Datasets:
dataesr
/
paragraph_classification_eval

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dataset
10.1038_s41467-021-27769-5
doi10.1038_s41467-021-27769-5
Data availability The data and code underlying Fig. 2a, c, d are provided in the github repository https:// github.com/ClaMtnez/Ocean_tags. The data underlying Figs. 3, 4 & 5 and Supplementary Figs. 1, 4 & 5 are provided as a Supplementary Data Files. The sequence data generated in this study have been deposited in the EMBL Nucleotide Sequence Database (ENA) database under Bioproject PRJEB35712 (metagenomic and metatranscriptomic raw reads, metagenomic and metatranscriptomic assemblies, metagenomic assembled genomes, and single-cell amplified genomes) and in the NCBI Sequence Read Archive (SRA) under Bioproject PRJNA593264 (16S rRNA gene amplicon reads). The following public databases were used in this study: Swiss-Prot database, https://www.uniprot.org/, release-2018_10; Genome Taxonomy Database, https://gtdb.ecogenomic.org/, release 80; SILVA non-redundant SSU Ref database, https://www.arb-silva.de/, v.138; UniRef 100 VIROME database, http:// virome.dbi.udel.edu; Greening lab metabolic marker gene database, https://doi.org/ 10.26180/c.5230745; CAZyme HMM database, https://bcb.unl.edu/dbCAN2/, v.8.0; Pfam HMM database, http://pfam.xfam.org/, release 32.0; and TIGRFAM HMM database, https://www.ncbi.nlm.nih.gov/genome/annotation_prok/tigrfams/, release 15.0
false
true
true
dataset
10.1371_journal.pone.0240176
doi10.1371_journal.pone.0240176
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1073_pnas.2220576120
doi10.1073_pnas.2220576120
Data, Materials, and Software Availability Sequencing data is available at National Center for Biotechnology Information Gene Expression Omnibus under accession GSE214456 (52). All other data are included in the manuscript and/or SI Appendix.
true
true
true
dataset
10.1088_1748-3190_ad00a2
doi10.1088_1748-3190_ad00a2
Data availability statementAll data that support the findings of this study are included within the article (and any supplementary files).
false
true
false
dataset
10.1093_nar_gkad633
doi10.1093_nar_gkad633
Data AvailabilityAnalyses and data acquisition codes are upload on lab GitHub account and archived in Zenodo with the following doi. Additionally, raw data that support our findings have been uploaded and archived in Zenodo, corresponding to each individual figure.GitHub: https://github.com/Ha-SingleMoleculeLabAnalyses, data acquisition codes, and raw data are archived in Zenodo:Raw data analysis DOI: 10.5281/zenodo.4925617Data acquisition DOI: 10.5281/zenodo.4925630Raw data DOI: 10.5281/zenodo.8088172
false
true
true
dataset
10.1186_s12872-022-02488-x
doi10.1186_s12872-022-02488-x
Availability of data and materials The data that support the findings of this study are available from the National Health Insurance Service in the Republic of Korea, but restrictions apply to the availability of these data, which were used under license for the current study and so are not publicly available. Data are, however, available from the authors upon reasonable request and with permission from the National Health Insurance Service.
false
true
false
dataset
10.1088_1402-4896_ad075b
doi10.1088_1402-4896_ad075b
Data availability statementAll data that support the findings of this study are included within the article (and any supplementary files).
false
true
false
dataset
10.1038_s41467-022-35112-9
doi10.1038_s41467-022-35112-9
Data availability Data from this study is available at https://zenodo.org/badge/ latestdoi/566835035. Code availability The version of the model code used in this study is tagged as release v1.0 and is available at https://zenodo.org/badge/latestdoi/566835035. Necessary boundary condition files and observational data are inclu- ded as part of the code release.
false
true
true
dataset
10.1016_j.celrep.2023.112408
doi10.1016_j.celrep.2023.112408
Data and code availability Original small-RNA sequencing datasets are publicly available in NCBI under the accession number BioProject: PRJNA874806.
false
true
true
dataset
10.1088_1402-4896_ad0b51
doi10.1088_1402-4896_ad0b51
Data availability statementThe data cannot be made publicly available upon publication because they are not available in a format that is sufficiently accessible or reusable by other researchers. The data that support the findings of this study are available upon reasonable request from the authors.
false
true
false
dataset
10.1371_journal.pone.0241692
doi10.1371_journal.pone.0241692
Data Availability Statement Data are contained within the paper.
