Find research datasets worth reusing

opencc-by-4.0Feb 2019View details →

MAPNET Population Genomics Workshop Content: Whole genome sequencing of Bactericera cockerelli

Materials for the Workshop "Getting Started with Low Coverage Population Genomics" , Otago University, 22 March 2019. Alignment files for whole-genome sequence of N=143 Tomato and Potato Psyllids (Bactericera cockerelli)  from 4 New Zealand , 1 Californian and 1 Honduran populations.  Data files represent 250 kbp of one scaffold of a draft assembly. This data was  generated by the  Plant and Food Research in research programme  funded by the Ministry of Business, Innovation and Employment (MBIE) .    <a href="https://github.com/MapNetNZ/Pop-Genomics-Workshop2019">Wokshop GitHub Repo</a>

opencc-by-4.0Dec 2023View details →

Intra-host single-genome sequences of SARS-CoV-2 spike from people without HIV and people living with HIV

Supporting data and code for the study "Rapid Intra-host Diversification and Evolution of SARS-CoV-2 in Advanced HIV Infection" (2024) by Ko & Radecki et al. See <a href="https://github.com/niaid/UMI-pacbio-pipeline/releases/tag/SC2-HIV-demo">the GitHub</a> for demo of SGS and haplotype generation using example data from the study. Raw sequencing data are deposited at <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1055920">PRJNA1055920</a>. READMEs are available within individual folders and releases.

CodonTransformer - Genomic and CodonTransformer-Generated Sequences for Fine-tuned Organisms

This dataset is used in creating Fig. 2a and Supplementary Figs. 2-16 of the paper, mainly including the predictions of base (pretrained) and finetuend CodonTransformer model along with various metrics.

Phylogenetic tree of 1819 YfaL protein sequences identified in 2053 E. coli genomes.

Phylogenetic tree of 1819 YfaL protein sequences identified in 2053 E. coli genomes. The purple circles on the branches represent bootstrap values > 0.8. The different strain’s phylogroups are displayed outside of the tree.

opencc-by-4.0May 2024View details →

Genome sequence of the sugarcane aphid, Melanaphis sacchari (Hemiptera: Aphididae)

The sugarcane aphid, Melanaphis sacchari (Zehntner, 1897), is an agricultural pest that causes damage to plants in the <a name="OLE_LINK12"></a>Poaceae (the grasses) family, such as sorghum and sugarcane. However, genomic resources of this species are currently limited. Here, we used Nanopore long reads and Hi-C interaction map to generate a chromosome-level assembly with a total length of 356.1 Mb, of which 85.5% (304.6 Mb) is contained within the three autosomes and the X chromosome. <a name="OLE_LINK4"></a>Repetitive sequences accounted for 16.29% of the chromosomes and a total of 12,350 protein-coding genes were annotated, achieving 95.8% benchmarking universal single-copy orthologs (BUSCO) gene completeness. Phylogenomic analysis by comparing M. sacchari with twenty-four published aphid genomes representing three aphid tribes reveals that M. sacchari belongs to the tribe Aphidini and maintained a conserved chromosome structure with other Aphidini species. The genomic resources reported in this study will be useful for understanding the evolution of aphid genomes and studying pest management of M. sacchari.

1200 artificial genome sequences containing a single-or-multistep NAHR event each.

This is a companion dataset to Höps et al. 2024: Impact and characterization of serial structural variations across humans and great apes   600 'ancestor'; i.e. source sequences with two pairs of SDs were mutated first. The SD sequences of the two pairs are not overlapping, however the space between SD pairs IS. There are two possible configurations for this: 1-2-2-1 or 1-2-1-2, with 1 and 2 denoting the identity of repeat pair 1 and 2. This configuration as well as the relative orientation of the two SDs (same direction / inverse direction) were randomly chosen. We used four target SD lenghts [100bp, 500bp, 1000bp, 10000bp] and three SD similarity scores [90%, 95%, 99%], totalling 12 combinations. Here, we created 50 artifical sequences for each of these configurations, totalling 600 sequences.  From the 600 ancestor sequences, we then simulated several, again randomly chosen NAHR chains up to depth-3 using the mutate_sequences.py script in the attached github. Finally, we chose two 'representative' mutated seuqnces for each ancestor, totalling 1200 sequences published here.  This upload contains two (zipped) folders; ancestors and mutated_seqs. The ancestors are enumerated 1-600, and mutated seqs likewise have their corresponding ancestor in the beginning of their filename.  The data was created using the generate_mutate script in https://github.com/WHops/nahrwhals_simulate_events release v0.2.    contact: wolfram.hoeps@gmail.com

