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Experimental data for "An End-to-End Coding Scheme for DNA-Based Data Storage With Nanopore Sequenced Reads"

The experimental dataset used in "An End-to-End Coding Scheme for DNA-Based Data Storage With Nanopore Sequenced Reads." A set of 91,766 150-nt oligos were synthesised with GenScript (oligos.fasta). Each oligo consists of a pseudo-random 110-nt payload flanked by 20-nt primers at each end. The strands are split in three roughly equal groups (two groups of 30,589 and one group of 30,588). Each group has a dedicated primer pair for targeted PCR amplification (the primer pairs used for amplification are provided in primers_synthesis.fasta). The pseudo-random payload was designed to avoid primer-payload collisions. For each file, a sample from the synthesised pool was PCR amplified using the corresponding primer pair and sequenced using Oxford Nanopore Technologies MinION sequencing device following the standard library preparation protocol for amplicon DNA. The raw reads were basecalled using guppy, either in fast- ("acc-false") or high-accuracy ("acc-true") regime. The basecaller generated two groups of reads—"passQ-true" for the reads that passed the quality-score threshold of 8 and "passQ-false" for those that did not. For each group of reads, a BLAST-based fuzzy search for primer sequences was performed and, based on the resulting alignments, the segments containing the correct primer pairs and located at a distance of 150+-15nt were extracted (separately for forward and reverse-complemented reads). The segments are then assigned to the closest synthesized strand based on Levenshtein distance. The resulting clusters are used to estimate the parameters of the end-to-end DNA storage channel model and to test the proposed error-correction scheme. The archive clustered_read_segments.tar.gz contains 12 sub-archives, for each file (0,1,2), accuracy ("acc-true" or "acc-false"), and Q-score ("passQ-true" or "passQ-false"). Within each sub-archive, there are two folders (one for forward read segments and one for backward read segments), and each folder contains two files: one for the reference synthesised (or "transmitted") sequences that correspond to the file in question ("TX__" — e.g., "TX__file=0_accBaCa=true_passQ=true_filter=true_forward_.txt") and another file for the sequenced (or "received") segment clusters ("RX__" — e.g., "RX__file=0_accBaCa=true_passQ=true_filter=true_forward_.txt"). The received clusters in the "RX__" file are ordered in correspondence with the synthesised sequences in the "TX__" file, and a line "===============================" is used as a separator.

Pulse sequences for measurement of magnetization exchange and effective 1H relaxation rates in condensed phase

- ddHSQC based 4D pulse sequence for measurement of magnetization exchange in condensed phase samples, using gradients for coherence selection. Processing scripts for processing the data.  - ddHMQC based 3D pulse sequence for measurement of effective proton transverse relaxation rates in condensed phase samples, using gradients for coherence selection

opencc-by-4.0Apr 2023View details →

ddRAD sequencing of Fagus sylvatica sensu lato

ddRAD sequencing data from Stacks (SNPs) along with corresponding information. Exon-only genotypes in file "genotypes_exons-only.7z".

Genome sequence resources from three isolates of the apple canker pathogen Neonectria ditissima infecting forest trees

Neonectria ditissima is a generalist ascomycete plant pathogen causing canker diseases on a variety of hardwood tree species and can cross-infect many of them. The fungus enters the plants through wounds throughout the year. N. ditissima is considered a major threat to apple production responsible for the fruit tree canker disease which damages trees and causes rotting of fruits in storage. Nearby forests and shelter belts can serve as source of inoculum for well-managed apple orchards. Thus, knowledge about the N. ditissima isolates infecting different host species is essential for designing integrated pest management strategies. Here, we describe the genomes of three N. ditissima isolates, Nd_iso34, Nd_iso35, and Nd_iso36, infecting European beech, American tulip tree, and American beech, respectively. We obtained genome assemblies of ca. 45 megabases for all isolates, covering 94% of the N. ditissima reference annotation, and 97% of the universal single-copy orthologs (BUSCOs). We conclude that these genome assemblies are a highly relevant resource considering the scarcity of genomic data available for N. ditissima.

Strainy: phasing and assembly of strain haplotypes from long-read metagenome sequencing - Real and mock datasets

This repository contains the reads, assemblies, and references required to replicate the real and mock results presented in the paper: https://doi.org/10.1101/2023.01.31.526521

Strainy: phasing and assembly of strain haplotypes from long-read metagenome sequencing - Simulated datasets

This repository contains the reads, assemblies, and references required to replicate the simulated results presented in the paper: https://doi.org/10.1101/2023.01.31.526521

opencc-by-4.0Mar 2024View details →

Mini In Situ Sequencing mouse brain dataset using Cartana technology

<div> <div> <div> A subset of an ISS dataset is being utilized here to showcase the data format without replicating the ISS decoding procedure (for this first version). There are in total 3 data objects: <ol> <li>A 5-channel raw microscope image</li> <li>The corresponding single cell segmentation image (label image)</li> <li>The correspdoning single-cell gene expression data object (.h5ad)</li> </ol> </div> </div> </div>

opencc-by-4.0Nov 2023View details →

Data supporting publication "Metagenomic Immunoglobulin Sequencing (MIG-Seq) Exposes Patterns of IgA Antibody Binding in the Healthy Human Gut Microbiome"

