Datasets:
dataesr
/
paragraph_classification_eval

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dataset
10.1038_s41467-020-14824-w
doi10.1038_s41467-020-14824-w
Data availability The data generated during the study are available in a public repository (https://osf.io/mktdb/).
false
true
false
dataset
10.1016_j.xcrm.2023.101003
doi10.1016_j.xcrm.2023.101003
Data and code availabilityThis paper does not report original code. NGS data have been deposited at NCBI sequence read archive (SRA) under accession numbers 32312762-32312784 and are publicly available as of the date of publication. The crystal structure reported in this manuscript has been deposited at the Protein Data Bank (PDB) under accession number 8E1P. Any additional information is available from the lead contacts upon request.
false
true
true
dataset
10.1371_journal.pone.0252389
doi10.1371_journal.pone.0252389
Data Availability Statement All relevant data are within the manuscript and its S1 File.
false
true
true
dataset
10.1088_1361-6501_ad0939
doi10.1088_1361-6501_ad0939
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
10.18063_ijb.v9i2.668
doi10.18063_ijb.v9i2.668
Availability of data The datasets used and analyzed during the present study can be obtained from the corresponding author on request.
false
true
false
dataset
10.1371_journal.pgph.0003036
doi10.1371_journal.pgph.0003036
Data Availability Statement: Data are publicly available using the following Harvard Dataverse repository links: https://doi.org/10.7910/DVN/NTXO8M; https://doi.org/10.7910/DVN/RNLU3J; https://doi.org/10.7910/DVN/ETQZO2; https://doi.org/10.7910/DVN/ZF6SJE.
false
true
true
dataset
10.1088_1367-2630_ad06da
doi10.1088_1367-2630_ad06da
Data availability statementThe data that support the findings of this study are openly available at the following URL/DOI: https://github.com/fine-group-us/disordered-resetting.
false
true
true
dataset
10.1016_j.isci.2022.105093
doi10.1016_j.isci.2022.105093
Data and code availability d All data reported in this paper will be shared by the lead contact upon request. d This paper does not report original code. d Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.
false
true
true
dataset
10.1371_journal.pntd.0007421
doi10.1371_journal.pntd.0007421
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1186_s12877-021-02434-0
doi10.1186_s12877-021-02434-0
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
10.1038_s41590-023-01527-9
doi10.1038_s41590-023-01527-9
Data availabilityThe data supporting this publication have been deposited at ImmPort (https://www.immport.org) under study accession SDY2213. An h5ad file for CELLXGENE interactive data viewer is also available for download. Source data are provided with this paper.Code availabilityThe customized code used in the present study is publicly available at: https://github.com/viannegao/RA_Fibroblast_Multiome_Analysis.git
false
true
true
dataset
10.1038_s41467-019-12557-z
doi10.1038_s41467-019-12557-z
Data availability The data underlying all figures are provided as part of the Open Science Framework (OSF; https://osf.io/y325a; Digital Object Identifier (DOI): 10.17605/OSF.IO/Y325A). The OSF project contains a zip folder with all source Data files (.mat), a spreadsheet detailing the names of the source data files and all scripts relevant for producing the figures (make_figX.m). Unthresholded fMRI maps of all contrasts are available on Neurovault (https://identifiers.org/neurovault.collection:5765).
false
true
true
dataset
10.3389_fonc.2022.895544
doi10.3389_fonc.2022.895544
DATA AVAILABILITY STATEMENT The datasets studied for this study is collected from a clinical trial; due to PHI protection, the original image data cannot be published in the public domain. The studied deep learning design model will be available upon direct request to the corresponding author. Requests to access the datasets should be directed to chunhao.wang@duke.edu.
false
true
false
dataset
10.1093_mnras_stab3539
doi10.1093_mnras_stab3539
DATA AVAILABILITY All of the data presented in this paper are publicly available. The HST data can be found under the programme 15701 (PI S. Chap- man), the Spitzer-IRAC data can be found under the four pro- grammes 60194 (PI J. Vieira), 80032 (PI S. Stanford), 13224 (PI S. Chapman), and 14216 (PI S. Chapman), the Gemini-South data can be found under the programme GS-2017B-Q-7 (PI A. Chap- man), and the ALMA data can be found under the two programmes 2017.1.00273.S (PI S. Chapman) and 2018.1.00058.S (PI S. Chap- man).