EGP Mitochondrial Genome Analysis on Human Genome Diversity Project Whole-Genome Sequencing Data

Summary: This dataset consists of running EGP version 1.3 on whole-genome sequencing data from the HGDP. The link to EGP is here https://github.com/tycheleturner/ElGenomaPequeno. Author: Tychele N. Turner, Ph.D. Short Writeup: EGP version 1.3 on Simons Genome Diversity Project: Short-read WGS CRAM files were downloaded from the EMBL-EBI Public Data Globus Endpoint from the <code>/1000g/ftp/data_collections</code> directory. Post-download, the data was run through EGP version 1.3. The results are shown below: <div> <table> <tbody> <tr> <td>Public Dataset</td> <td>EGP Result File Type</td> <td>MD5</td> </tr> <tr> <td>Human Genome Diversity Project</td> <td>Mitochondrial Genome Fasta Files for MEGA</td> <td>2b388c1fa446ecec70e33ea0471e06f8</td> </tr> <tr> <td>Human Genome Diversity Project</td> <td>Mitochondrial Genome MitoMaster Result File</td> <td>50b80ed32b1ae542c8967cc31986dd19</td> </tr> <tr> <td>Human Genome Diversity Project</td> <td>Mitochondrial Genome Variant Tables</td> <td>995f30b74c4bb094a674b1a994853246</td> </tr> <tr> <td>Human Genome Diversity Project</td> <td>Mitochondrial Genome Copy Number</td> <td>e79e61efab4c491fa2825b7d1853df58</td> </tr> </tbody> </table> </div> <div>Please note: I have found that with Zenodo you must use "Download All" for the copy number table to properly open.</div>

EGP Mitochondrial Genome Analysis on Simons Genome Diversity Project Whole-Genome Sequencing Data

Summary: This dataset consists of running EGP version 1.3 on whole-genome sequencing data from the SGDP. The link to EGP is here https://github.com/tycheleturner/ElGenomaPequeno. Author: Tychele N. Turner, Ph.D. Short Writeup: EGP version 1.3 on Simons Genome Diversity Project: Short-read WGS CRAM files were downloaded from the EMBL-EBI Public Data Globus Endpoint from the <code>/1000g/ftp/data_collections</code> directory. Post-download, the data was run through EGP version 1.3. The results are shown below: <table> <tbody> <tr> <th>Public Dataset</th> <th>EGP Result File Type</th> <th>MD5</th> </tr> </tbody> <tbody> <tr> <td>Simons Genome Diversity Project</td> <td>Mitochondrial Genome Fasta Files for MEGA</td> <td>86b09553f80926c1c29c57000ec1a88f</td> </tr> <tr> <td>Simons Genome Diversity Project</td> <td>Mitochondrial Genome MitoMaster Result File</td> <td>010026d77bee81e7b8daf5836bd12da3</td> </tr> <tr> <td>Simons Genome Diversity Project</td> <td>Mitochondrial Genome Variant Tables</td> <td>f1ea3edf4a82b42f2028467fb3544dc4</td> </tr> <tr> <td>Simons Genome Diversity Project</td> <td>Mitochondrial Genome Copy Number</td> <td>4872eeb792c214ad49662e98e4b14620</td> </tr> </tbody> </table> Please note: I have found that with Zenodo you must use "Download All" for the copy number table to properly open.

Whole-genome sequencing reveals contribution of rare and common variation to structural kidney and urinary tract malformations

Supplementary tables detailing analysis of whole-genome sequencing data from 992 patients with congenital anomalies of the kidneys and urinary tract (CAKUT).