false
true
false
dataset
10.1371_journal.pclm.0000184
doi10.1371_journal.pclm.0000184
Data Availability Statement Causal loop diagrams refined during workshop discussion comprise the major data source of the study and are included in the submitted manuscript. Search terms and the extraction matrix used for the literature search to develop preliminary causal loop models are included as Supplementary material. Listing of the literature accessed and data extracted are lodged on the QMU eData repository: https://eresearch.qmu.ac.uk/handle/20.500.12289/12889.
false
true
false
dataset
10.1186_s12917-019-2170-8
doi10.1186_s12917-019-2170-8
Availability of data and materials The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.
false
true
false
dataset
10.1088_1402-4896_ad0a2a
doi10.1088_1402-4896_ad0a2a
Data availability statementThe data that support the findings of this study are openly available at the following URL/DOI: https://orcid.org/0000-0003-3389-9318.
false
true
false
dataset
10
doi10
Data availability The data that support the findings of this study are available from the corresponding authors upon request.
false
true
false
dataset
10.1371_journal.pone.0262844
doi10.1371_journal.pone.0262844
Data Availability Statement All relevant data are within the paper.
false
true
false
dataset
10.3389_fmicb.2021.711073
doi10.3389_fmicb.2021.711073
DATA AVAILABILITY STATEMENT The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author/s.
false
true
false
dataset
10.1038_s42003-021-02716-8
doi10.1038_s42003-021-02716-8
Data availabilitySeveral public databases were used in this study, including Immune Epitope Database and Analysis Resource (IEDB) (https://www.iedb.org/) for experimental measurements, UniProt (https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz) for decoy peptides, and IPD-IMGT/HLA (https://github.com/ANHIG/IMGTHLA/tree/3410) for MHC-I allele sequences. Research data files supporting this study, including the peptide-binding cleft sequence of MHC-I alleles; the training, validation, and benchmark datasets; the prediction of the validation and benchmark datasets; and the prediction of the allele expansion are available from Mendeley Data (10.17632/c249p8gdzd.3)33. Source data for all figures are provided in Supplementary Data. Code availabilityThe source code of the research and the MHCfovea’s predictor are freely available at GitHub (https://github.com/kohanlee1995/MHCfovea) and Mendeley Data33 for academic non-commercial research purposes. All source codes are based on Python (v3.6.9) and its packages, including numpy (v1.18.2), pandas (v1.0.3), scikit-learn (v0.22.2), pytorch (v1.4.0), matplotlib (v3.2.1), seaborn (v0.10.0), logomaker (v0.8). Numpy, pandas, and scikit-learn, are used for data analysis; pytorch is used for deep learning; matplotlib, seaborn, and logomaker are used for visualization. The website for the summarization of MHCfovea is available at https://mhcfovea.ailabs.tw.
false
true
true
dataset
10.1111_sapm.12544
doi10.1111_sapm.12544
DATA AVA ILAB IL ITY STATEMENT Data sharing not applicable to this article as no datasets were generated or analyzed during the current study.
true
true
false
dataset
10.1073_pnas.2221809120
doi10.1073_pnas.2221809120
Data, Materials, and Software AvailabilityAll study data are included in the article and/or SI Appendix. Sequencing data are available through the National Center for Biotechnology Information Gene Expression Omnibus, accession number GSE234805 (74).
true
true
true
dataset
10.3390_bs13010066
doi10.3390_bs13010066
Data Availability Statement: Data supporting the reported results is kept by the first author.
false
true
false
dataset
10.1371_journal.pone.0265477
doi10.1371_journal.pone.0265477
Data Availability Statement The raw data was collected from Taiwan Centers for Disease Control (CDC) and it is available at www.cdc.gov.tw/En. The tool and dataset are publicly available at github.com/mahsaashouri/Taiwan-COVID-19-Interactive-tool.
false
true
true
dataset
10.2196_41005
doi10.2196_41005
Data Availability The deidentified data analyzed in this study are available from the corresponding author upon reasonable request.
false
true
false
dataset
10.3389/fnbeh.2020
doi10.3389/fnbeh.2020
DATA AVAILABILITY STATEMENT The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.
false
true
false
dataset
10.1073_pnas.2301852120
doi10.1073_pnas.2301852120
Data, Materials, and Software Availability Cryo-EM images data have been deposited in Electron Microscopy Public Image Archive (EMPIAR) database with accession number EMPIAR-11544 (https://www.ebi.ac.uk/empiar/EMPIAR-11544/) (41).
