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opencc-by-4.0Apr 2022View details →

Course 27255 - Sequencing Results

This dataset contains the raw fastq data of the microbial isolates collected during the course 27255 - Advanced Experimental Prokaryotic Molecular Biology and Ecology (Spring 2022) at DTU.

opencc-by-4.0Sep 2021View details →

Comprehensive discovery of CRISPR-targeted terminally redundant sequences in the human gut metagenome: viruses, plasmids, and more

S1 Data Dataset including the discovered CRISPR spacers, direct repeats, protospacers, co-occurrence-based spacer clustering results, predicted protein sequences, built HMMs, database comparison results, phylogenetic analysis results, predicted targeting hosts, and CRISPR-targeted TR sequences.

opencc-by-4.0Mar 2022View details →

Insertion sequences and other mobile elements associated with antibiotic resistance genes in Enterococcus isolates from an inpatient with prolonged bacteremia.

Insertion sequences (ISs) and other transposable elements are associated with the mobilization of antibiotic resistance determinants and the modulation of pathogenic characteristics. In this work, we aimed to investigate the association between ISs and antibiotic resistance genes, and their role in dissemination and modification of the antibiotic resistant phenotype. To that end, we leveraged fully resolved Enterococcus faecium and Enterococcus faecalis genomes of isolates collected over five days from an inpatient with prolonged bacteremia. Isolates from both species harbored similar IS family content but showed significant species-dependent differences in copy number and arrangements of ISs throughout their replicons. Here, we describe two inter-specific IS-mediated recombination events and IS-mediated excision events in plasmids of E. faecium isolates. We also characterize a novel arrangement of the ISs in a Tn1546-like transposon in E. faecalis isolates likely implicated in a vancomycin genotype-phenotype discrepancy. Furthermore, an extended analysis revealed a novel association between daptomycin resistance mutations in liaSR genes and a putative composite transposon in E. faecium, offering a new paradigm for the study of daptomycin resistance and novel insights into the dissemination of daptomycin resistance. In conclusion, our study highlights the role ISs and other transposable elements play in the rapid adaptation and response to clinically relevant stresses such as aggressive antibiotic treatment in enterococci.

opencc-by-4.0Mar 2022View details →

Supporting information for "An Atlas of Convection in Main-Sequence Stars"

The contents of 'code.zip' are the plotting and analysis scripts used in generating the plots in this work. The contents of 'atlas_Z_MW_time_2022_05_06_13_40_06_sha_94d5.zip' are the history files for the MESA runs which the plotting scripts analyze. Each file is in its own directory, labelled by the mass of the star in solar units.