EGP Mitochondrial Genome Analysis on 1000 Genomes Project 2504 Whole-Genome Sequencing Data

Summary: This dataset consists of running EGP version 1.3 on whole-genome sequencing data from the 1000 Genomes Project 2504 Dataset. The link to EGP is here https://github.com/tycheleturner/ElGenomaPequeno. Author: Tychele N. Turner, Ph.D. Short Writeup: EGP version 1.3 on 1000 Genomes Project 2504 Dataset: Short-read WGS CRAM files were downloaded through the paths present in this file <code>https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/1000G_2504_high_coverage.sequence.index</code>. Please note that the index files are there as well. You just have to append a <code>.crai</code>. The results are shown below: <div> <table> <tbody> <tr> <td>Public Dataset</td> <td>EGP Result File Type</td> <td>MD5</td> </tr> <tr> <td>1000 Genomes Project 2504</td> <td>Mitochondrial Genome Fasta Files for MEGA</td> <td>dbf39d6ff0e4389b900f9d985f2e6c64</td> </tr> <tr> <td>1000 Genomes Project 2504</td> <td>Mitochondrial Genome MitoMaster Result File</td> <td>4d53ef60ec16f3e4b566c45fdf0fb977</td> </tr> <tr> <td>1000 Genomes Project 2504</td> <td>Mitochondrial Genome Variant Tables</td> <td>16925b546051d37cce27df8ec57ccc5e</td> </tr> <tr> <td>1000 Genomes Project 2504</td> <td>Mitochondrial Genome Copy Number</td> <td>365c1b360ea327795d981356064658a6</td> </tr> </tbody> </table> Please note: I have found that with Zenodo you must use "Download All" for the copy number table to properly open. </div>

EGP Mitochondrial Genome Analysis on 1000 Genomes Project 698 Related Whole-Genome Sequencing Data

<div> Summary: This dataset consists of running EGP version 1.3 on whole-genome sequencing data from the 1000 Genomes Project 698 Related Dataset. The link to EGP is here https://github.com/tycheleturner/ElGenomaPequeno. Author: Tychele N. Turner, Ph.D. Short Writeup: EGP version 1.3 on 1000 Genomes Project 698 Related Dataset: Short-read WGS CRAM files were downloaded through the paths present in this file <code>https://ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp/1000G_2504_high_coverage/additional_698_related/1000G_698_related_high_coverage.sequence.index</code>. The results are shown below: <div> <table> <tbody> <tr> <td>Public Dataset</td> <td>EGP Result File Type</td> <td>MD5</td> </tr> <tr> <td>1000 Genomes Project 698 Related</td> <td>Mitochondrial Genome Fasta Files for MEGA</td> <td>322038d61b4da2e937b32410613c3532</td> </tr> <tr> <td>1000 Genomes Project 698 Related</td> <td>Mitochondrial Genome MitoMaster Result File</td> <td>36c782c12245100478903f7fa191a402</td> </tr> <tr> <td>1000 Genomes Project 698 Related</td> <td>Mitochondrial Genome Variant Tables</td> <td>68b2a51361ffae4e7ad9d420b8becd38</td> </tr> <tr> <td>1000 Genomes Project 698 Related</td> <td>Mitochondrial Genome Copy Number</td> <td>1e83c8ae132b0a7ef33b090757b29063</td> </tr> </tbody> </table> Please note: I have found that with Zenodo you must use "Download All" for the copy number table to properly open. </div>   </div> <h2> </h2>

EGP Mitochondrial Genome Analysis on Gambian Genome Variation Project Whole-Genome Sequencing Data

Summary: This dataset consists of running EGP version 1.3 on whole-genome sequencing data from the GGVP. The link to EGP is here https://github.com/tycheleturner/ElGenomaPequeno. Author: Tychele N. Turner, Ph.D. Short Writeup: EGP version 1.3 on Gambian Genome Variation Project: Short-read WGS CRAM files were downloaded from the EMBL-EBI Public Data Globus Endpoint from the <code>/1000g/ftp/data_collections</code> directory. Post-download, the data was run through EGP version 1.3. The results are shown below: <div> <table> <tbody> <tr> <td>Public Dataset</td> <td>EGP Result File Type</td> <td>MD5</td> </tr> <tr> <td>Gambian Genome Variation Project</td> <td>Mitochondrial Genome Fasta Files for MEGA</td> <td>d21e1e91e8b4c00627171fae79a1f54d</td> </tr> <tr> <td>Gambian Genome Variation Project</td> <td>Mitochondrial Genome MitoMaster Result File</td> <td>b359d1068d4f84f7746d1ebde82df29a</td> </tr> <tr> <td>Gambian Genome Variation Project</td> <td>Mitochondrial Genome Variant Tables</td> <td>ee2b93aa93d2177d92ec0f8f308b43ed</td> </tr> <tr> <td>Gambian Genome Variation Project</td> <td>Mitochondrial Genome Copy Number</td> <td>fda509ba1d2bf33fd2d6b77b92e76c03</td> </tr> </tbody> </table> Please note: I have found that with Zenodo you must use "Download All" for the copy number table to properly open. </div>