false
true
true
dataset
10.7554_elife.76554
doi10.7554_elife.76554
Data availability Sequencing data have been deposited in GEO under accession code GSE157681. The following dataset was generated: Author(s) Year Dataset title Dataset URL Database and Identifier Brown JM, Helsley R, Kadam A, Neumann C 2021 The Gut Microbe-Derived Metabolite Trimethylamine is a Biomarker of and Therapeutic Target in Alcohol-Associated Liver Disease http://www.ncbi. nlm.nih.gov/geo/ query/acc.cgi?acc= GSE157681 NCBI Gene Expression Omnibus, GSE157681
false
true
true
dataset
10.1088_1758-5090_acfb3c
doi10.1088_1758-5090_acfb3c
Data availability statementThe data that support the findings of this study are openly available at the following URL/DOI: www.ncbi.nlm.nih.gov/bioproject/PRJNA953644. The other data that supports the findings of this study are available upon reasonable request.
false
true
false
dataset
10.1371_journal.pclm.0000285
doi10.1371_journal.pclm.0000285
Data Availability Statement: R code and aggregated data used in climate risk calculations are available at https://github.com/groundfish-climatechange/fish-footprints. Confidential vessel-level logbook, landings, and registration data may be acquired by direct request from the California, Oregon, and Washington Departments of Fish and Wildlife, subject to a non-disclosure agreement.
false
true
true
dataset
10.1371_journal.pone.0256592
doi10.1371_journal.pone.0256592
Data Availability Statement The data underlying the results presented in this study are from the Centers for Medicare and Medicaid Services and CMS does not permit data sharing as per their legally binding and standard data use agreements. The exact data used in this study can be purchased directly from the Centers for Medicare and Medicaid Services (https://www.cms.gov/Research-Statistics-Data-and-Systems/Research-Statistics-Data-and-Systems).
false
true
false
dataset
10
doi10
Data availability The data that support this study are available from the corresponding author upon reasonable request. The crystal structure described in this study has been deposited in the Protein Data Bank under the accession number 7TD5. The LC-MS/MS data files have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange. org) via the MassIVE partner repository with the dataset identifier MSV000088683. Source Data are provided with this paper.
false
true
true
dataset
10.1088_1361-6463_ad0ac1
doi10.1088_1361-6463_ad0ac1
Data availability statementAll data that support the findings of this study are included within the article (and any supplementary files).
false
true
false
dataset
10.1186_s12866-020-01881-w
doi10.1186_s12866-020-01881-w
Availability of data and materials All data generated or analyzed during this study are included in this published article [and its supplementary information files].
false
true
false
dataset
10.1016_j.isci.2022.104876
doi10.1016_j.isci.2022.104876
Data and code availability d Microscopy images published in this paper will be shared by the lead contact upon request. d Original code is uploaded in the supplementary documents and is publicly available as of the date of publication. Section 1: Data All data reported in this paper will be shared by the lead contact upon request. Section 2: Code All original code is available in this paper’s supplemental information. Section 3: Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.
false
true
true
dataset
10.1088_1361-6641_acfa1f
doi10.1088_1361-6641_acfa1f
Data availability statementAll data that support the findings of this study are included within the article (and any supplementary files).
false
true
false
dataset
10.1371_journal.pone.0232007
doi10.1371_journal.pone.0232007
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10
doi10
DATA AVAILABILITY The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.
false
true
false
dataset
10.3389/fmicb.2019
doi10.3389/fmicb.2019
DATA AVAILABILITY STATEMENT The raw data supporting the conclusions of this article are made available by the authors, without undue reservation, through Zenodo (doi: 10.5281/zenodo.3582838).
true
true
false
dataset
10.1128_mbio.01039-23
doi10.1128_mbio.01039-23
DATA AVAILABILITYCrystallographic data have been deposited to the RCSB protein data bank (accessions 8FZY, 8FZZ, and 8G0K). Metagenomic sequencing data were previously published (32) and are publicly available at the NCBI sequence read archive (BioProject PRJNA398089). Plasmids and bacterial strains generated in the study are listed in Table S3 and will be available upon reasonable request to the corresponding author.
false
true
false
dataset
10.1038_s41467-022-28771-1
doi10.1038_s41467-022-28771-1
Data availability Data supporting the results of this study are presented within the article and supplementary figures. NGS data are available in the NCBI Sequence Read Archive database (BioProject accession code PRJNA803881). Additional details and data to support the findings of this study are available from the corresponding authors upon reasonable request. Source data for Figs. 1a, 2a, c, 3b, d–f, 4, 5b, d, S1, S2, S4, S5a are provided as Source Data file. Source data are provided with this paper.
false
true
true
dataset
10.1073_pnas.2301121120
doi10.1073_pnas.2301121120
Data, Materials, and Software Availability Cryo-EM maps and atomic models for all structures described in this work have been deposited to the Electron Microscopy Data Bank (EMDB) and the Protein Data Bank (PDB), respectively. Accession codes are as follows: PLCβ3 in solution-8EMV and EMD-28266, PLCβ3 in complex with Gβγ on vesicles-8EMW and EMD-28267, and PLCβ3 in complex with Gβγ on nanodiscs-8EMX and EMD-28268.