Marine sponge Haliclona fulva hologenome sequences - total contigs assembled

Dataset (multifasta) of DNA contig sequences assembled from Illumina metagenomic reads of Haliclona fulva hologenome. The sequences analyses are described in the peer-reviewed article at https://doi.org/10.3389/fmars.2021.736817 entitled: "The Hologenome of Haliclona fulva (Porifera, Demospongiae) Reveals an Abundant and Diverse Viral Community" by Erika García-Bonilla1,2&dagger;, Diego Chaves-Moreno3&dagger;, Diego Riaño-Pachón4, Wilson Terán5, Alberto Acosta1 and Howard Junca2* 1Laboratorio Ecosistemas Marinos Estratégicos, Unidad de Ecología y Sistemática - UNESIS, Facultad de Ciencias - Departamento de Biología, Pontificia Universidad Javeriana, Bogotá, Colombia 2RG Microbial Ecology: Metabolism, Genomics & Evolution, Division of Ecogenomics & Holobionts, Microbiomas Foundation, Chía, Colombia 3Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany 4Laboratório de Biologia Computacional, Evolutiva e de Sistemas, Centro de Energía Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, Brazil 5Biología de Plantas y Sistemas Productivos, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia "Sample Collection Three specimens of H. fulva (HF1, HF2, and HF3) were collected by SCUBA diving in the Mediterranean Sea at the Grotte du Lido, in the bay of Villefranche-sur-Mer, France (latitude: 43° 41′ 31.49″ N; longitude: 7° 19′ 12.19″ E) at 35 m depth. After collection, all individual samples were placed in independent plastic bags. They were preserved in ethanol 70% (v/v) and stored at −20°C until further analysis. The samples were selected based on the findings of our previous study (<a href="https://www.frontiersin.org/articles/10.3389/fmars.2021.736817/full#B11">García-Bonilla et al., 2019</a>) and are coming from exactly the same spots and colonies/specimens analyzed regarding microbiome content by 16S amplicons, showing a stable and consistent microbial composition of low microbial abundance and diversity. DNA Extraction and Sequencing Metagenomic DNA was extracted from 15 g sponge wet weight using a MagAttract® HMW DNA kit (Qiagen, Germany) following the manufacturer’s instructions. Tissue lysis was made for 16 h according to protocol. Extracted DNA was eluted with 50 μl water, and its concentration determined by fluorescence using the Qubit® dsDNA BR assay kit (Thermo Fisher Scientific). Nucleic acid integrity was verified by 0.8% agarose gel electrophoresis. Sponge DNA extracts were used as template to perform isothermal multiple displacement hologenome amplification with a phi29 polymerase of high processivity and fidelity in order to increase total DNA concentrations (<a href="https://www.frontiersin.org/articles/10.3389/fmars.2021.736817/full#B36">Lasken, 2007</a>) and to avoid the effect of coextracted enzymatic inhibitors detected in H. fulva, improving further downstream processes (library construction and sequencing). The amplification process was made using REPLI-g Mini kit (Qiagen, Germany), according to manufacturer’s recommendations. Briefly, samples were incubated at 30°C for 11 h followed by 3 min at 65°C for polymerase inactivation. For all assays, a negative control was run to evaluate the presence of contaminants during amplification. Quantity and quality of DNA was measured as described previously. Genomic libraries were constructed using TruSeq DNA PCR free kit (Illumina, United States). Shotgun hologenome sequencing was performed using paired-end Illumina technology (Macrogen, South Korea). The complete raw sequencing data obtained is publicly accessible at NCBI GenBank SRA under Bioproject PRJNA741981. Raw Data Processing and Assembly An initial filtering of the sequencing reads was done after visual evaluation using FastQC (v.0.11.8) consisting of a quality and length-based filtering performed with Trimmomatic (v.0.31). Filtered and processed reads were assembled using Megahit (v.1.0) (<a href="https://www.frontiersin.org/articles/10.3389/fmars.2021.736817/full#B37">Li et al., 2014</a>) and IDBA-UD (<a href="https://www.frontiersin.org/articles/10.3389/fmars.2021.736817/full#B46">Peng et al., 2012</a>) with default parameters. To compare, identify and join overlaps between reads from each assembly, we used minimus2 from the AMOS suite with default parameters (<a href="https://www.frontiersin.org/articles/10.3389/fmars.2021.736817/full#B65">Treangen et al., 2011</a>). Obtained contigs were filtered and those <500 bp were removed."

Point-of-care monitoring of head and neck cancer treatment response and recurrence development using nanopore-based ctDNA consensus sequencing

Circulating tumor DNA (ctDNA) in blood may become a generic biomarker for non-invasive cancer diagnosis and monitoring. However, detection of ctDNA is challenged by the presence of many circulating DNA molecules from healthy cells. We found that single ctDNA molecules can be sequenced with high accuracy by a three-step process consisting of capturing, copying and concatenation of the original double-stranded ctDNA molecules. This innovative approach - called CyclomicsSeq -  is unparalleled by any other method in terms of cost-efficiency and speed, allowing point-of-care cancer diagnostics. Within this CPOC, subsidized by the Oncode institute, we have applied our CyclomicsSeq ctDNA test in patients with advanced head and neck cancer squamous cell carcinoma (HNSCC). Head and neck cancer (HNSCC) accounts for 380,000 cancer-related deaths worldwide. For these patients, determining whether a patient responds to the primary chemoradiation treatment is challenging, and non-responders are sometimes identified when other treatment options are no longer possible. By measuring the ctDNA levels in the blood of these patients prior to and during treatment, we aim to identify non-responders at an earlier stage. This dataset contains base calls of TP53 of 47 nanopore sequencing runs. We included 10 patients and 7 controls. For the patients, we have samples of multiple time points (0 = prior to treatment, 1 = 1 week after treatment initiation, etc).