EGP Mitochondrial Genome Analysis on GIAB Whole-Genome Sequencing Data

<div> Summary: This dataset consists of running EGP version 1.3 on whole-genome sequencing data from the GIAB. The link to EGP is here https://github.com/tycheleturner/ElGenomaPequeno. Author: Tychele N. Turner, Ph.D. Short Writeup: EGP version 1.3 on GIAB: Short-read WGS CRAM files were downloaded through the paths present in this file <code>https://raw.githubusercontent.com/genome-in-a-bottle/giab_data_indexes/refs/heads/master/AshkenazimTrio/alignment.index.AJtrio_Illumina300X_wgs_novoalign_GRCh37_GRCh38_NHGRI_07282015</code> <div> <table> <tbody> <tr> <td>Public Dataset</td> <td>EGP Result File Type</td> <td>MD5</td> </tr> <tr> <td>GIAB</td> <td>Mitochondrial Genome Fasta Files for MEGA</td> <td>5eac6ec7d36307aa401fd5441b38a506</td> </tr> <tr> <td>GIAB</td> <td>Mitochondrial Genome MitoMaster Result File</td> <td>1151ae74c8e515f4f39bef816bb55d6a</td> </tr> <tr> <td>GIAB</td> <td>Mitochondrial Genome Variant Tables</td> <td>b3e342fe9827df2e399f5685f84cd4dc</td> </tr> <tr> <td>GIAB</td> <td>Mitochondrial Genome Copy Number</td> <td>3c45c19f76f71b3ccaad155565ead5e4</td> </tr> </tbody> </table> </div> <div>Please note: I have found that with Zenodo you must use "Download All" for the copy number table to properly open.</div>     </div> <h2> </h2>

Melange (COGs and Pfams) and AntiSMASH (BGCs) annotations of the genome sequence of Lentilitoribacter sp. EG35

Secondary Metabolite Encoding Biosynthetic Gene Cluster (BGC) annotation files from antiSMASH bacterial version 7.1.0 as well as Clusters of Orthologous Groups of proteins (COG) and Protein families (Pfam) annotations from the Melange pipeline (<a href="https://github.com/sandragodinhosilva/melange">https://github.com/sandragodinhosilva/melange</a>) of the genome assembly of Lentilitoribacter sp. strain EG35, isolated from the temperate octocoral Eunicella gazella sampled in the Northeast Atlantic Ocean, Portugal.  The data correspond to the genome assembly of EG35 available under the BioProject accession number<a href="https://www.ncbi.nlm.nih.gov/bioproject/1075806"> PRJNA1135483</a>. To interactively view the AntiSMASH results, please download and extract the entire content of the AntiSMASH folder, and open the HTML file named "index". This dataset is part of the following study: Tina Keller-Costa, Selene Madureira, Ana S. Fernandes, Lydia Kozma, Jorge M.S. Gonçalves, Cristina Barroso, Conçeicão Egas, & Rodrigo Costa 2024. Genome sequence of the marine alphaproteobacterium Lentilitoribacter sp. EG35 isolated from the temperate octocoral Eunicella gazella. Microbiology Resource Announcements. MRA00872-24.

Raw data for whole plasmid and whole genome sequencing

Original data for plasmid and genomic DNA sequencing in the paper: Tailoring Microbial Fitness Through Computational Steering and CRISPRi-Driven Robustness Regulation

opencc-by-4.0Oct 2024View details →

Supplementary dataset to publication: Whole-genome sequencing of Streptococcus uberis isolated from cows with mastitis in Thuringia

