Find research datasets worth reusing

opencc-by-4.0Sep 2022View details →

Combination of whole genome sequencing and Supervised Machine Learning provides unambiguous identification of enterohemorrhagic Escherichia coli in raw milk

These dataset are used in the "rename_list_of_groups.ipynb" notebook

opencc-by-4.0Jun 2022View details →

CRAG: De novo characterization of cell-free DNA fragmentation hotspots in plasma whole-genome sequencing

Supplementary dataset for the manuscript: CRAG: De novo characterization of cell-free DNA fragmentation hotspots in plasma whole-genome sequencing  Xionghui Zhou1,*, Haizi Zheng1,*, Hailu Fu1,*, Kelsey L. Dillehay McKillip2-3, Susan M. Pinney2,4, Yaping Liu1-2,5-7 # Affiliations: 1 Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 2 University of Cincinnati Cancer Center, Cincinnati, OH 45229 3 Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45229 4 Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45229 5 Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 6 Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229 7 Department of Electrical Engineering and Computing Sciences, University of Cincinnati College of Engineering and Applied Science, Cincinnati, OH 45229 * These authors contributed equally # Email: lyping1986@gmail.com

Figure 5 in Phylogenetic relationships of Brachycera (Insecta: Diptera) inferred from mitochondrial genome sequences

Figure 5. Chronogram for major clades of Brachycera estimated by BEAST 1.8.4 based on 107-taxon_PCG_nt12 (scale on x-axis in mya). At the branching nodes, numbers show the estimated divergence times and blue bars represent the time interval for 95% probability of actual node age.

Figure 4 in Phylogenetic relationships of Brachycera (Insecta: Diptera) inferred from mitochondrial genome sequences

Figure 4. The simplified ML tree inferred from the dataset 107-taxon_PCG_aa by using IQ-TREE, under the data partitions and best-fitting models selected by PartitionFinder 2. Node numbers show the bootstrap support values (> 50). The insect pictures are provided by Yuqiang Xi.

Figure 1 in Phylogenetic relationships of Brachycera (Insecta: Diptera) inferred from mitochondrial genome sequences

Figure 1. Representations of previous hypotheses for the relationships among major groups of Brachycera inferred from morphologically-based or molecular studies by authors cited. A, Woodley (1989) based on morphological data; B, Wiegmann et al. (2003) based on morphological and molecular data; C, Yeates (2002) based on morphological data; D, Wiegmann et al. (2011) based on morphological and molecular data; E, Shin et al. (2018) based on molecular data; F, Bayless et al. (2021) based on molecular data.

Figure 3. The Bayesian tree inferred from the dataset 107 in Phylogenetic relationships of Brachycera (Insecta: Diptera) inferred from mitochondrial genome sequences

Figure 3. The Bayesian tree inferred from the dataset 107-taxon_PCG_nt12 using PhyloBayes, under the site-heterogeneous mixture model (CAT-GTR). Node numbers show the posterior probability values (> 0.90). The insect pictures are provided by Yuqiang Xi.

Figure 2 in Phylogenetic relationships of Brachycera (Insecta: Diptera) inferred from mitochondrial genome sequences

Figure 2. The simplified ML tree inferred from the dataset 187-taxon_PCG_nt123 using IQ-TREE, under the data partitions and best-fitting models selected by PartitionFinder 2. Node numbers show the bootstrap support values (> 50). For the full tree, see Supporting Information, Fig. S3A. The insect pictures are provided by Yuqiang Xi.

opencc-zeroJan 2018View details →

Supplementary material 1 from: Yuhui X, Lijun Z, Yue H, Xiaoqi W, Chen Z, Huilun Z, Ruoran W, Da P, Hongying S (2017) Complete mitochondrial genomes from two species of Chinese freshwater crabs of the genus Sinopotamon recovered using next-generation sequencing reveal a novel gene order (Brachyura, Potamidae). ZooKeys 705: 41-60. https://doi.org/10.3897/zookeys.705.11852

Figure S1 : Explanation note: Comparisons of the consensus sequence and variable sites in the entire mNCR for Sinopotamon yaanense, S. yangtsekiense and S. xiushuiense. The conserved central domain is grey shaded, and the extended termination associated sequences (ETAS) is underlined.

opencc-by-nc-nd-4.0Apr 2024View details →

Draft genome sequences of Arabidopsis thaliana-associated micro-organisms from Reijerscamp soil, the Netherlands

Methodological summary and relevant references Compressed tar archive containing 447 draft bacterial genomes and their annotations used in several studies including Fourie et al. (2024; in review) and Selten et al. (2024; in prep). Genome sequences are obtained by Illumina-only sequencing of microbial cultures. Illumina reads were demultiplexed and cleaned with cutadapt (version 2.8) (Martin, 2011) and assembled into genomes using A5 (A5-miseq version 20160825) (Coil et al., 2014). Genome contamination and heterogeneity was checked with CheckM (version 1.1.3) (Parks et al., 2015) and any genomes with multiple single copy gene occurrences were subjected to MaxBin (version 2.2.7) (Wu et al., 2014) to separate the genomes from contaminated bacterial cultures. Any non-bacterial contigs in the genome assemblies were removed using MMSeqs2 (version 13.45111) (Steineigger & Schöding, 2017). Open reading frames were found and annotated by PROKKA (version 1.14.6) (Seemann, 2014) and EggNOG (version 2.1.4-2) (Cantalapiedra et al., 2021) respectively. Microbial cultures were derived from Arabidopsis thaliana roots grown in Reijerscamp soil, described in Stringlis et al., 2018 https://doi.org/10.1073/pnas.1722335115. The uploaded files are <ol> <li>Genome assemblies</li> <li>Prokka gene predictions in GFF3 format</li> <li>Predicted transcripts from genes in (2)</li> <li>Predicted proteins from genes in (2), and</li> <li>EggNOG annotations for the proteins in (4)</li> </ol> Genomes and annotations pending upload om NCBI GenBank (April 2024)

