolic activity changes in response to warming.
The work (proposal:https://doi.org/10.46936/10.25585/60008115) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.
2024-11-06 | MSV000096317 | MassIVE
Project description:Paenibacillus polymyxa is an agriculturally important plant growth promoting rhizobacterium (PGPR). Many Paenibacillus species are known to be engaged in complex bacteria-bacteria and bacteria-host interactions, which in other bacteria were shown to necessitate quorum sensing communication, but to date no quorum sensing systems have been described in Paenibacillus. Here we show that the type strain P. polymyxa ATCC 842 encodes at least 16 peptide-based communication systems. Each of these systems comprises a pro-peptide that is secreted to the growth medium and further processed to generate a mature short peptide. Each peptide has a cognate intracellular receptor of the RRNPP family, and we show that external addition of P. polymyxa communication peptides to the medium leads to reprogramming of the transcriptional response. We found that these quorum sensing systems are conserved across hundreds of species belonging to the Paenibacillaceae family, with some species encoding more than 25 different peptide-receptor pairs, representing a record number of quorum sensing systems encoded in a single genome.
2020-08-05 | PXD015319 | Pride