true
true
true
dataset
10.1371_journal.pntd.0009999
doi10.1371_journal.pntd.0009999
Data Availability Statement All relevant data are within the paper and its Supporting Information files.
false
true
false
dataset
10.1088_1361-6595_ad05f5
doi10.1088_1361-6595_ad05f5
Data availability statementThe data cannot be made publicly available upon publication because they are not available in a format that is sufficiently accessible or reusable by other researchers. The data that support the findings of this study are available upon reasonable request from the authors.
false
true
false
dataset
10.1038_s41598-020-79151-y
doi10.1038_s41598-020-79151-y
Data availability The raw data of the study are available at http://www.nature.com/srep.
false
true
false
dataset
10.1038_s41467-022-30736-3
doi10.1038_s41467-022-30736-3
Data availability The data used in this paper are available at the following url: https://figshare.com/ articles/dataset/Manuscript_Data/16695592. In addition, Source Data are provided with this paper, which can be used to reproduce figures without rerunning analyses. Source data are provided with this paper. Code availability Analysis code used in this study is in the repository available at https://github.com/ Brody-Lab/dynamic_ephys36.
false
true
true
dataset
10.1088_1751-8121_ad0b5c
doi10.1088_1751-8121_ad0b5c
Data availability statementNo new data were created or analysed in this study.
false
true
false
dataset
10.3390_genes14061231
doi10.3390_genes14061231
Data Availability Statement Not applicable.
false
true
false
dataset
10.1088_1361-665x_ad1426
doi10.1088_1361-665x_ad1426
Data availability statementAll data that support the findings of this study are included within the article (and any supplementary files).
false
true
false
dataset
10
doi10
Data availability Data supporting the findings of this manuscript are available from the corresponding author upon request. The source data underlying all figures are available as a Source Data file provided with this paper. Source data are provided with this paper. Code availability All codes used for data analysis may be requested from the authors.
false
true
true
dataset
10.1371_journal.pgen.1011201
doi10.1371_journal.pgen.1011201
Data Availability Statement: The consensus sequence of Spoink as well as the sequences of the six PCR amplicons are available at https://github.com/rpianezza/Dmel-Spoink/tree/main/releasedseqs. The tool LTRtoTE is available on GitHub (https://github.com/Almo96/LTRtoTE). The analysis performed in this work have been documented with RMarkdown and have been made publicly available, together with the resulting figures, at GitHub (https://github.com/rpianezza/Dmel-Spoink; see *.md files).
false
true
true
dataset
10.1371_journal.pone.0222013
doi10.1371_journal.pone.0222013
Data Availability Statement All relevant data are within the paper and its Supporting Information files.
false
true
false
dataset
10.1007_s00208-022-02489-3
doi10.1007_s00208-022-02489-3
Data Availability Data sharing not applicable to this article as no data sets were generated or analysed during the current study.
false
true
false
dataset
10.1158_1078-0432.ccr-21-3817
doi10.1158_1078-0432.ccr-21-3817
Data availability The somatic variant calls and normalized RNA-seq intensity data, code, and deidentified clinical data are available here: https://github. com/kbolton-lab/Bolton_OCCC. This will enable all the figures and tables to be re-generated and also provide data for others for future analyses. We will also make the BAMs/FASTQs available to researchers through contacting Kelly Bolton (bolton@wustl.edu).
true
true
true
dataset
10.1371_journal.pdig.0000221
doi10.1371_journal.pdig.0000221
Data Availability Statement Public deposition of raw data points would breach compliance with the protocol approved by the Danish Data Protection Agency. In the paper, we have also had to limit the number of indirect identifiers in cases where there might be a risk of compromising patient privacy (e.g. Tables 1 and 2). Reviewers and others may obtain access to the data by request, and after a data processing agreement has been signed. There will be no limitation to data sharing as long as a data sharing agreement is signed. As per Danish research code, we are required to store research data for a minimum of 5 years starting from the time of publication. We will ensure this by standard data management and storage at our institution. Please address any correspondence to Dr Thomas Bandholm; thomas.quaade.bandholm@regionh.dk (corresponding author) or the Department of Clinical Research, Hvidovre Hospital, Kettegaard Alle 30, DK-2650 Hvidovre, Copenhagen, Denmark. Phone: +45 3862 3862.
false
true
false
dataset
10.1016_j.envres.2023.115368
doi10.1016_j.envres.2023.115368
Data availabilityData will be made available on request.
false
true
false
dataset
10.1371_journal.pone.0263447
doi10.1371_journal.pone.0263447
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1038_s41598-021-03032-1
doi10.1038_s41598-021-03032-1
Data availability All data are available in the manuscript.