false
true
false
dataset
10.1371_journal.pone.0230651
doi10.1371_journal.pone.0230651
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1371_journal.pone.0277927
doi10.1371_journal.pone.0277927
Data Availability Statement All relevant data are within the paper and its Supporting information files. In Jordan, the engraved slab from Jibal al-Khashabiyeh is stored at the French Institute for the Near East (Ifpo, Amman) and is expected to be soon housed in the Hussein Bin Talal University exhibition room of the South-Eastern Badia Archaeological Project in Wadi Musa. In Saudi Arabia, the engraved boulder at Jebel az-Zilliyat has not been removed from its original location.
false
true
false
dataset
10.1371_journal.pgph.0002801
doi10.1371_journal.pgph.0002801
Data Availability Statement: The datasets upon which our findings are based belong to the US Centers for Disease Control and Prevention. For confidentiality reasons, the datasets are not publicly available. However, the data sets can be availed upon reasonable request from the secretariat of the Uganda Public Health Fellowship program at jnamagulu@musph.ac.ug, and with permission from the US Centers for Disease Control and Prevention.
false
true
true
dataset
10.1371_journal.ppat.1011448
doi10.1371_journal.ppat.1011448
Data AvailabilityAll relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1186_s12879-021-06753-w
doi10.1186_s12879-021-06753-w
Availability of data and materialsThe datasets used and/or analyzed in the current study are available from the corresponding author upon reasonable request.
false
true
false
dataset
10.14814_phy2.15703
doi10.14814_phy2.15703
DATA AVAILABILITY STATEMENT The data that support the findings of this study are avail- able from the corresponding author upon reasonable request.
false
true
false
dataset
10.1371_journal.pone.0239702
doi10.1371_journal.pone.0239702
Data Availability Statement All SAXS data used in the analysis are available as supplementary data. The data averaged series with a 5.0 mg/ml protein concentration at pH 7.5 have been deposited in SASBDB (the Small Angle Scattering Biological Data Bank) as SASDHG6. The crystal structure has been deposited in the Protein Data Bank (PDB) as 6VE1.
false
true
true
dataset
10.1371_journal.pbio.3002555
doi10.1371_journal.pbio.3002555
Data Availability Statement: All relevant data are within the paper and its Supporting information files, and from OSF: https://osf.io/wzrdk/ and https://osf.io/sc7pr/. Raw sequencing reads available from the SRA database under accession PRJNA949791.
true
true
false
dataset
10.1140_epjc_s10052-023-11191-w
doi10.1140_epjc_s10052-023-11191-w
Data Availability Statement This manuscript has no associated data or the data will not be deposited. [Authors’ comment: All the results in this paper can be reproduced using the HEPfit package, publicly available at https://github.com/silvest/HEPfit/. The configuration file adopted for this study can be provided upon request.]
false
true
true
dataset
10.1038_s41467-020-15693-z
doi10.1038_s41467-020-15693-z
Data availability The data that support the findings of this study are available from the corresponding authors on request (total data size approximately 1 TB). The source data underlying Figs. 2, 3, and 4c–f are provided as a Source Data file. Code availability All computer code (in MATLAB) developed for this study is available from the corresponding authors on request.
false
true
true
dataset
10
doi10
Software: Athena (Stone et al. 2008), VisIt (Department Of Energy (DOE) Advanced Simulation & Computing Initiative (ASCI), 2011).
true
false
true
dataset
10.3390_v14112464
doi10.3390_v14112464
Data Availability Statement: All nonsimulated data on COVID-19’s development used in this paper were pulled from the tool developed in [33]. The tool aggregates data from a variety of data sources including the WHO, each state’s individual department of health, and the CDC. The data used included reports on case counts, active cases, and deaths within each individual U.S. state. We also include a direct link to the github for the tool here: https://github.com/CSSEGISandData/COVID-19 (accessed on 29 August 2022).
