Kveik_sample6_1a
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB90461 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Genome assembly of kveik (Selland kveik) from Vossestrand, Norway
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Project description:Genome assembly of kveik (Laerdal kveik) from Ljosne, Laerdal, Norway
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Project description:Genome assembly of kveik (Tore Hjelle kveik) from Hjelle, Eidsdal, Norway
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Project description:28 Streptomyces strains isolated from common scab lesions of potato tubers from a wide geographic range in Norway, were selected for microarray analysis. The selected strains were subjected to species identification by microarray, 16S phylogenetic analysis and PCR; and microarray-based comparative genome analysis. To our knowledge, this is the first report of S. turgidiscabies and S. europaeiscabiei in Norway.
2010-05-01 | GSE20487 | GEO
Project description:We have completed the high quality reference genome for domestic sheep (Oar v3.1). Early-stage Illumina GA sequence platform sequenced less reads in high GC content regions than in other regions. To read through higher GC content regions, we generated 2 Gb MeDIP-seq data for filling gaps in sheep reference genome assembly.
2014-06-06 | E-GEOD-56644 | biostudies-arrayexpress
Project description:<p> The casuarina moth (Lymantria xylina) is a notorious forestry pest, posing severe ecological and economic threats due to its destructive defoliation outbreaks and high invasive potential. Despite its significance, a high-quality reference genome has been lacking, limiting molecular-level investigations into its biology and hindering the development of effective pest management strategies. In this study, we report the first chromosome-level genome assembly of L. xylina generated through a combination of illumina short-reads, Oxford Nanopore long-reads, and Hi-C scaffolding. The final assembly spans 977.74 Mb, with 95.17% anchored to 31 pseudo-chromosomes, achieving a scaffold N50 of 34.15 Mb. Importantly, telomeric sequences were identified at both ends of all 31 pseudo-chromosomes, underscoring the exceptional quality and completeness of this reference genome. Quality assessment further revealed a BUSCO completeness of 94.5% and a consensus QV of 31.72. We also annotated 18,484 protein-coding genes, 95.21% of which were functionally assigned, and characterized genome-wide repetitive elements (77.18%).</p><p> Beyond the genome assembly, we generated comprehensive RNA-seq and metabolomic datasets across multiple diapause stages, enabling insights into gene expression dynamics and metabolic regulation during egg development. Together, these resources provide a valuable foundation for studying the genetic basis of host adaptation, invasiveness, and interactions with natural enemies such as nucleopolyhedrovirus and Beauveria bassiana.</p>
2025-12-26 | MTBLS13575 | MetaboLights
Project description:Genome sequencing of traditional kveik yeast used in farmhouse brewing on the west-coast of Norway
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Project description:We have sequenced a wild Prunus mume and constructed a reference sequence for this genome. In order to improve quality of gene models, RNA samples of five tissues (bud, leaf, root, stem, fruit) were extracted from the Prunus mume. To investigate tissue specific expression using the reference genome assembly and annotated genes, we extracted RNA samples of different tissues and conducted transcriptome sequencing and DEG analysis.
2012-12-27 | GSE40162 | GEO
Project description:Centromeres are chromosomal regions that serve as platforms for kinetochore assembly and spindle attachments, ensuring accurate chromosome segregation during cell division. Despite functional conservation, centromeric sequences are diverse and usually repetitive across species, making them challenging to assemble and identify. Here, we describe centromeres in the model oomycete Phytophthora sojae by combining long-read sequencing-based genome assembly and chromatin immunoprecipitation for the centromeric histone CENP-A followed by high-throughput sequencing (ChIP-seq). P. sojae centromeres cluster at a single focus in the nucleus at different life stages and during nuclear division. We report a highly contiguous genome assembly of the P. sojae reference strain, which enabled identification of 15 highly enriched CENP-A binding regions as putative centromeres. By focusing on 10 intact regions, we demonstrate that centromeres in P. sojae are regional, spanning 211 to 356 kb. Most of these regions are transposon-rich, poorly transcribed, and lack the euchromatin mark H3K4me2 but are embedded within regions with the heterochromatin marks H3K9me3 and H3K27me3.
2020-01-07 | GSE143137 | GEO
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