Data supporting publication "Metagenomic Immunoglobulin Sequencing (MIG-Seq) Exposes Patterns of IgA Antibody Binding in the Healthy Human Gut Microbiome"

Rapid Inference of Antibiotic Susceptibility Phenotype of Uropathogens using Metagenomic Sequencing with Neighbour Typing - RASE Database for EuSCAPE

RASE databases used for the prediction of antibiotic phenotype in the paper titled "Rapid Inference of Antibiotic Susceptibility Phenotype of Uropathogens using Metagenomic Sequencing with Neighbour Typing". A database for Klebsiella pneuomiae constructed from EuSCAPE isolates.

Datasets accompanying "Deciphering the heterogeneity of differentiating hPSC-derived corneal limbal stem cells through single-cell RNA-sequencing"

Datasets include two seurat objects: one with all unfiltered cells and raw expression data (seu_unfiltered.rds) and one dataset with normalised expression and latest annotations (differentiation_object_latest.rds). Additionally, a single-cell object containing post-(py)SCENIC analysis is added (ipsc_scenic.h5ad).

Sequencing data for seabird eDNA in long-nosed fur seal diets from southeastern Australia

Wildlife conflicts require robust quantitative data on incidence and impacts, particularly among species of conservation and cultural concern. We apply a multi-assay framework to quantify predation in a southeastern Australian scenario where complex management implications and calls for predator culling have grown despite a paucity of data on seabird predation by recovering populations of long-nosed fur seals (Arctocephalus forsteri). We apply two ecological surveillance techniques to analyse this predator's diet – traditional morphometric (prey hard-part) and environmental DNA metabarcoding (genetic) analyses using an avian specific primer for the 12S ribosomal RNA (rRNA) gene – to provide managers with estimated predation incidence, number of seabird species impacted and inter-prey species relative importance to the predator. DNA metabarcoding identified additional seabird taxa and provided relative quantitative information where multiple prey species occur within a sample; while parallel use of both genetic and hard-part analyses revealed a greater diversity of taxa than either method alone. Using data from both assays, the estimated frequency of occurrence of predation on seabirds by long-nosed fur seals ranged from 9.1–29.3% of samples and included up to 6 detected prey species. The most common seabird prey was the culturally valued little penguin (Eudyptula minor) that occurred in 6.1–25.3% of samples, higher than previously reported from traditional morphological assays alone. We then explored DNA haplotype diversity for little penguin genetic data, as a species of conservation concern, to provide a preliminary estimate of the number of individuals consumed. Polymorphism analysis of consumed little penguin DNA identified five distinct mitochondrial haplotypes – representing a minimum of 16 individual penguins consumed across 10 fur seal scat samples from 99 sampled across southeastern Australia. We recommend rapid uptake and development of cost-effective genetic techniques and broader spatiotemporal sampling of fur seal diets to further quantify predation and hotspots of concern for wildlife conflict management.

DNA sequences for: Synthetic control of actin polymerization and symmetry breaking in active protocells

Non-linear biomolecular interactions on membranes drive membrane remodeling crucial for biological processes including chemotaxis, cytokinesis, and endocytosis. The complexity of biomolecular interactions, their redundancy, and the importance of spatiotemporal context in membrane organization impede understanding of the physical principles governing membrane mechanics. Developing a minimal in vitro system that mimics molecular signaling and mem- brane remodeling while maintaining physiological fidelity poses a significant challenge. Inspired by chemotaxis, we reconstructed chemically regulated actin polymerization inside vesicles, guiding membrane self-organization. An external, undirected chemical input induced directed actin polymerization and membrane deformation uncorrelated with upstream biochemical cues, suggesting symmetry breaking. A biophysical model incorporating actin dynamics and membrane mechanics proposes that uneven actin distributions cause non-linear membrane deformations, consistent with experimental findings. This protocellular system illuminates the interplay between actin dynamics and membrane shape during symmetry breaking, offering insights into chemotaxis and other cell biological processes.

Nanopore sequencing assay to detect and diagnose tuberculous meningitis via cerebrospinal fluid

This study aimed to evaluate the efficiency of nanopore sequencing for the early diagnosis of tuberculous meningitis (TBM) using cerebrospinal fluid and compared it with acid-fast bacilli (AFB) smear, mycobacterial growth indicator tube (MGIT) culture, and Xpert MTB/Rifampicin (RIF). We enrolled 64 adult patients with presumptive TBM admitted to our hospital from August 2021 to August 2023. We calculated the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of AFB smear, culture, Xpert MTB/RIF, and nanopore sequencing to evaluate their diagnostic efficacy compared with a composite reference standard for TBM. Among these 64 patients, all tested negative for TBM by AFB smear. The sensitivity, specificity, PPV, and NPV were 11.11%, 100%, 100%, and 32.2% for culture, 13.33%, 100%, 100%, and 2.76% for Xpert MTB/RIF, and 77.78%, 100%, 100% and 65.52% for nanopore sequencing, respectively. The diagnostic accuracy of the nanopore sequencing test was significantly higher than that of conventional testing methods used to detect TBM.