false
true
true
dataset
10.1371_journal.pone.0241981
doi10.1371_journal.pone.0241981
Data Availability Statement The mobile phone data at the antenna- and commune-level aggregated to the year 2013 including noisy antenna locations as well as instructions for replicating the study results have been added as part of the Supporting information. In order to access record-level mobile phone data and exact antenna locations, one would need to contact Sonatel directly and present the research project that would require the data (contact: Mr El Hadji Birahim Gueye, Direction des Systèmes d’information Sonatel, ebgueye@orange-sonatel.com or post mail: Orange-Sonatel, 46 Boulevard de la République, BP 69 Dakar, Senegal). GUF data cannot be shared publicly because third-party access conditions apply (for scientific, non-commercial use). However, it is available for research purposes under a data user agreement. For data access, please contact the German Aerospace Agency under guf@dlr.de (https://www.dlr.de/eoc/en/PortalData/60/Resources/dokumente/guf/DLR-GUF_LicenseAgreement-and-OrderForm.pdf). Census data used in the study cannot be shared publicly because third-party access conditions apply. However, it is available for research purposes under a data user agreement. For data access, please visit the microdata catalogue of the statistical office in Senegal (http://anads.ansd.sn/index.php/catalog/51) or send the inquiry to statsenegal@ansd.sn. All code required for replicating the findings of this study is fully available in the Supporting information of this submission (S1 and S2 Files) and under https://github.com/tilluz/geomatching_open.
false
true
true
dataset
10.1371_journal.pone.0276413
doi10.1371_journal.pone.0276413
Data AvailabilityThe PDB file and structure factors for the structure reported in this paper are available from the RCSB database (PDB ID 8E4T) doi 10.2210/pdb8e4t/pdb
false
true
false
dataset
10.1088_1361-648x_ad1217
doi10.1088_1361-648x_ad1217
Data availability statementAll data that support the findings of this study are included within the article (and any supplementary files).
false
true
false
dataset
10.5194_gmd-14-7155-2021
doi10.5194_gmd-14-7155-2021
Code availability. The commented OMEN-SED-RCM source code (MATLAB) to this article is available for download in the two links provided below or see Pika and Hülse (2021). The specific version of the OMEN-SED model used in this pa- per is tagged as release v1.1, has been assigned a DOI of https://doi.org/10.5281/zenodo.4029488 (Hülse and Pika, 2021) and is hosted on GitHub. A version including the code to plot some of the presented results has the DOI of https://doi.org/10.5281/zenodo.4421777 (Pika and Hülse, 2021) and is hosted on GitHub. Data availability. Data sets used in this study are available from the studies cited in the text and figures.
false
true
true
dataset
10.3389_fnbeh.2023.1111908
doi10.3389_fnbeh.2023.1111908
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 authors.
false
true
false
dataset
10.1186_s12882-021-02303-3
doi10.1186_s12882-021-02303-3
Availability of data and materials The data support the findings of this study are available on request, with permission of the study group, DAK Gesundheit and SBK.
false
true
false
dataset
10.1016_j.jbc.2022.102523
doi10.1016_j.jbc.2022.102523
Data availability Coulomb potential maps were deposited in the Electron Microscopy Data Bank (EMDB) with accession numbers EMD-24964, EMD-26342, and EMD-26341, corresponding to retromer heterotrimer, dimers, and 3KE mutant particles. Substructure maps were deposited for C-VPS35 dimers as EMD-26343 and EMD-26345 and for the 3KE mutant as EMD-26340. The heterotrimer dataset was first reported very briefly (44), but its refinement and analysis are reported here. Coordinates for this updated retromer heterotrimer were deposited in the PDB as 7U6F.
false
true
true
dataset
10.1242_bio.059967
doi10.1242_bio.059967
Data availability All data supporting this study have been made available in the Dryad Digital Repository (https://doi.org/10.5061/dryad.8sf7m0cth).
false
true
false
dataset
10.1371_journal.pone.0283318
doi10.1371_journal.pone.0283318
Data Availability Statement Due to the limitations of the consent provided by the subjects in our study, we cannot disclose the data to the public. Only researchers who have formally applied to and been approved by the human research ethics committee of Kyushu University Hospital can access the data (ijkseimei@jimu.kyushu-u.ac.jp).