Sequence Similarity Network (SSN) and Genome Neighbourhood Network (GNN) for Mycobacterium Cytochrome P450 enzymes

This dataset was generated in the context of the Horizon 2020 MSCA IF action deCrYPtion (Grant 839116). The aim of this project is to use comparative genomics in order to propose and then test the function of uncharacterised Cytochrome P450 enzymes that are present among Mycobacterium species. More information about this project can be found at: https://cordis.europa.eu/project/id/839116. This dataset contains: - The FASTA sequences files obtained from the UniProt database, for members of the PF00067 protein family (CYP). - A set of reference FASTA sequences, matching the supplementary material from the following publication: Parvez, M. et al. (2016) ‘Molecular evolutionary dynamics of cytochrome P450 monooxygenases across kingdoms: Special focus on mycobacterial P450s’, Scientific Reports, 6(1), p. 33099. doi:<a href="https://doi.org/10.1038/srep33099">10.1038/srep33099</a>. - A combined FASTA files of both previously described, that was used for the generation of SSNs - A PNG image produced from the analysis of the Sequence Similarity Networks generated at AST78 (corresponding to 40% identity, defining CYP families) - A PNG image produced from the analysis of the Sequence Similarity Networks generated at AST141 (corresponding to 55% identity, defining CYP subfamilies) - A Cytoscape session for the Sequence Similarity Networks from the combined FASTA file generated using the Enzyme Function Initiative web tools (https://efi.igb.illinois.edu), at AST78 - A Cytoscape session containing Sequence Similarity Networks and Genome Neighborhood Network from the combined FASTA file  generated using the Enzyme Function Initiative web tools (https://efi.igb.illinois.edu), at AST141

Polymorphism-aware estimation of species trees and evolutionary forces from genomic sequences with RevBayes

Supplementary files of Polymorphism-aware estimation of species trees and evolutionary forces from genomic sequences with RevBayes by Borges, Boussau, Höhna, Pereira and Kosiol

Data in support of "An exploration of linkage fine-mapping on sequences from case-control studies"

These data were simulated for an exploration of linkage fine-mapping on sequences from case-control studies. The code to generate and analyze the data is available on GitHub in the scripts at <a href="https://github.com/SFUStatgen/PBJ0">https://github.com/SFUStatgen/PBJ0</a>. Queries may be directed to Payman Nickchi at <a href="mailto:pnickchi@sfu.ca">pnickchi@sfu.ca</a> or Charith (Bhagya) Karunarathna at <a href="mailto:ch757276@dal.ca">ch757276@dal.ca</a>.

Phylogenetic analysis of policistronic amino-acid sequences encoded by 116 flavivirus genomes

Recently, Genome Biology and Evolution (11:3341-3352) published three statistical tests for testing whether alignments of sequence data violate the phylogenetic assumption of evolution under homogeneous conditions. The tests extend the matched-pairs tests of symmetry, marginal symmetry, and internal symmetry for pairs of aligned homologous sequences to the case where a whole alignment is considered. Here we reveal that the new tests are misleading. We explain why this is so, reveal how the tests of whole alignments may be done, and release new bioinformatics tools that implement statistically sound methods of dealing with multiple comparisons (i.e., by controlling the family-wise error rate or the false discovery rate). Using the new software to analyse an alignment of amino acids encoded by 116 flavivirus genomes, we reveal, for the first time, that these genomes are unlikely to have evolved under stationary, reversible, and homogeneous Markovian conditions.