false
true
false
dataset
10.1371_journal.pcbi.1008853
doi10.1371_journal.pcbi.1008853
Data Availability Statement BCI FDP data are available from https://repository.si.edu/handle/10088/11. The authors do not own the data and are unable to share it in a public repository, as the majority of the data is held by various government agencies. However interested researchers are able to access all the data through the Smithsonian Institution’s ForestGeo project (https://forestgeo.si.edu/explore-data) The EAA analysis programs, written in R, along with their documentation, are freely available from https://github.com/wangbinzjcc/EAAr.
false
true
true
dataset
10.1088_1361-6463_ad146b
doi10.1088_1361-6463_ad146b
Data availability statementAll data that support the findings of this study are included within the article (and any supplementary files).
false
true
false
dataset
10.1371_journal.pgen.1010857
doi10.1371_journal.pgen.1010857
Data AvailabilityHi-C data were deposited in the Gene Expression Omnibus (accession no. GSE225771). The scripts used for analyzing Hi-C data have been deposited to Github (https://github.com/hbbrandao/Borrelia_HiC_Analysis). All other relevant data are within the paper and its Supporting Information files.
false
true
true
dataset
10.1038_s41598-020-65766-8
doi10.1038_s41598-020-65766-8
Data availability Data are available at http://bicresources.jcbose.ac.in/ssaha4/drag/browse.php. Supporting figures and tables are included in Supplementary Files 1–3.
false
true
false
dataset
10.1007_s00127-023-02428-w
doi10.1007_s00127-023-02428-w
Data Availability The datasets generated during and/or analysed dur- ing the current study are not publicly available under current ethical approvals but are available from the corresponding author on reason- able request.
false
true
false
dataset
10.1088_1402-4896_ad0c11
doi10.1088_1402-4896_ad0c11
Data availability statementAll data that support the findings of this study are included within the article (and any supplementary files).
false
true
false
dataset
10.1371_journal.pone.0248369
doi10.1371_journal.pone.0248369
Data Availability Statement All relevant data are within the paper and its Supporting information files.
false
true
false
dataset
10.1371_journal.pone.0298960
doi10.1371_journal.pone.0298960
Data Availability Statement: All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1016_j.cell.2023.05.028
doi10.1016_j.cell.2023.05.028
Data and Code availabilityAll raw and processed sequencing data in this study, including single-cell DNA methylation sequencing, single-cell RNA-seq, ChIP-seq, Cut and Run assay and Nanopore sequencing, have been deposited to the NCBI Gene Expression Omnibus (GEO) database under accession GSE208449. All data are publicly available as of the date of publication.This paper analyses existing, publicly available data or available upon request to the authors. These accession numbers for the datasets are listed in the key resources table.This paper does not report original code. All the scripts and mathematical algorithms used in this study will be available from the corresponding authors upon request.
false
true
true
dataset
10.1016_j.enpol.2022.113277
doi10.1016_j.enpol.2022.113277
Data availabilityNo data was used for the research described in the article.
false
true
false
dataset
10.1371_journal.pgen.1008460
doi10.1371_journal.pgen.1008460
Data Availability Statement The RNA sequencing data of human cell lines and zebrafish tissues are available from NCBI Sequence Read Archive (SRA) (accession numbers PRJNA542249 and PRJNA543385). All other relevant data are available within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1371_journal.ppat.1009995
doi10.1371_journal.ppat.1009995
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1038_s41467-023-39627-7
doi10.1038_s41467-023-39627-7
Data availabilityThe sequencing data generated in this study have been deposited in the NCBI Gene Expression Omnibus (GEO) database under accession code GSE192447. The publicly available whole blood bulk short-read RNA-Seq data from healthy samples and samples infected with Makona Ebola Virus data used in this study are available in the NCBI Gene Expression Omnibus (GEO) database under accession code GSE115785. The single-cell RNA-Seq data used in this study are available in the NCBI Gene Expression Omnibus (GEO) database under accession code GSE158390. Raw Seurat Objects for both single-cell datasets used in this study are available at Zenodo. The full co-expression network file is also provided (10.5281/zenodo.7997135). The reference genome of EBOV used in this study is available in the GenBank database under accession code KU182905.1. The assembly and reference genome of Macaca Mulatta used in this study are available in the Ensembl database (Mmul_10) (https://ftp.ensembl.org/pub/release-100/fasta/macaca_mulatta/dna/Macaca_mulatta.Mmul_10.dna.toplevel.fa.gz, https://ftp.ensembl.org/pub/release-100/gtf/macaca_mulatta/Macaca_mulatta.Mmul_10.100.gtf.gz). The assembly and reference genome of human used in this study are available in the Gencode database (release_23) (https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_23/gencode.v23.annotation.gtf.gz, https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_23/GRCh38.primary_assembly.genome.fa.gz). Source data are provided with this paper.Code availabilityThe code used for this study is available at: https://github.com/Mele-Lab/2023_SingleCellEbolaLncRNAs_NatComms.