false
true
false
dataset
10.1371_journal.pmed.1004327
doi10.1371_journal.pmed.1004327
Data Availability Statement: The data underlying the results presented in the study are hosted by the Hong Kong Hospital Authority. Due to local regulation, the data are not available to the public. Request for data can be made via Hong Kong Hospital Authority: https://www3.ha.org.hk/data.
true
true
false
dataset
10.1371_journal.pwat.0000210
doi10.1371_journal.pwat.0000210
Data Availability Statement: All data can be found in the manuscript and the supporting information file.
false
true
true
dataset
10.1088_1361-6501_ad0e3a
doi10.1088_1361-6501_ad0e3a
Data availability statementThe data cannot be made publicly available upon publication because no suitable repository exists for hosting data in this field of study. The data that support the findings of this study are available upon reasonable request from the authors.
false
true
false
dataset
10.1088_1751-8121_ad02ec
doi10.1088_1751-8121_ad02ec
Data availability statementNo data were used to obtain the findings of this study/ Not applicable.
false
true
false
dataset
10.1038_s41598-021-86143-z
doi10.1038_s41598-021-86143-z
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
10.1088_1748-9326_ad114a
doi10.1088_1748-9326_ad114a
Data availability statementNo new data were created or analysed in this study.
false
true
false
dataset
10.1371_journal.pone.0239797
doi10.1371_journal.pone.0239797
Data Availability Statement Replication codes and data for this study have been uploaded to the Harvard Dataverse and can be accessed at: https://doi.org/10.7910/DVN/7WX5UU.
false
true
false
dataset
10.1371_journal.pgph.0002467
doi10.1371_journal.pgph.0002467
Data Availability Statement: Our data came from four publicly available datasets: World Bank’s World Development Indicators; U.S. government’s foreignassistance.gov database; OECD Creditor Reporting System database; and the Institute of Health Metrics and Evaluation GBD Result’s Tool.
false
true
false
dataset
10.1371_journal.pone.0250576
doi10.1371_journal.pone.0250576
Data Availability Statement All relevant data are within the paper and its Supporting information files.
false
true
false
dataset
10.1088_1367-2630_ad1418
doi10.1088_1367-2630_ad1418
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.0270562
doi10.1371_journal.pone.0270562
Data Availability Statement Data will be made available on request. The request can be sent to Ms. KV. Sripriya, administrative officer, Samarth. She can be contacted at admin@samarthngo.org.
false
true
false
dataset
10.1088_1361-6463_ad10d4
doi10.1088_1361-6463_ad10d4
Data availability statementThe data that support the findings of this study are available from the corresponding author upon reasonable request.
false
true
false
dataset
10.1371_journal.pgen.1010754
doi10.1371_journal.pgen.1010754
Data Availability Statement All DNA sequence files used for MFA analysis are available from NCBI (SRA accession number: PRJNA738450). Numerical data for qPCR are provided in Supplementary data.
false
true
false
dataset
10.1371_journal.pbio.3002472
doi10.1371_journal.pbio.3002472
Data Availability Statement: The raw sequencing reads for the metagenomic samples used in this study were downloaded from public repositories listed in the following publications: 10.1038/nature11209, 10.1038/nature11450, 10.1016/j.cels.2016.10.004, and 10.1101/gr.233940.117. Data underlying all figures, such as the numerical values of bar plots, can be found in 10.5281/zenodo.10304481. All other metadata, as well as the source code for the sequencing pipeline, downstream analyses, and figure generation are available at Zenodo (10.5281/zenodo.10368227) or GitHub (https://github.com/zhiru-liu/microbiome_evolution).
false
true
true
dataset
10.1371_journal.pone.0284899
doi10.1371_journal.pone.0284899
Data Availability Statement All relevant data are within the paper and its Supporting Information file.
false
true
false
dataset
10.1371_journal.pone.0217829
doi10.1371_journal.pone.0217829
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1371_journal.pone.0256297
doi10.1371_journal.pone.0256297
Data Availability Statement The data was derived from the second and third wave of the China Health and Retirement Longitudinal Study (CHARLS) (data and documentation are available at http://charls.pku.edu.cn/).
