Ontology highlight
ABSTRACT:
PROVIDER: PRJNA591165 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Single-fly sequencing and genome assembly
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Project description:The Personalized Discovery Process is the only program offering patients treatment recommendations based on an empirically constructed Drosophila "fly" model of their disease. Special committee selects one of the one of the few 2-3 FDA approved drug combinations or single agents that improved survival in the fly cancer model.
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Project description:One ONT-ULK sequencing run from the kidney of a single male CDMR (Bathyergus suillus) sample used to make the mBatSui1.1.primary genome assembly as an evolutionary comparator to our telomere-to-telomere naked mole-rat genome assembly. Specifically, we assembled a CDMR from a wild-derived sample in South African cape and sequenced in Toronto, Canada, using PacBio HiFi (89 Gb, read N50 = 18 Kb) and ONT-ULK (55 Gb, read N50 = 43 Kb) reads (contig N50 = 33 Mb, Compleasm S = 99%, QV = 71.0). This accession stores the ONT-ULK data for this assembly.
2026-08-05 | E-MTAB-17420 | biostudies-arrayexpress
Project description:One PacBio Hifi sequencing run from the kidney of a single male CDMR (Bathyergus suillus) sample used to make the mBatSui1.1.primary genome assembly as an evolutionary comparator to our telomere-to-telomere naked mole-rat genome assembly. Specifically, we assembled a CDMR from a wild-derived sample in South African cape and sequenced in Toronto, Canada, using PacBio HiFi (89 Gb, read N50 = 18 Kb) and ONT-ULK (55 Gb, read N50 = 43 Kb) reads (contig N50 = 33 Mb, Compleasm S = 99%, QV = 71.0). This accession stores the Pacbio Hifi data for this assembly.
2026-08-05 | E-MTAB-17312 | biostudies-arrayexpress
Project description:Two PacBio Hifi sequencing runs from the kidney of a single male NMR sample used to make the mHetGla4.1.primary genome assembly. Specifically, we assembled a second NMR genome from an unrelated male of a separate captive colony in Toronto, Canada, using PacBio HiFi (155.8 Gb, read N50 = 11.45 Kb) and ONT-LSK (299.6 Gb, read N50 = 10.1 Kb) reads (contig N50 = 75.7 Mb, Compleasm S = 98%). This accession stores the Pacbio Hifi data for this independent assembly.
2026-08-05 | E-MTAB-17313 | biostudies-arrayexpress
Project description:Two PacBio Hifi sequencing runs from the kidney of a single male NMR sample used to make the mHetGla4.1.primary genome assembly. Specifically, we assembled a second NMR genome from an unrelated male of a separate captive colony in Toronto, Canada, using PacBio HiFi (155.8 Gb, read N50 = 11.45 Kb) and ONT-LSK (299.6 Gb, read N50 = 10.1 Kb) reads (contig N50 = 75.7 Mb, Compleasm S = 98%). This accession stores the ONT-LSK data for this independent assembly.
2026-08-06 | E-MTAB-17334 | biostudies-arrayexpress
Project description:Advances in sequencing and assembly technology has led to the creation of genome assemblies for a wide variety of non-model organisms. The rapid production and proliferation of updated, novel assembly versions can create create vexing problems for researchers when multiple genome as-sembly versions are available at once, requiring researchers to work with more than one reference genome. Multiple genome assemblies are especially problematic for researchers studying the genetic makeup of individual cells as single cell RNA sequencing (scRNAseq) requires sequenced reads to be mapped and aligned to a single reference genome. Using the Astyanax mexicanus this study highlights how the interpretation of a single cell dataset from the same sample changes when aligned to its two different available genome assemblies. We found that the number of cells and expressed genes detected were drastically different when aligning to the different assemblies. When the genome assemblies were used in isolation with their respective annotation, cell type identification was confounded as some classic cell type markers were assembly-specific, whilst other genes showed differential patterns of expression between the two assemblies. To overcome the problems posed by multiple genome assemblies, we propose that researchers align to each available assembly and then integrate the resultant datasets to produce a final dataset in which all genome alignments can be used simultaneously. We found this approach increased the accuracy of cell type identification and maximised the amount of data that could be extracted from our single cell sample by capturing all possible cells and transcripts. As scRNAseq becomes more widely available, it is imperative that the single cell community is aware how genome assembly alignment can alter single cell data and its interpretation, especially when reviewing studies on non-model organisms.
2022-02-10 | GSE194093 | GEO
Project description:<p class='ql-align-justify'>Megasphaera hexanoica KCCM 43214T, isolated from cow rumen, is capable of producing medium-chain carboxylic acids such as n-caproate and n-caprylate. In this study, we present a high-quality genome assembly, along with intracellular metabolomic profiling and pangenomic analysis. Illumina sequencing generated 2.3 Mbp from 15,293,634 reads with a GC content of 49.5%, while PacBio HiFi sequencing produced 331.5 Mbp across 45,266 reads, with an average read length of 7,323 bp and a HiFi read N50 of 8,214 bp. Hybrid assembly of short and long reads resulted in a single 2.88 Mbp contig, containing 2,075-2,083 unique genes. A genome-scale metabolic model was constructed, to evaluate its metabolic capabilities under specific growth conditions. Intracellular metabolomic analysis of cells grown in fructose medium and lactate medium revealed key metabolic activities associated with chain elongation. Pangenomic analysis across nine annotated genomes identified 6,721 orthologous gene using OrthoMCL, emphasizing the genetic and functional diversity within the Megasphaera genus. This dataset offers valuable insights into the metabolism and biotechnological potential of M. hexanoica KCCM 43214T.</p>
2026-04-03 | MTBLS14019 | MetaboLights
Project description:We utilized Comparative Genomic Hybridization (CGH), using probes designed from de novo assembly of a testes transcriptome, to identify genes located on the sex chromosomes and autosomes of a stalk-eyed fly, Sphyracephala beccarii. Analysis of X chromosome gene content revealed the evolution of a neo-X chromosome that originated prior to the diversification of the family. Comparison of X-linkage across three species spanning the phylogenetic breadth of the family indicates abundant chromosomal gene movement, particularly for genes expressed exclusively in the testes.
2015-12-11 | GSE75873 | GEO
Project description:We utilized Comparative Genomic Hybridization (CGH), using probes designed from de novo assembly of a testes transcriptome, to identify genes located on the sex chromosomes and autosomes of a stalk-eyed fly, Teleopsis quinqueguttata. Analysis of X chromosome gene content revealed the evolution of a neo-X chromosome that originated prior to the diversification of the family. Comparison of X-linkage across three species spanning the phylogenetic breadth of the family indicates abundant chromosomal gene movement, particularly for genes expressed exclusively in the testes.
2015-12-11 | GSE75872 | GEO