false
true
true
dataset
10.15252_embj.2022112987
doi10.15252_embj.2022112987
Data availability Original high resolution Z stacks for all images used in figures have been deposited in the BioImage Archive: accession number S‐BIAD651 (https://www.ebi.ac.uk/biostudies/BioImages/studies/S‐BIAD651?query=S‐BIAD651).
false
true
false
dataset
10.1371_journal.pone.0287008
doi10.1371_journal.pone.0287008
Data Availability Statement The data underlying the results presented in the study are available from Table 1.
false
true
false
dataset
10.1038_s41598-021-00119-7
doi10.1038_s41598-021-00119-7
Data availability The data presented in this study are available on request from the corresponding authors.
false
true
false
dataset
10.1038_s41593-023-01409-1
doi10.1038_s41593-023-01409-1
Data availabilityAll primary data for the figures and extended data figures are available from the corresponding author (K.D.) upon request.Code availabilityThe code used for data processing and analysis is available from the corresponding author (K.D.) upon request.
true
true
true
dataset
10.1038_s42003-023-04981-1
doi10.1038_s42003-023-04981-1
Data availabilityPlasmid sequences are available through the PLSDB database (https://ccb-microbe.cs.uni-saarland.de/plsdb/) while plasmid metadata files are hosted in a Github repository (https://github.com/LBHarrison/Lociq/). Source data for Figs. 3, 6 and 8 are provided in Supplementary Data 3, 7 and 8, respectively.Code availabilityThe Lociq program is available through the Github repository https://github.com/LBHarrison/Lociq/38.
false
true
true
dataset
10.1038_s41588-023-01451-6
doi10.1038_s41588-023-01451-6
Data availabilityPublic and private data can be accessed through their respective portals. Private data will require prior authorization. Data can be cleaned and normalized using any standard or well-established procedure for variant analysis or the procedures described in this paper, including referenced papers or procedures. The integrated, curated and de-duplicated data (to the best of our ability) are available in Supplementary Table 1. No additional data or intermediate results will be available upon request given the high manual burden to verify access to a variety of private portals, repositories and patients.Code availabilityVariants were processed using well-established procedures described in the referenced papers. Datasets from diverse sources were integrated using a combination of code (to automate certain steps) and manual curation. Thus, the standalone code is not sufficient to regenerate the integrated dataset. Therefore, this code and intermediate results from dataset integration and curation is not available upon request. The code used for analysis and to generate figures is available under Creative Commons license through Zenodo at 10.5281/zenodo.8008632. Analyses were executed in Python (v3.7), R (v4.1.1), GraphPad Prism (v92.2), matplotlib(v3.3.1), circos (v0.69-9) and seaborn (v0.11.1).PyMOL v2.4.0 was used to visualize structures. The Consurf online server was used for conservation analysis. Geneious Prime v2021.2.2 was used for multiple sequence alignmentss. The PolyPhen2 online server using the HumVar model was used to predict the severity/pathogenicity of the compiled NDD mutations. Unless otherwise noted, mutational counts, bar plots, pie charts, and Venn diagrams throughout were made using a combination of Python (v3.7), R (v4.1.1), GraphPad Prism (v92.2), matplotlib(v3.3.1) and seaborn (v0.11.1). The lollipop portion of the 2D schematics were created using the St. Jude PeCan Protein Paint software. Missense substitutions were visualized as a Sankey diagram using Google Charts. The Circos plot was made using the Circos software (v0.69-9). Missense substitutions were visualized as a Sankey diagram using Google Charts. The code used to process and visualize the data are available under the MIT license at Zenodo at 10.5281/zenodo.8008632.
false
true
true
dataset
10.1371_journal.pone.0240269
doi10.1371_journal.pone.0240269
Data Availability Statement Genomics data are now available at the NCBI repository: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE156993.
false
true
false
dataset
10.1186_s12889-023-15632-9
doi10.1186_s12889-023-15632-9
Data availability All datasets used for supporting the conclusions of this paper are available from the corresponding author on request.
