Find research datasets worth reusing

opencc-by-4.0Jul 2023View details →

Alliance of Genome Resources Sequence Variants

Variant Call Format (VCF) formatted spreadsheets of sequence variants associated with phenotypic alleles from the Alliance of Genome Resources. Variants are in Human Genome Variation Society (HGVS) nomenclature syntax. Files include variants in VCF format for the following organisms: <ul> <li>Caenorhabditis elegans (nematode; NCBI:txid 6239)</li> <li>Danio rerio (zebrafish;NCBI:txid 7955)</li> <li>Drosophila melanogaster (fruit fly; NCBI:txid 7227)</li> <li>Mus musculus (mouse; NCBI:txid10090)</li> <li>Rattus norvegicus (rat; NCBI:txid 10116)</li> </ul>

Whole-genome sequences of Cercospora beticola isolates from Germany and Italy.

Sequences used in the manuscript "Large-scale analyses reveal the contribution of adaptive evolution in pathogenic and non-pathogenic fungal species"

opencc-by-4.0Feb 2022View details →

Supplemental material of "An annotated whole-genome multilocus sequence typing schema for scalable high resolution typing of Streptococcus pyogenes"

This supplemental material includes the genome assemblies, associated metadata and analysis results for five datasets used to define a publicly available annotated wgMLST schema for S. pyogenes and to evaluate its suitability for high resolution typing. A brief description for each file in the dataset is available in the included README file. Raw sequencing data and sample metadata for the 265 isolates included in Dataset1 have been deposited in the European Nucleotide Archive (ENA) under Project <a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB49967?show=reads">PRJEB49967</a>. The wgMLST schema was created with <a href="https://github.com/B-UMMI/chewBBACA">chewBBACA</a> and is publicly available at <a href="https://chewbbaca.online/species/1/schemas/1">chewie-NS</a>, where a more detailed description of schema creation, annotation and curation can be found.

Whole genome sequence and annotation dataset of rare actinobacteria, Barrientosiimonas humi gen. nov., sp. nov. 39T from Antarctica

The present data files are the source files of the annotation output from the whole genome sequencing of rare actinobacteria, Barrientosiimonas humi gen. nov., sp. nov. 39T from Antarctica. The dataset of the whole-genome sequence of B. humi had been deposited in European Nucleotide Archive (ENA) repository under the accession number PRJEB44986 / ERP129097, direct URL to data: <a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB44986">https://www.ebi.ac.uk/ena/browser/view/PRJEB44986</a>

Supplementary dataset for Enzyme promiscuous profiles for protein sequence and reaction annotation

The data and scripts used to produce, analyze, and visualize the results of the manuscript Enzyme promiscuous profiles for protein sequence and reaction annotation by Homa MohammadiPeyhani, Anastasia Sveshnikova, Ljubisa Miskovic, and Vassily Hatzimanikatis. The detailed description of the datafiles and scripts is provided in the accompanying README.rtf file.

Geodetic dataset and slip models of the 2022 Chihshang earthquake sequence in eastern Taiwan

This repository contains the geodetic dataset and corresponding slip models presented in Tang et al. (2023), "Nearby fault interaction within the double-vergence suture in eastern Taiwan during the 2022 Chihshang earthquake sequence".

opencc-by-4.0Jul 2023View details →

Coseismic Kinematics of the 2023 Kahramanmaras, Turkey Earthquake Sequence from InSAR and Optical Data

We upload the supporting information and  four high-resolution images Figures 1-4 in the manuscript accepted by the GRL journal (2023.07.31).

Sequence-based identification of amyloidogenic β-hairpins

Data for: Heid et al., Sequence-based identification of amyloidogenic β-hairpins reveals a prostatic acid phosphatase fragment promoting semen amyloid formation   The dataset contains code and output sequences for sequence-based identification of amyloidogenic β-hairpins

opencc-by-4.0Oct 2022View details →

Integrative QTL mapping and selection signatures in Groningen White Headed cattle inferred from whole-genome sequences

Here, we aimed to identify and characterize genomic regions that differ between Groningen White Headed (GWH) breed and other cattle, and in particular to identify candidate genes associated with coat color and/or eye-protective phenotypes. Firstly, whole genome sequences of 170 animals from eight breeds were used to evaluate the genetic structure of the GWH in relation to other cattle breeds by carrying out principal components and model-based clustering analyses. Secondly, the candidate genomic regions were identified by integrating the findings from: a) a genome-wide association study using GWH, other white headed breeds (Hereford and Simmental), and breeds with a non-white headed phenotype (Dutch Friesian, Deep Red, Meuse-Rhine-Yssel, Dutch Belted, and Holstein Friesian); b) scans for specific signatures of selection in GWH cattle by comparison with four other Dutch traditional breeds (Dutch Friesian, Deep Red, Meuse-Rhine-Yssel and Dutch Belted) and the commercial Holstein Friesian; and c) detection of candidate genes identified via these approaches. The alignment of the filtered reads to the reference genome (ARS-UCD1.2) resulted in a mean depth of coverage of 8.7X. After variant calling, the lowest number of breed-specific variants was detected in Holstein Friesian (148,213), and the largest in Deep Red (558,909). By integrating the results, we identified five genomic regions under selection on BTA4 (70.2–71.3 Mb), BTA5 (10.0–19.7 Mb), BTA20 (10.0–19.9 and 20.0–22.7 Mb), and BTA25 (0.5–9.2 Mb). These regions contain positional and functional candidate genes associated with retinal degeneration (e.g., CWC27 and CLUAP1), ultraviolet protection (e.g., ERCC8), and pigmentation (e.g. PDE4D) which are probably associated with the GWH specific pigmentation and/or eye-protective phenotypes, e.g. Ambilateral Circumocular Pigmentation (ACOP). Our results will assist in characterizing the molecular basis of GWH phenotypes and the biological implications of its adaptation.

