Ontology highlight
ABSTRACT:
PROVIDER: PRJEB66264 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This BioProject includes the reference genomes generated by the Spanish chapter of the European Reference Genome Atlas.
| PRJEB43471 | ENA
Project description:Purpose: To demonstrate that gene expression and splicing analysis varies considerably depending on the mapping reference genome. Methods: We mapped and analyzed submitted RNA reads using different tools and reference genomes to evaluate the influence of genome on DEG and alternative splicing tools. Results: We observed that these differences in transcriptome analysis are, in part, due to the presence of single nucleotide polymorphisms between the sequenced individual and each respective reference genome, as well as annotation differences between the reference genomes that exist even between syntenic orthologs. Conclusion: We conclude that even between two closely related genomes of similar quality, using the reference genome that is most closely related to the species being sampled significantly improves transcriptome.
2019-02-16 | GSE126650 | GEO
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:Sixteen individual rhesus macaque genomes were compared to a reference macaque genome (R354) on custom-designed sure-print 1M oligonucleotide microarray Agilent (Agilent Technologies) aCGH slide per manufacturer’s recommendations.
2011-05-11 | GSE19881 | GEO
Project description:Bufotes viridis (European green toad) genomic and assembly data, ERGA pilot
| PRJEB71764 | ENA