Morphological and DNA sequence data generated by Sanger sequencing and target capture methods for moss plants in the genus Fissidens from herbarium specimens

Morphological evolution in mosses has long been hypothesized to accompany shifts in microhabitats and can be tested using comparative phylogenetics. These lines of inquiry have developed substantially, in part, by target capture sequencing allowing for phylogenomic scale data generated from herbarium specimens. In the present study, we test the relationship between taxonomically important morphological characters in the moss genus Fissidens, using both a 400-locus dataset generated using a target-capture approach as well as a three-locus phylogeny generated using sanger sequencing. Phylogenetic trees were generated using ASTRAL and Bayesian Inference and used to test the monophyly of subgenera/sections and provided the basis for ancestral character reconstruction and phylogenetic correlation analyses among five morphological characters as well as habitat moisture scored from literature. The characters axillary hyaline nodules, limbidium, costa, and peristome morphology as well as sexual system, minimum habitat moisture, average habitat moisture, maximum habitat moisture, and habitat moisture niche breadth each exhibit statistically significant phylogenetic signal. Significant correlations were found between the limbidium (phyllid/leaf border) and habitat moisture niche breadth, which could be interpreted as a more extensive limbidium enabling species to survive across a wider variety of habitats. Correlations were also found between costa anatomy and the limbidum of the gametophyte and sporophyte peristome morphology, as well as average habitat moisture and sexual system. Continued exploration of the relationships between morphological evolution, life history, and habitat will enable us to expand our understanding of functional morphology in mosses.

Mitochondrial DNA sequencing results control and MELAS fibroblasts. Povea-Cabello, S. et al 2022.

Mitochondrial DNA sequencing results from control and MELAS patients-derived dermal fibroblasts. Povea-Cabello, S. et al 2022.

Sequence-structure-function relationships in the microbial protein universe

The Microbiome Immunity Project (MIP) dataset contains models predicted with both Rosetta and DMPFold (folder `dataset/`). It also contains DeepFRI function predictions for all models.  The `metadata` folder contains additional data which may be useful for searching the MIP database (FASTA files, BLAST databases and useful scripts for structure/function search) as well as retrieving the sequence/structural annotations. The `intermediate_data` folder contains preprocessed output for reproducing many of the figures in our manuscript in conjunction with scripts and Juypter notebooks found in our git repository: https://github.com/microbiome-immunity-project/protein_universe . More information about the dataset and associated metadata is provided in the `README.md` file). We are also providing workflows to search the MIP database against a protein sequence or structure or function of interest (see `SEARCHING.md` for more details).

Data in support of "An exploration of linkage fine-mapping on sequences from case-control studies"

