Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1040111 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Aeromonas salmonicida genomes WGS
| PRJEB37195 | ENA
Project description:WGS of five Ochrobactrum isolates from Israel
| PRJEB37004 | ENA
Project description:To elucidate the target genes of ArgR in Aeromonas veronii, we engineered an Aeromonas veronii strain that expresses the ArgR protein fused to a 3× FLAG tag, and FLAG antibodies were employed for the immunoprecipitation of DNA-protein complexes.
2024-09-15 | GSE277129 | GEO
Project description:We performed shallow whole genome sequencing (WGS) on circulating free (cf)DNA extracted from plasma or cerebrospinal fluid (CSF), and shallow WGS on the tissue DNA extracted from the biopsy in order to evaluate the correlation between the two biomaterials. After library construction and sequencing (Hiseq3000 or Ion Proton), copy number variations were called with WisecondorX.
2021-11-17 | E-MTAB-10548 | biostudies-arrayexpress
Project description:Whole genome sequencing (WGS) of tongue cancer samples and cell line was performed to identify the fusion gene translocation breakpoint. WGS raw data was aligned to human reference genome (GRCh38.p12) using BWA-MEM (v0.7.17). The BAM files generated were further analysed using SvABA (v1.1.3) tool to identify translocation breakpoints. The translocation breakpoints were annotated using custom scripts, using the reference GENCODE GTF (v30). The fusion breakpoints identified in the SvABA analysis were additionally confirmed using MANTA tool (v1.6.0).
2024-02-17 | E-MTAB-12534 | biostudies-arrayexpress
Project description:Aeromonas are ubiquitous inhabitants of both natural and anthropogenic aquatic ecosystems. Occasionally, Aeromonas also grows in drinking water distribution systems, which is highly undesired due to the pathogenicity of some members of this genus. The growth of Aeromonas in such highly oligotrophic environments is currently poorly understood. Possible nutrient sources are biopolymers. For example, chitin is the structural component of the exoskeleton of insects, some invertebrates and the cell walls of fungi which makes it one of the most abundant carbon and nitrogen sources in nature. In this study we demonstrate the ability of two Aeromonas strains, Aeromonas bestiarum and Aeromonas rivuli to efficiently grow on chitin. The secreted proteins confirm the presence of the functional hydrolytic enzymes that enable the efficient degradation and utilization of this abundant biopolymer. Further quantitative cellular proteomic study unravels the remarkable reorganization of the Aeromonas metabolism when switching to chitin as sole carbon and nitrogen source. This proves that Aeromonas is not only chitinolytic but also a chitinotrophic microorganism.
2024-12-12 | PXD047459 | Pride
Project description:Plasmodium falciparum WGS from Northern Cambodia
| PRJNA682991 | ENA
Project description:In principle, whole-genome sequencing (WGS) of the human genome even at low coverage offers higher resolution for genomic copy number variation (CNV) detection compared to array-based technologies, which is currently the first-tier approach in clinical cytogenetics. There are, however, obstacles in replacing array-based CNV detection with that of low-coverage WGS such as cost, turnaround time, and lack of systematic performance comparisons. With technological advances in WGS in terms of library preparation, instrument platforms, and data analysis algorithms, obstacles imposed by cost and turnaround time are fading. However, a systematic performance comparison between array and low-coverage WGS-based CNV detection has yet to be performed. Here, we compared the CNV detection capabilities between WGS (short-insert, 3kb-, and 5kb-mate-pair libraries) at 1X, 3X, and 5X coverages and standardly used high-resolution arrays in the genome of 1000-Genomes-Project CEU genome NA12878. CNV detection was performed using standard analysis methods, and the results were then compared to a list of Gold Standard NA12878 CNVs distilled from the 1000-Genomes Project. Overall, low-coverage WGS is able to detect drastically more (approximately 5 fold more on average) Gold Standard CNVs compared to arrays and is accompanied with fewer CNV calls without secondary validation. Furthermore, we also show that WGS (at ≥1X coverage) is able to detect all seven validated deletions larger than 100 kb in the NA12878 genome whereas only one of such deletions is detected in most arrays. Finally, we show that the much larger 15 Mbp Cri-du-chat deletion can be clearly seen at even 1X coverage from short-insert WGS.
2018-06-26 | GSE105092 | GEO