Introduction. Streptococcus uberis is a common cause of mastitis in cattle, leading to significant economic losses. The widespread use of antimicrobials has contributed to the emergence of resistance, which poses a severe challenge in controlling S. uberis infection. Aim. The objective of this study was to gain insights into the antimicrobial resistance (AMR) and epidemiological typing of S. uberis isolated from milk collected from bovine mastitis on dairy farms in Thuringia. Methodology. In this study, 84 S. uberis isolates were obtained from cattle with clinical mastitis in Thuringia, their phenotypic and genotypic AMR were analyzed and their phylogenetic relationship was explored using whole-genome sequencing. Results. Genetically heterogeneous strains were found on the farms, but clusters of highly similar strains also circulated within the same farms. All isolates were sensitive to ampicillin, penicillin, ceftiofur, and vancomycin. However, 42.9%, 42.9%, 22.6%, 19.0%, and 13.0% were resistant to tetracycline, doxycycline, clindamycin, pirlimycin, and erythromycin, respectively. Thirty-nine strains were phenotypically resistant to two or more tested antibiotics. We identified a plasmid associated with macrolide and lincosamide resistance in 12% of the strains. Conclusion. The emergence of S. uberis strains resistant to multiple antibiotics highlights the importance of S. uberis surveillance and the prudent use of antimicrobials.

dryad36/100

Data from: A RAD-sequencing approach to genome-wide marker discovery, genotyping, and phylogenetic inference in a diverse radiation of primates

Until recently, most phylogenetic and population genetics studies of nonhuman primates have relied on mitochondrial DNA and/or a small number of nuclear DNA markers, which can limit our understanding of primate evolutionary and population history. Here, we describe a cost-effective reduced representation method (ddRAD-seq) for identifying and genotyping large numbers of SNP loci for taxa from across the New World monkeys, a diverse radiation of primates that shared a common ancestor ~20-26 mya. We also estimate, for the first time, the phylogenetic relationships among 15 of the 22 currently-recognized genera of New World monkeys using ddRAD-seq SNP data using both maximum likelihood and quartet-based coalescent methods. Our phylogenetic analyses robustly reconstructed three monophyletic clades corresponding to the three families of extant platyrrhines (Atelidae, Pitheciidae and Cebidae), with Pitheciidae as basal within the radiation. At the genus level, our results conformed well with previous phylogenetic studies and provide additional information relevant to the problematic position of the owl monkey (Aotus) within the family Cebidae, suggesting a need for further exploration of incomplete lineage sorting and other explanations for phylogenetic discordance, including introgression. Our study additionally provides one of the first applications of next-generation sequencing methods to the inference of phylogenetic history across an old, diverse radiation of mammals and highlights the broad promise and utility of ddRAD-seq data for molecular primatology.

opencc-zeroDec 2017View details →

opencc-by-4.0Jun 2021View details →

Supplementary Data for: Whole genome sequencing elucidates the species-wide diversity and evolution of fungicide resistance in the early blight pathogen Alternaria solani

Supplementary Data for: Whole genome sequencing elucidates the species-wide diversity and evolution of fungicide resistance in the early blight pathogen Alternaria solani This repository contains: SNP call data / VCF file Scripts for all processing steps from mapping up to PCA and phylogenetic analyses (script.ts) Scripts for population genomic analyses with LEA and PopGenome (scripts.SE) All script names are self explanatory.

dryad36/100

Sequence-based genome-wide association study of individual milk mid-infrared wavenumbers in mixed-breed dairy cattle

Fourier-transform mid-infrared (FT-MIR) spectroscopy provides a high-throughput and inexpensive method for predicting milk composition and other novel traits from milk samples. Whilst there have been many genome-wide association studies (GWAS) conducted on FT-MIR predicted traits, there have been few GWAS for individual FT-MIR wavenumbers. Here we examine associations between genomic regions and individual FT-MIR wavenumber phenotypes within a population of 38,085 mixed-breed New Zealand dairy cattle with imputed whole-genome sequence. GWAS were conducted for each of 895 individual FT-MIR wavenumber phenotypes and three FT-MIR predicted milk composition traits, and gene annotation and mammary tissue gene expression datasets were employed to identify candidate causative genes and variants. This resulted in the identification of 38 co-locating, co-segregating expression QTL (eQTL), and 31 protein-sequence mutations for FT-MIR wavenumber phenotypes, the latter including a null mutation in ABO that has a potential role in changing milk oligosaccharide profiles. For the candidate causative genes implicated in these analyses, the strength of association between relevant loci and each wavenumber across the mid-infrared spectrum revealed shared association patterns for groups of genomically-distant loci, highlighting clusters of loci linked through their biological roles in lactation and their presumed impacts on the chemical composition of milk.

opencc-zeroDec 2020View details →