Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA723884 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Chromatin boundary elements contribute to the partitioning of mammalian genomes into topological domains to regulate gene expression. Certain boundary elements are adopted as DNA insulators for safe and stable transgene expression in mammalian cells. These elements, however, are ill-defined and less characterized in the non-coding genome, partially due to the lack of a platform to readily evaluate boundary-associated activities of putative DNA sequences. Here we report SHIELD (Site-specific Heterochromatin Insertion of Elements at Lamina-associated Domains), a novel platform tailored for the high-throughput screening of barrier-type DNA elements in human cells. SHIELD takes advantage of the high specificity of serine integrase at heterochromatin, and exploits the natural heterochromatin spreading inside LADs for the discovery of potent barrier elements. We adopted SHIELD to evaluate the barrier activity of 1000 DNA elements in a high-throughput manner and identified 8 novel elements with barrier activities comparable to the core region of cHS4 element. SHIELD should greatly facilitate the discovery of novel barrier DNA elements from the non-coding genome in human cells.
2023-08-01 | GSE236198 | GEO
Project description:Illumina PCR Free sequencing of 1000 Genomes Trios for SV discovery
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Project description:Taxonomic outliers of Pseudomonas aeruginosa recently emerged as infectious for humans. Here we present the first analysis of a hyper-virulent isolate that cause hemorrhagic pneumonia. We demonstrated that, in two sequential clones CLJ1 and CLJ3 recovered from a patient with chronic obstructive pulmonary disease undergoing antibiotic therapy, insertion of a mobile genetic element into the P. aeruginosa chromosome affected major virulence-associated phenotypes and led to increased resistance to antibiotics used to treat the patient. Our work reveals insertion sequences as major players in enhancing the pathogenic potential of a P. aeruginosa taxonomic outlier by modulating both the virulence and resistance to antimicrobials. This also explains the ability of this bacterium to adapt to an infected host and cause a serious disease.
2019-03-18 | PXD011105 | Pride
Project description:High Coverage PCR Free sequencing of Individuals from 24 1000 Genomes populations
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Project description:High-coverage whole genome sequencing of Han Chinese populations (1000 Genomes Project)
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Project description:1000 Genomes Project Pilot 2. High coverage sequencing of 2 Trios (6 individuals).
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Project description:<p>This study combined whole exome (103 samples) and whole genome (22 samples) sequencing over a total of 108 breast tumors and matched normal DNA to identify novel mutations and translocations. Samples were subjected to paired-end Illumina sequencing with goal of 30x coverage of tumor/normal for whole genomes and 100x tumor/normal coverage for whole exomes. From these sequences, we used various computational techniques to identify somatic point mutations, insertion/deletions and structural rearrangements in these tumors. From these data, we identified new insights into the rates of background mutations in these cancers, novel recurrent mutated genes, and multiple gene rearrangements. One of these rearrangements appears to be a recurrent event in breast cancer.</p>
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Project description:Low-pass sequencing (sequencing a genome to an average depth less than 1× coverage) combined with genotype imputation has been proposed as an alternative to genotyping arrays for trait mapping and calculation of polygenic scores. To empirically assess the relative performance of these technologies for different applications, we performed low-pass sequencing (targeting coverage levels of 0.5× and 1×) and array genotyping (using the Illumina Global Screening Array (GSA)) on 120 DNA samples derived from African and European-ancestry individuals that are part of the 1000 Genomes Project. We then imputed both the sequencing data and the genotyping array data to the 1000 Genomes Phase 3 haplotype reference panel using a leave- one-out design. We evaluated overall imputation accuracy from these different assays as well as overall power for GWAS from imputed data, and computed polygenic risk scores for coronary artery disease and breast cancer using previously derived weights. We conclude that low-pass sequencing plus imputation, in addition to providing a substantial increase in statistical power for genome wide association studies, provides increased accuracy for polygenic risk prediction at effective coverages of ∼ 0.5× and higher compared to the Illumina GSA.
2021-01-31 | GSE165845 | GEO
Project description:1000 Genomes Full Production low coverage WGS population sequencing
| PRJNA59771 | ENA