false
true
false
dataset
10.1016_j.yjsbx.2023.100085
doi10.1016_j.yjsbx.2023.100085
Data availability Micrographs are available at EMPIAR-11397. Reconstructions are available on EMDB with the following accession codes: for Glacios 0-50 nm, EMD-29566; 50-100 nm, EMD-29567; 100-150 nm, EMD-29568; 150-200 nm, EMD-29569; 200-500 nm, EMD-29570. For Arctica in counting mode 0-50 nm, EMD-29573; 50-100 nm, EMD-29574; 100-150 nm, EMD-29575; 150-200 nm, EMD-29576; 200-500 nm, EMD-29577. For Arctica in super resolution mode 0-50 nm, EMD-29589; 50-100 nm, EMD-29591; 100-150 nm, EMD-29592; 150-200 nm, EMD-29593; 200-500 nm, EMD-29594. For Krios unfiltered 0-50 nm, EMD-29554; 50-100 nm EMD-29555; 100-150 nm, EMD-29556; 150-200 nm, EMD- 29557; 200-500 nm, EMD-29558. For Krios filtered 0-50 nm, EMD- 29536; 50-100 nm, EMD-29535; 100-150 nm, EMD-29559; 150-200 nm, EMD-29513; 200-500 nm, EMD-29393.
false
true
true
dataset
10.1016_S2213-2600(20)30559-2
doi10.1016_S2213-2600(20)30559-2
Data sharing Access to all data and samples collected by ISARIC4C are controlled by an Independent Data and Materials Access Committee composed of representatives of research funders, academia, clinical medicine, public health, and industry. The application process for access to the data is available on the ISARIC4C website.
false
true
false
dataset
10.1371_journal.pgph.0002891
doi10.1371_journal.pgph.0002891
Data Availability Statement: Data are included in supporting materials.
false
true
false
dataset
10.1038_s41467-023-38529-y
doi10.1038_s41467-023-38529-y
Data availability Spike recording data in NWB format are available for download at https://dandiarchive.org/dandiset/000060/draft. Source data are provided with this paper.
false
true
false
dataset
10.3390_biom11010118
doi10.3390_biom11010118
Data Availability StatementAll data are contained within the article or supplementary material.
false
true
false
dataset
10.1088_1402-4896_ad1320
doi10.1088_1402-4896_ad1320
Data availability statementAll data used are available in the manuscript. The data that support the findings of this study are available upon reasonable request from the authors.
false
true
false
dataset
10.1038_s41467-023-37865-3
doi10.1038_s41467-023-37865-3
Atomic coordinates that support the findings of this study are available in the RCSB Protein Data Bank (PDB) under accession numbers: 7LV2 [10.2210/pdb7LV2/pdb], 7LTU [10.2210/pdb7LTU/pdb] (form 1), 7LUX [10.2210/pdb7LUX/pdb] (form 2), and 7LUZ [10.2210/pdb7LUZ/pdb]. The amino acid sequences of the Nucleocapsid proteins of SARS-CoV-2 and SARS-CoV analyzed in this study are available on UniProtKB, accession numbers: P0DTC9, and P59595 respectively. Amino acid sequences of other coronavirus Nucleocapsid proteins were accessed from the European Nucleotide Archive [ENA; https://www.ebi.ac.uk/genomes/virus.html]. Raw EM images, light and fluorescence microscopy images and fiber diffraction source files generated in this study have been deposited in the Figshare respiratory at [https://figshare.com/projects/Low_Complexity_Domains_of_the_Nucleocapsid_Protein_of_SARS-CoV-2_Form_Amyloid_Fibrils/162391]. Data for all plots presented in this manuscript are provided with this paper in the Source Data file. Source data are provided with this paper.
false
true
true
dataset
10.1111_jbfa.12686
doi10.1111_jbfa.12686
DATA AVA ILAB IL ITY STATEMENT The data that support the findings of this study are available from third parties. Restrictions apply to the availability of these data, which were used under license for this study. Data are available from the authors with the permission of third parties.
false
true
true
dataset
10.1371_journal.pcbi.1007774
doi10.1371_journal.pcbi.1007774
Data Availability Statement All relevant data are available at the github repository: https://github.com/mdkarcher/BEAST-XML.
false
true
true
dataset
10.1088_1361-6382_ad0749
doi10.1088_1361-6382_ad0749
Data availability statementAll data that support the findings of this study are included within the article (and any supplementary files).
false
true
false
dataset
10.1371_journal.pone.0280975
doi10.1371_journal.pone.0280975
Data Availability Statement All relevant data are within the paper and its Supporting Information files.
false
true
false
dataset
10.1186_s12934-021-01548-9
doi10.1186_s12934-021-01548-9
Availability of data and materials The original contributions presented in the study are publicly available. The raw sequence data reported in this paper have been deposited in the Genome Sequence Archive (Genomics, Proteomics & Bioinformatics 2017) in National Genomics Data Center (Nucleic Acids Res 2020), Beijing Institute of Genomics (China National Center for Bioinformation), Chinese Academy of Sciences, under accession number CRA003010 that are publicly accessible at https://bigd.big.ac.cn/gsa.