Automatic message sequence chart creation from simulation run of the Chandy-Lamport algorithm modeled by colored Petri net

Videos of two message sequence chart creation from simulation runs of the Chandy-Lamport algorithm modeled by colored Petri net using the CPN tool. Message Sequence Chart Of Model With Automatic Simulation Run_SuppInfo.mp4: This video shows the automatic generation of a message sequence chart of a proposed colored Petri net model of the Chandy-Lamport distributed global snapshot algorithm using the CPN tool version 4.0.1. The video has been generated by the authors' updated extension server of the CPN tool. The automatic simulation run of the model has been used to create this video. The CPN tool randomly selects the enabled transition in an automatic simulation run. Message Sequence Chart Of Model With Step-By-Step Simulation Run_SuppInfo.mp4: This video shows the automatic generation of a message sequence chart of the proposed colored Petri net model of the Chandy-Lamport algorithm in a step-by-step simulation run with our updated extension server of the CPN tools version 4.0.1. We fired our selected enabled transition of the model to create this video.

Sequence and HMM libraries

This repository contains the data specified in the paper entitled "A refined picture of the native Amine Dehydrogenase family revealed by extensive biodiversity screening". It includes: 1. NAD-dependent_enzymes.fa.gz - The library of 20,315,745 sequences of NADPH-dependent enzymes recovered from genomic and metagenomic sequence databases. 2. ref-AmDHs17959_nr.fa.gz - The library of 17,959 ref-AmDH sequences recovered from genomic and metagenomic sequence databases. Considered as the updated nat-AmDH family. 3. NAD_subfams_HMMs.tar.gz - The library of 104,686 Hidden Markov Models (HMMs) of NADPH-dependent protein subfamilies. As described in the paper, those HMMs were obtained by clustering the set uploaded here as NAD-dependent_enzymes.fa.gz and building one HMM per subfamily. 4. ref-AmDHs_HMMs.tar.gz - This repertory includes the HMMs used to update the nat-AmDH family (all_ASMC_no_nad,hmm and all_ASMC_nad_dom.hmm) as well as the ones used to search for distant homologs; HMMs designed for the phylogenetic and structure-based groups built from the set uploaded here as ref-AmDHs17959_nr.fa.gz (asmc_*.hmm and phylo_*.hmm) . 5. ref-AmDH_ASMC_models.tar.gz - The library of 9886 ref-AmDH models built using the ASMC pipeline. 6. 72_ref-AmDH_seqs_representatives.txt.gz - Sequences of the 72 representative ref-AmDHs experimentally tested and found to be active. 7. 17_nat-AmDH_seqs_specific_feature.txt.gz - Sequences of the 17 nat-AmDHs with specific feature that have been heterologously expressed and tested.

Inferring B cell phylogenies from paired heavy and light chain BCR sequences with Dowser

In our publication, we created simulations of paired heavy and light chain BCR sequences. Uploaded here is all the data needed to rerun the simulations, as well as the output of the simulations we ran. The output of BCR phylo included here are the lineage trees, unpickled and put into one file (true_trees.tsv), and the fasta files ('starting_fastas' folder). The naive BCR sequences we used as a starting point are found in the 'naive_data' folder. The post-simulation data for all 20 iterations (combined heavy and light chain data through both simulation frameworks) can be found in the 'simulation_data' folder.

Next-generation sequencing of AAV.CAP-Mac from Chuapoco et al. (2023) Nature Nanotechnology

Dataset of next-generation sequencing of enrichment of AAV.CAP-Mac in various tissues from the publication: Chuapoco, M.R., Flytzanis, N.C., Goeden, N. et al. Adeno-associated viral vectors for functional intravenous gene transfer throughout the non-human primate brain. Nat. Nanotechnol. (2023). https://doi.org/10.1038/s41565-023-01419-x

18S sequences from eDNA surveys of a coral reef in the Maldives

18S sequence data for eDNA samples collected in the Maldives and the associated metadata and tag codes. The title of the study/publication is: Field collections and environmental DNA surveys reveal topographic complexity of coral reefs as a predictor of cryptobenthic biodiversity across small spatial scales

opencc-zeroSep 2023View details →

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Comparative seagulls of gut microbiota by using metagenomics and 16S rDNA sequencing

Shotgun metagenomic and 16S rDNA sequencing are commonly used methods to identify the taxonomic composition of microbial communities. We compared the metagenome and 16S rDNA amplicon results to demonstrate the features of this animal. In general, relatively consistent patterns and reliability could be identified by both sequencing methods, but the results varied following the refinement of taxonomic levels. Metagenomic sequencing was more suitable for the discovery and detection of pathogenic bacteria of gut microbiota in seagulls. Although there were large differences in the numbers and abundance of bacterial species of the two methods in terms of taxonomic levels, the patterns and reliability results of the samples were consistent.