false
true
false
dataset
10.1371_journal.pcbi.1010680
doi10.1371_journal.pcbi.1010680
Data AvailabilityAll data are available in the main text or as supplementary materials. Scripts, computational methods, and design models are available on GitHub at https://github.com/willsheffler/rpxdock. For O43-rpxdock-EK1, coordinates are deposited in the Protein Data Bank with the accession code 8FWD; the cryo-EM density map is deposited in the Electron Microscopy Data Bank (EMDB) with the accession code EMD-29502.
false
true
true
dataset
10.1093_nar_gkad329
doi10.1093_nar_gkad329
DATA AVAILABILITY Raw sequencing data has been submitted to the NCBI SRA under accession numbers SRR19744356-SRR19744369. The corresponding BioSample accession numbers are SAMN29198687-SAMN29198700. Processed RNA-seq data are provided in the supplementary materials.
false
true
false
dataset
10.1371_journal.pone.0260553
doi10.1371_journal.pone.0260553
Data Availability Statement All relevant data are within the paper and its Supporting information files.
false
true
false
dataset
10.1016_j.celrep.2023.112657
doi10.1016_j.celrep.2023.112657
Data and code availabilityStructures and coordinates have been deposited in the Protein DataBank with identification number PDB: 8ENT. X-ray diffraction images have been deposited in the SBGrid DataBank with accession 974. Cryo-EM maps have been deposited to the Electron Microscopy DataBank (EMDB) under accession ID EMDB: EMD-28278.This paper does not report original code.
true
true
true
dataset
10
doi10
Data availability The coordinates and structure factors in this study have been deposited in the Protein Data Bank under accession codes 7KIH, 7KIL, and 7KIQ. The mass spectrometry proteomics data in this study have been deposited in the ProteomeXchange Consortium via the PRIDE partner repository45 with the dataset identifier PXD022172. Source data are provided with this paper.
false
true
true
dataset
10.3390_ijms24129783
doi10.3390_ijms24129783
Data Availability StatementNot applicable.
false
true
false
dataset
10.1186_s12867-019-0122-2
doi10.1186_s12867-019-0122-2
Availability of data and materials All data generated or analysed during this study are included in this article.
false
true
false
dataset
10.1371_journal.pone.0244789
doi10.1371_journal.pone.0244789
Data Availability Statement All relevant data are within the manuscript.
false
true
false
dataset
10.1371_journal.pbio.3000622
doi10.1371_journal.pbio.3000622
Data Availability Statement All relevant data are within the paper and its Supporting Information files.
false
true
false
dataset
10.1371_journal.pgen.1008228
doi10.1371_journal.pgen.1008228
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1021_acssynbio.3c00078
doi10.1021_acssynbio.3c00078
NotesPlasmids and their maps available for requests at Addgene (addgene.org/browse/article/28233817/). The key cell lines are available upon request. EM-Seq raw and processed data is deposited at Gene Expression Omnibus (GSE224403). Data and codes for analysis and generating figures are available at data.caltech (doi: 10.22002/ct5kt-cv878).
true
true
true
dataset
10.1371_journal.pone.0284380
doi10.1371_journal.pone.0284380
Data Availability Statement All relevant data are within the manuscript and its Supporting information files.
false
true
true
dataset
10.1088_1402-4896_ad0c14
doi10.1088_1402-4896_ad0c14
Data availability statementThe data cannot be made publicly available upon publication because no suitable repository exists for hosting data in this field of study. The data that support the findings of this study are available upon reasonable request from the authors.
false
true
false
dataset
10.1371_journal.pclm.0000173
doi10.1371_journal.pclm.0000173
Data Availability Statement The data that support the findings of this study are openly available in Zenodo at http://doi.org/10.5281/zenodo.3524917. The codes can be retrieved from: https://git.idiv.de/fm58hufi/discounting-the-future.git.
false
true
true
dataset
10.1371_journal.pone.0237574
doi10.1371_journal.pone.0237574
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1088_1402-4896_ad0695
doi10.1088_1402-4896_ad0695
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.1011003
doi10.1371_journal.pgen.1011003
Data Availability Statement: All relevant data are within the paper and its Supporting Information files. The whole genome sequencing data are available at the Sequencing Read Archive (PRJNA1044129). Raw and processed mRNA-Seq data have been deposited in GEO (GSE236037).