opencc-zeroFeb 2025View details →

Data from: Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR

"Mid-density" targeted genotyping-by-sequencing (GBS) combines trait-specific markers with thousands of genomic markers at an attractive price for linkage mapping and genomic selection. A 2.5K targeted GBS assay for potato was developed using the DArTagTM technology and later expanded to 4K targets. Genomic markers were selected from the potato InfiniumTM SNP array to maximize genome coverage and polymorphism rates. The DArTag and SNP array platforms produced equivalent dendrograms in a test set of 298 tetraploid samples, and 83% of the common markers showed good quantitative agreement, with RMSE (root-mean-squared-error) less than 0.5. DArTag is suited for genomic selection candidates in the clonal evaluation trial, coupled with imputation to a higher-density platform for the training population. Using the software polyBreedR, an R package for the manipulation and analysis of polyploid marker data, the RMSE for imputation by linkage analysis was 0.15 in a small half-diallel population (N=85), which was significantly lower than the RMSE of 0.42 with the Random Forest method. Regarding high-value traits, the DArTag markers for resistance to potato virus Y, golden cyst nematode, and potato wart appeared to track their targets successfully, as did multi-allelic markers for maturity and tuber shape. In summary, the potato DArTag assay is a transformative and publicly available technology for potato breeding and genetics.

Gene and protein sequence features augment HLA class I ligand predictions

Dataset and analyses supporting the manuscript "Gene and protein sequence features augment HLA class I ligand predictions". The "peptides" files contain the mass-spec detected peptides obtained from HLA ligandomics performed on the indicated tumor lines.  The "protein data" files contain the RNAseq data (TPM) and Ribosome profiling data (ribosome occupancy) per protein, for each tumor line.  The "source data" zip archive contains the source data underlying the figures of the manuscript. The "HLA ligandome analyses" zip archive contains the R scripts used for all data analysis in the manuscript, including all data and output files. These analyses can also be found at https://github.com/kasbress/HLA_Ligandome_Analyses/

Selection pressure analysis of dengue virus complete genome and E gene nucleotide sequences from Pakistan

This dataset comprises 43 E gene and 44 complete genome nucleotide sequences of the dengue virus from serotypes DENV-1 to DENV-4, representing all documented sequences in Pakistan to date, sourced from the Virus Pathogen Resource (ViPR) database and NCBI. The E gene is critical as it is involved in serotype changes of the dengue virus, making it a pivotal target for understanding shifts in viral pathogenicity and immune escape mechanisms. The aim of compiling this dataset is to facilitate comprehensive genetic analysis and enhance understanding of the evolutionary dynamics of the dengue virus within the region. To assess the evolutionary pressures acting on these sequences, we conducted a selection pressure analysis utilizing computational methods. These methods include the Single Likelihood Ancestor Counting (SLAC), Fixed Effects Likelihood (FEL), adaptive Branch Site Random Effects Likelihood (aBSREL), Mixed Effects Model of Evolution (MEME), and the Genetic Algorithm for Recombination Detection (GARD), all implemented in the HyPhy software package. Our analysis focused on identifying genomic sites under both positive and negative selection pressures, providing insights into the adaptive evolutionary processes affecting the E gene of the dengue virus in Pakistan. Understanding the molecular evolution of this gene is crucial for predicting serotype evolution, potentially aiding in the development of effective vaccines and therapeutic strategies.

FLAIR2 results from LRGASP R2C2 sequencing of Human WTC11 and Mouse ES cell lines

FLAIR2 results from Oxford Nanopore sequencing of R2C2 libraries generated from Human WTC11 and Mouse ES cell lines from the Long-read RNA-seq Genome Annotation Assessment Project (LRGASP) (Pardo-Palacios et al. Nature Methods 2024). FLAIR2 high-confidence isoforms are provided for WTC11 and ES cells. For Mouse ES cells, sequence variants were identified with Longshot and incorporated into transcript isoforms using FLAIR2. These data are associated with the FLAIR2 publication (Tang et al. 2024)

Machine-Learning Based Location of the 2021 MW 7.4 Maduo Earthquake Sequence: Insight into Intraplate Seismogenesis

This file is the Machine-Learning Based earthquake catalog of the 2021 MW 7.4 Maduo Earthquake. It is only used for scientific research. ATTENTION!!! The data for the paper "Relocation of the 2024 MS 7.1 Wushi, Xinjiang earthquake sequence and implications for seismogenic structure" is accessible at the website "https://zenodo.org/records/12790377". ATTENTION!!!

opencc-by-4.0Dec 2023View details →

Nucleotide sequence database of Copper-containing membrane monooxygenases genes for analysing primer pairs targeting the ammonia monooxygenase subunit A gene of complete ammonia oxidising Nitrospira

Nucleotide sequences of 487 Cu-mmo genes, including amoA comammox clade A and clade B, amoA ammonia oxidizing bacteria as well as other Cu-mmo genes.