These data were simulated for an exploration of linkage fine-mapping on sequences from case-control studies. The scripts to generate and analyze the data are available at <a href="https://github.com/SFUStatgen/PBJ0">https://github.com/SFUStatgen/PBJ0</a>. Queries may be directed to Payman Nickchi at <a href="mailto:pnickchi@sfu.ca">pnickchi@sfu.ca</a> or Charith (Bhagya) Karunarathna at <a href="mailto:ch757276@dal.ca">ch757276@dal.ca</a>. README file for All_data directory Directory structure The All_data directory consists of this README file and 500 sub-directories named DatasetX, for X=1 to 500. Within each DatasetX sub-directory are further sub-directories named alt and null containing files named pop_data.RData and sample_data.RData. alt versus null directories The files in the alt and null directories contain the same variant data but different phenotype data. In particular, under the null hypothesis, disease status is simulated at random according to a 5% prevalence in the population, whereas under the alternative hypothesis disease status is simulated according to a penetrance model that depends on causal SNVs. The R script to simulate data under the alternative hypothesis is in the file 1_SimulateData.R in the Github repository <a href="https://github.com/SFUStatgen/PBJ0">https://github.com/SFUStatgen/PBJ0</a>. pop_data.RData and sample_data.RData files The data structures contained in the pop_data.RData and sample_data.RData files are described below. The structure is the same under both the null and alternative hypothesis. pop_data.RData From R, load("pop_data.RData") loads a list named pop_data whose elements describe the population’s haplotype and phenotype data. The list elements are as follows. <ul> <li>Variants: a matrix of variants for the population of 6200 haplotypes <ul> <li>rows are SNVs,</li> <li>columns are sequences</li> </ul> </li> <li>Positions: a data frame of SNV positions <ul> <li>rows are SNVs,</li> <li>column 1 is the SNV name and column 2 is the SNV position in base pairs</li> </ul> </li> <li>Population.Mapping: a data frame telling us how the sequences are paired into individuals <ul> <li>rows are individuals</li> <li>First column 1 is an individual ID from 1,…,3100; columns 2 and 3 are the sequence IDs of the first and second sequence for that individual where the sequence IDs are the column names of the Variants matrix.</li> </ul> </li> <li>Genotype.Matrix: a matrix of genotypes (i.e. variant counts) for the 3100 individuals <ul> <li>rows are SNVs</li> <li>columns are the individuals</li> </ul> </li> <li>causal_region: a vector containing the lower- and upper-limit of the causal region in base pairs.</li> <li>cSNV: a vector containing the IDs of the causal SNVs, where the SNV IDs are the row names of the Variants matrix.</li> <li>DISCRETE: a list with the following elements. <ul> <li>CaseIndividuals: vector of IDs of the affected individuals in the population.</li> <li>ControlIndividuals: vector of IDs of the unaffected in the population.</li> <li>BinaryTrait: a vector of trait status (0=unaffected, 1=affected) for each individual.</li> </ul> </li> </ul> Note: Within the same DatasetX directory, the only difference between the pop_data data structures under the null and alternative hypothesis is the phenotype information contained in their respective DISCRETE list elements. Both the null and alternative pop_data data structure share list elements: Variants, Positions, Population.Mapping, Genotype.Matrix, causal_region and cSNV. sample_data.RData From R, load("sample_data.RData") loads a list whose elements describe the sequences and phenotypes of the sample of 50 affected individuals (cases) and 50 unaffected individuals (controls) from the population. <ul> <li>Haps: a list with two elements. <ul> <li>sample_haps: a matrix of 200 sequences for the 50 cases and 50 controls. Rows are SNVs and columns are sequences, with the sequences of sampled cases appearing first (i.e. first 100 columns), followed by the sequences of sampled controls (i.e. last 100 columns). Sequences include only those SNVs that are polymorphic in the sample.</li> <li>ccStatus: a vector indicating the case/control status of the individual to which the sequence belongs, with case=1 and control=0.</li> </ul> </li> <li>Genos: a list with two elements. <ul> <li>sample_genos: a matrix of 100 genotypes for the 50 cases and 50 controls. Rows are SNVs and columns are genotypes, with genotypes of cases appearing first, followed by genotypes of controls.</li> <li>ccStatus: a vector indicating the case/control status of each individual, with case=1 and control=0.</li> </ul> </li> <li>Posn: a data frame of SNV positions for each SNV that is polymorphic in the sample. The first column is the SNV name and the second is the SNV position in base pairs. Posn is a subset of pop_data$Positions.</li> <li>poly_cSNV: a vector of IDs for causal SNVs that are polymorphic in the sample.</li> <li>CaseIND: a vector of individual IDs for the case individuals (see pop_data$Population.Mapping).</li> <li>ControlIND: a vector of individual IDs for the control individuals (see pop_data$Population.Mapping).</li> <li>CaseHapID: a vector of IDs for the sequences that belong to cases (see the sequence IDs in the column names of the matrix pop_data$Variants).</li> <li>ControlHapID: a vector of IDs for the sequences that belong to controls (see the sequence IDs in the column names of the matrix pop_data$Variants).</li> </ul>

Sequence diagram of the RIPOSTE framework

Sequence diagram of the RIPOSTE framework This directory contains the sequence diagram supporting the publication Riposte. R. Jolak, T. Rosenstatter, S. Aldaghistani, and R. Scandariato, "A Collaborative Cyber Attack Response Framework for the Automotive Systems" to be published at the 48th Euromicro Conference Series on Software Engineering and Advanced Applications (SEAA), Gran Canaria, Spain, 2022.