opencc-by-4.0Apr 2023View details →

Gene annotation of complete genome sequence of Achromobacter sp. strain E1

Open the record for dataset details and reuse information.

opencc-by-4.0Apr 2024View details →

Transposase-Assisted Tagmentation: An Economical and Scalable Strategy for Single-Worm Whole-Genome Sequencing (elegans)

AlphaMissense identifies 23 million human missense variants as likely pathogenic, but only 0.1% have been clinically classified. To experimentally validate these predictions, chemical mutagenesis presents a rapid, cost-effective method to produce billions of mutations in model organisms. However, the prohibitive costs and limitations in the throughput of whole-genome sequencing (WGS) technologies, crucial for variant identification, constrain its widespread application. Here, we introduce a Tn5 transposase-assisted tagmentation technique for conducting WGS in C. elegans, E. coli, S. cervisiae, and C. reinhardtii. This method, demands merely 20 minutes of hands-on time for a single worm or single-cell clones and incurs a cost below 10 US dollars. It effectively pinpoints causal mutations in mutants defective in cilia or neurotransmitter secretion and in mutants synthetically sterile with a variant analogous to the oncogenic BRAF(V600E) mutation. Integrated with chemical mutagenesis, our approach can generate and identify missense variants economically and efficiently, facilitating experimental investigations of missense variants in diverse species.

Supplementary information to the data note The genome sequence of the Sandhill Rustic moth Luperina nickerlii (Freyer, 1845) subspecies leechi Goater, 1976"

Supplementary information to the data note: "The genome sequence of the Sandhill Rustic moth Luperina nickerlii (Freyer, 1845) subspecies leechi Goater, 1976" . The LSU analysis of the Luperina nickerlii subsp. leechi genome, presenting evidence that this is a ZO female.

CARACTERIZAÇÃO GENÉTICA DE SOROVARES DE Salmonella spp. ISOLADOS NA AVICULTURA POR WHOLE GENOME SEQUENCING

Table S1. Metadata for the 21 Salmonella enterica genomes used to perform phylogenetic analysis. Table S2. Comprehensive overview of sequences of targeted serovars present in the genomic database by prescribed selection criteria.

CARACTERIZAÇÃO GENÉTICA DE SOROVARES DE Salmonella spp. ISOLADOS NA AVICULTURA POR WHOLE GENOME SEQUENCING

Table S1: Metadata for the 317 Salmonella Heidelberg genomes retrieved from the Enterobase database to perform genomic analysis in this study.

1000 Genomes Data: Sequencing Data in BAM Format - LPA Region

Open the record for dataset details and reuse information.

Genome Sequence of Colletotrichum karsti isolated from rose leaves exhibiting anthracnose symptoms in Potchefstroom, South Africa.

Open the record for dataset details and reuse information.

Fig 6 in Whole-Genome Optical Mapping and Finished Genome Sequence of Sphingobacterium deserti sp. nov., a New Species Isolated from the Western Desert of China

Fig 6. Venn diagram depicting orthologous groups of predicted proteins encoded in four sphingobacterial genomes. C1: Sphingobacterium spiritivorum ATCC 33300; C2: Sphingobacterium paucimobilis HER1398; C3: Sphingobacterium thalpophilum DSM11723; and C4: Sphingobacterium deserti ZWT. doi:10.1371/journal.pone.0122254.g006

Fig 4 in Whole-Genome Optical Mapping and Finished Genome Sequence of Sphingobacterium deserti sp. nov., a New Species Isolated from the Western Desert of China

Fig 4. Genome map of Sphingobacterium deserti sp. nov. ZWT. Concentric tracks from the inside to the outside represent the GC nucleotide bias; the GC content; tRNA and rRNA genes on the reverse strand; tRNA and rRNA genes on the forward-strand; reverse-strand coding sequences (CDSs); and forwardstrand CDSs. doi:10.1371/journal. pone.0122254.g004

Fig 1 in Whole-Genome Optical Mapping and Finished Genome Sequence of Sphingobacterium deserti sp. nov., a New Species Isolated from the Western Desert of China

Fig 1. Electron micrograph of the cell morphology of strain ZWT. doi:10.1371/journal.pone.0122254.g001

Fig 5 in Whole-Genome Optical Mapping and Finished Genome Sequence of Sphingobacterium deserti sp. nov., a New Species Isolated from the Western Desert of China

Fig 5. Whole-genome optical mapping barcode of Sphingobacterium deserti sp. nov. ZWT. Vertical lines represent restriction sites; distances between lines represent fragment sizes.