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Whole genome sequence and annotation of Penstemon davidsonii

Penstemon is the most speciose flowering plant genus endemic to North America. Penstemon species' diverse morphology and adaptation to various environments have made them a valuable model system for studying evolution, but the absence of publicly available reference genomes limits possible research directions. Here we report the first reference genome assembly and annotation for Penstemon davidsonii. Using PacBio long-read sequencing and Hi-C scaffolding technology, we constructed a de novo reference genome of 437,568,744 bases, with a contig N50 of 40 Mb and L50 of 5. The annotation includes 18,199 gene models, and both the genome and transcriptome assembly contain over 95% complete eudicot BUSCOs. This genome assembly will serve as a valuable reference for studying the evolutionary history and genetic diversity of the Penstemon genus.

opencc-zeroOct 2023View details →

De novo nanopore sequencing overrepresents RNA modification landscape

RNA modifications are critical to the functional diversity and regulatory complexity of the transcriptome. With increasing frequency, direct nanopore RNA sequencing is applied to identify RNA modifications de novo. Here, we directly compare the MS2 phage genome RNA modification profiles determined using nanopore to orthogonal LC-MS/MS assays. The results reveal very different views of the modification landscape, suggesting caution when calling new RNA modifications using nanopore alone.

SMRT PacBio Sequel sequencing of 12 Silene herbarium specimens

The folder includes reads sequenced with SMRT PacBio Sequel from twelve Silene herbarium specimens. Both demultiplexed and non demultiplexed reads are included. The demultiplexed reads are in folder called "demultiplexed.zip", in files starting with "Barcodenumber_speciesnamesamplingyear.fastq". The barcode number and sequence can be found below, in the description. The non demultiplexed reads are in file called "ps_248_001.ccsreads.fastq.gz". #NebNext Barcodes             #Adapter('Barcode 1 (forward)',             #        start_sequence=('BC01', 'CGTGAT'),             #        end_sequence=('BC01_rev', 'ATCACG')),             #Adapter('Barcode 2 (forward)',             #        start_sequence=('BC02', 'ACATCG'),             #        end_sequence=('BC02_rev', 'CGATGT')),             #Adapter('Barcode 3 (forward)',             #        start_sequence=('BC03', 'GCCTAA'),             #        end_sequence=('BC03_rev', 'TTAGGC')),             #Adapter('Barcode 4 (forward)',             #        start_sequence=('BC04', 'TGGTCA'),             #        end_sequence=('BC04_rev', 'TGACCA')),             #Adapter('Barcode 5 (forward)',             #        start_sequence=('BC05', 'CACTGT'),             #        end_sequence=('BC05_rev', 'ACAGTG')),             #Adapter('Barcode 6 (forward)',             #        start_sequence=('BC06', 'ATTGGC'),             #        end_sequence=('BC06_rev', 'GCCAAT')),             #Adapter('Barcode 7 (forward)',             #        start_sequence=('BC07', 'GATCTG'),             #        end_sequence=('BC07_rev', 'CAGATC')),             #Adapter('Barcode 8 (forward)',             #        start_sequence=('BC08', 'TCAAGT'),             #        end_sequence=('BC08_rev', 'ACTTGA')),             #Adapter('Barcode 9 (forward)',             #        start_sequence=('BC09', 'CTGATC'),             #        end_sequence=('BC09_rev', 'GATCAG')),             #Adapter('Barcode 10 (forward)',             #        start_sequence=('BC10', 'AAGCTA'),             #        end_sequence=('BC10_rev', 'TAGCTT')),             #Adapter('Barcode 11 (forward)',             #        start_sequence=('BC11', 'GTAGCC'),             #        end_sequence=('BC11_rev', 'GGCTAC')),             #Adapter('Barcode 12 (forward)',             #        start_sequence=('BC12', 'TACAAG'),             #        end_sequence=('BC12_rev', 'CTTGTA')),]

Distribution System Environmental and Sequencing Datasets for Assessing the Impacts of Lead Corrosion Control on the Microbial Ecology and Abundance of Drinking Water Associated Pathogens in a Full-Scale Drinking Water Distribution System

The dataset of environmental parameters and sequence fastqs used to create figures and do analysis in the paper Assessing the Impacts of Lead Corrosion Control on the Microbial Ecology and Abundance of Drinking Water Associated Pathogens in a Full-Scale Drinking Water Distribution System  submitted to Environmental Science & Technology

Genome sequencing of three Orestias species and the analysis of their phylogenetic relationships within the Cyprinodontiformes order

Relevant files and datasets for the paper: "Genomes of the Orestias pupfish from the Andean Altiplano shed light on their evolutionary history and phylogenetic relationships within Cyprinodontiformes." by Morales et al.