true
true
false
dataset
10.1038_s41586-023-05909-9
doi10.1038_s41586-023-05909-9
Data availability The atomic coordinates and experimental data of RPB_PEW3_R4–PAWx4, RPB_PLP3_R6–PLPx6, RPB_LRP2_R4–LRPx4, RPB_PLP1_R6–PLPx6, RPB_PLP1_R6–PLPx6 (alternative conformation 1), RPB_PLP1_R6–PLPx6 (alternative conformation 2) and RPB_LRP2_R4 (pseudopolymeric) have been deposited in the RCSB PDB with the accession numbers 7UDJ, 7UE2, 7UDK, 7UDL, 7UDM, 7UDN and 7UDO, respectively. The Rosetta macromolecular modelling suite (https://www.rosettacommons.org) is freely available to academic and non-commercial users. Commercial licences for the suite are available through the University of Washington Technology Transfer Office. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium through the PRIDE partner repository with the dataset identifiers PXD038492 and 10.6019/PXD038492. Source data are provided with this paper. All protein sequences for the binders described in this study are provided in Supplementary Table 2.
false
true
true
dataset
10.1161_CIRCRESAHA.121.319314
doi10.1161_CIRCRESAHA.121.319314
Data Availability The detailed methods are available in the Data Supplement. Please see also the Major Resources Table in the Data Supplement. The supporting data are available from the cor- responding author upon request.
false
true
false
dataset
10.1371_journal.pwat.0000213
doi10.1371_journal.pwat.0000213
Data Availability Statement: All data supporting this study is free access data and the sources and collections details are provided as supplementary information accompanying this paper. The code used for the analysis and results figures is also made available at: https://github.com/J-Marcal/WSF_IneqAnalysis.
false
true
true
dataset
10.1371_journal.pone.0283795
doi10.1371_journal.pone.0283795
Data Availability Statement Data and codes are available at: DOI:10.17605/OSF.IO/PS4RM.
false
true
false
dataset
10.1038_s41467-023-40247-4
doi10.1038_s41467-023-40247-4
Data availabilityThe raw reads, and complete pathogen genomes generated in this study have been deposited in the Sequence Read Archive (SRA) and NCBI GenBank, respectively, under BioProject accession codes PRJNA824010 and PRJNA436552. Sample metadata (collection date, state, age, sequencing machine, sequencing batch, etc.), metagenomic read classification data for all samples and controls, viral genome assembly data, reference sequence accession numbers, and RT-qPCR results generated in this study are provided in the Supplementary Data 1 file.Code availabilityOpen source software used in this study is available at https://github.com/broadinstitute/viral-ngs84 (i.e., pipelines for viral genomic analyses; v2.1.8) and at https://github.com/bpetros95/lassa-metagenomics94 (i.e., code for statistical analyses; developed in R v4.1.1 with packages bda v15.2.5, mediation v4.5.0, ROCR v1.0–11, stats v4.1.1, and tidyverse v2.0.0). Information about the Microsoft Premonition metagenomics pipeline is available at https://microsoft.com/premonition. Individuals can access the pipeline ahead of its public release by clicking the “Contact us for availability” button and mentioning this work or by emailing Simon Frost at Frost.Simon@microsoft.com.
false
true
true
dataset
10.1016_j.jbc.2023.105075
doi10.1016_j.jbc.2023.105075
Data availabilityAll data described within the article are contained in the document. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (73) partner repository with the dataset identifier PXD042589. Any further information and requests for resources and reagents should be directed to and will be fulfilled by the Lead Contact, Vamsi K. Mootha (vamsi@hms.harvard.edu).
false
true
false
dataset
10.1007_s00440-023-01195-8
doi10.1007_s00440-023-01195-8
Data availability Data sharing not applicable to this article as no datasets were generated or analysed during the current study.
false
true
false
dataset
10.1088_1361-648x_ad1135
doi10.1088_1361-648x_ad1135
Data availability statementAll data that support the findings of this study are included within the article (and any supplementary files).
false
true
false
dataset
10
doi10
Data Availability Anonymized data will be made available upon request.
false
true
false
dataset
10.1186_s12915-020-00859-4
doi10.1186_s12915-020-00859-4
Availability of data and materialsAll data generated or analysed during this study are included in this published article, its supplementary information files and publicly available repositories.
false
true
false
dataset
10.1088_1361-6587_acff7f
doi10.1088_1361-6587_acff7f
Data availability statementThe data that support the findings of this study are openly available at the following URL/DOI. https://github.com/YukiJajima/improved-spork/blob/main/NLD_data_CNN.
false
true
true