Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1013412 | 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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Project description:Sequencing of moonmilk dwelling actinobacterial species
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Project description:Insect derived cell-lines, from Spodoptera frugiperda (Sf21) and from Trichoplusia ni (High Five), are ones of the most widely used systems for recombinant protein expression in Baculoviral Expression Vector System (BEVS). Genomic sequences and annotations are still incomplete for Sf21 or absent for High Five. In this study we present an approach using different sequencing data types with short-read sequencing, long synthetic and Oxford Nanopore reads to build genomes at an unprecedented resolution. The Sf21 and High Five assemblies contain 4,020 scaffolds of size, 463 Mb with N50 of 364 Kb and 2,954 scaffolds of size, 332 Mb with N50 of 326 Kb, respectively. Furthermore, we build a new gene prediction workflow, which integrates transcriptome proteome information using pre-existing tools. Using this approach, we could predict 21,506 Sf21 genes and 14,159 High Five genes, which were then functionally annotated. Finally, we also generate and integrate proteomic datasets to validate predicted genes. This integrative approach could be theoretically applied to any uncharacterized genome and result in valuable new resources. With this information available, Sf21 and High Five cells will become even better tools for protein expression and could be used in a wider range of applications, from promoter identifications to genome engineering and editing.
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Project description:Actinobacterial Biodiversity from Indonesian Extremobiosphere
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Project description:The study is intended to collect specimens to support the application of genome analysis technologies, including large-scale genome sequencing. This study will ultimately provide cancer researchers with specimens that they can use to develop comprehensive catalogs of genomic information on at least 50 types of human cancer. The study will create a resource available to the worldwide research community that could be used to identify and accelerate the development of new diagnostic and prognostic markers, new targets for pharmaceutical interventions, and new cancer prevention and treatment strategies. This study will be a competitive enrollment study conducted at multiple institutions.
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Project description:This study aims to investigate the DNA methylation patterns at transcription factor binding regions and their evolutionary conservation with respect to binding activity divergence. We combined newly generated bisulfite-sequencing experiments in livers of five mammals (human, macaque, mouse, rat and dog) and matched publicly available ChIP-sequencing data for five transcription factors (CEBPA, HNF4a, CTCF, ONECUT1 and FOXA1). To study the chromatin contexts of TF binding subjected to distinct evolutionary pressures, we integrated publicly available active promoter, active enhancer and primed enhancer calls determined by profiling genome wide patterns of H3K27ac, H3K4me3 and H3K4me1.
2022-10-20 | E-MTAB-11946 | biostudies-arrayexpress
Project description:We determined Streptomyces coelicolor genes that are directly regulated by WblC (or WhiB7), an actinobacterial transcription factor that activates expression of intrinsic resistance in response to translation-inhibitory antibiotic stress. Identification of differentially expressed genes in wblC mutant by RNA-seq and WblC binding sites in wild type by ChIP-seq identified more than 300 genes as WblC regulon. This series encompasses the RNA-seq data of our study.
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