Whole genome re-sequencing of B. dorsalis in the Indian Ocean

Files containing essential data for the production of the paper: Bactrocera dorsalis in the Indian Ocean: a tale of two invasions (Deschepper et. al, 202X) DOI:####

BeerDEcoded Nanopore Sequencing workshop of la trappe Dez. 2019

The BeerDEcoded workshops are a project of the Street Science Community. https://streetscience.community/projects/beerdecoded/ We are extracting DNA from different Beers and sequence them using the Nanopore sequencing technique. The data contains the reads extracted from the beer of the brand la trappe and was performed on 08.12.2019.   The sequencing was performed on a MinION using a Flow Cell and the MinKNOW software. The Software collects sequencing data in real-time and has a base-calling integrated to convert the fast5 files into fastq files.

Deep-sequencing of viral genomes from treatment-naive HIV-infected persons shows positive association between intrahost genetic diversity and viral load

Background: Infection with human immunodeficiency virus type 1 (HIV) typically results from transmission of a small and genetically uniform viral population. Following transmission, the virus population becomes more diverse because of recombination and acquired mutations through genetic drift and selection. Viral intrahost genetic diversity remains a major obstacle to the cure of HIV; however, there is a disagreement whether intrahost viral genetic diversification associates positively or negatively with disease progression and progression markers. Viral load is a key progression marker and understanding its relationship to viral intrahost genetic diversity could help design future strategies for HIV monitoring and treatment. Methods: We analyzed deep-sequenced viral genomes from 2,650 treatment-naive HIV-infected persons to measure the intrahost genetic diversity of 2,447 genomic codon positions as calculated by Shannon entropy. We tested for associations between viral load (VL) and amino acid (AA) entropy accounting for sex, age, race, duration of infection, and HIV population structure. Results: We confirmed that the intrahost genetic diversity is highest in the env gene. Furthermore, we showed that mean Shannon entropy is significantly associated with VL, especially in infections of >24 months duration. We identified 16 significant associations between VL (p-value<2.0x10-5) and Shannon entropy at AA positions which in our association analysis explained 13% of the variance in VL. Conclusions: Our results elucidate that viral intrahost genetic diversity is associated with VL and could be used as a better disease progression marker than HIV consensus sequence variants, especially in infections of longer duration. We emphasize that viral intrahost diversity should be considered when studying viral genomes and infection outcomes.

Data file: Amino acid sequence Cm28; a scorpion toxin

The Data set contains the amino acid sequence of Cm28, a peptide toxin found in the venom of Centruroides margaritatus. The peptide sequence and functional data are reported in an article in the Journal of General Physiology (JGP) under this DOI 10.1085/jgp.202213146 and this data will appear in the UniProt Knowledgebase under the accession number C0HM22.

Joint analysis of microsatellites and flanking sequences enlightens complex demographic history of interspecific gene flow and vicariance in rear-edge oak populations

Inference of recent population divergence requires fast evolving markers and necessitates to differentiate shared genetic variation caused by ancestral polymorphism and gene flow. Theoretical research shows that the use of compound marker systems integrating linked polymorphisms with different mutational dynamics, such as a microsatellite and its flanking sequences, can improve estimation of population structure and inference of demographic history, especially in the case of complex population dynamics. However, empirical application in natural populations has so far been limited by lack of suitable methods for data collection. A solution comes from the development of sequence-based microsatellite genotyping which we used to study molecular variation at 36 sequenced nuclear microsatellites in seven Quercus canariensis and four Q. faginea rear-edge populations across Algeria. We aim to decipher their taxonomic relationship, past evolutionary history and recent demographic trajectory. First, we compare the estimation of population genetics parameters and simulation-based inference of demographic history from microsatellite sequence alone, flanking sequence alone or the combination of linked microsatellite and flanking sequence variation. Second, we apply random forest approximate Bayesian computation to identify which of these sequence types is most informative. Whereas analysing microsatellite variation alone indicates recent interspecific gene flow, additional information gained by integrating nucleotide variation in flanking sequences, by reducing homoplasy, suggests ancient interspecific gene flow followed by drift in isolation instead. The weight of each polymorphism in the inference also demonstrates the value of linked variations with contrasted mutation dynamic to improve estimation of both demographic and mutational parameters.