false
true
true
dataset
10.1186_s12961-020-00673-y
doi10.1186_s12961-020-00673-y
Availability of data and materialsQualitative data extracts are presented in the article to support the findings. The original transcripts are not available to the public as they may contain information that could compromise the confidentiality of study participants.
false
true
true
dataset
10.1088_1361-6552_ad11f8
doi10.1088_1361-6552_ad11f8
Data availability statementThe data cannot be made publicly available upon publication because they contain sensitive personal information. The data that support the findings of this study are available upon reasonable request from the authors.
false
true
false
dataset
10.1016_j.cell.2023.06.002
doi10.1016_j.cell.2023.06.002
Data and Code AvailabilityBulk-RNA seq and single cell RNA-seq data have been deposited at GEO (GSE211938, GSE212453) and are publicly available as of the date of publication.Codes used to process and analyze single-cell RNA-seq data are available at github.com/duncanmorgan/CAR_AgSpreading or Zenodo (10.5281/zenodo.7939518).
false
true
true
dataset
10.1371_journal.pone.0250041
doi10.1371_journal.pone.0250041
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1371_journal.pntd.0010777
doi10.1371_journal.pntd.0010777
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files. Data sourced from existing, open-access, databases are fully referenced and accession numbers are provided in the manuscript and supporting files. Accession numbers for the datasets used are as follows: RNA (transcriptomic data), accessed via NCBI: PRJEB3116, ERR146941-ERR146961. Genomic data, accessed via WormBase ParaSite v8: PRJEB528, PRJEB125, PRJEB530, PRJEB525. Protein coding sequences (genome-derived proteomes), accessed via WormBase ParaSite v8: PRJNA72581, PRJEB4950, PRJNA13758, PRJDA72781, PRJEB503, PRJNA72135, PRJEB513, PRJEB515, PRJEB525, PRJEB530, PRJEB125, PRJEB528, PRJEB524, PRJNA170813, PRJEB535. Human genome pep file, via Ensembl: GRCh38. Proteomic data, accessed from Supplementary Table 19 in Hunt et al., 2016, doi: 10.1038/ng.3495.
false
true
true
dataset
10.1371_journal.pone.0299479
doi10.1371_journal.pone.0299479
Data Availability Statement: The data underlying the results presented in the study are available from https://www.cdc.gov/nchs/nhanes/about_nhanes.htm
false
true
false
dataset
10.1186_s12875-020-01171-4
doi10.1186_s12875-020-01171-4
Availability of data and materials Anonymised transcript data will be stored on the University of Bristol’s Research Data Service repository. Bona fide researchers will be able to access this data subject to a data access agreement and following approval from the University of Bristol Data Access Committee.
false
true
true
dataset
10.1186_s13018-021-02394-6
doi10.1186_s13018-021-02394-6
Availability of data and materialsThe datasets used and analyzed during the current study are available from the corresponding author on reasonable request.
false
true
false
dataset
10.1371_journal.pone.0248381
doi10.1371_journal.pone.0248381
Data Availability Statement All relevant data are within the manuscript and its Supporting information files.
false
true
true
dataset
10.1038_s41467-021-25740-y
doi10.1038_s41467-021-25740-y
Data availabilityAll data generated in this study have been deposited in the OSF public repository (10.17605/OSF.IO/83WNU)80. Source data are provided with this paper. Code availabilityThe custom code used to analyze the data in this study (including the implementation used for the bGLS algorithm) and create all figures (except Figs. 1a, 3a, and 6a) is publicly available at Zenodo (10.5281/zenodo.4930034)81. Source data are provided with this paper.
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true
true
dataset
10.1371_journal.pone.0259135
doi10.1371_journal.pone.0259135
Data Availability Statement The dataset is available as supplementary material: https://figshare.com/s/01b2dd941d08b0fa6d9e).
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true
false
dataset
10.1371_journal.pone.0282823
doi10.1371_journal.pone.0282823
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1371_journal.pone.0284364
doi10.1371_journal.pone.0284364
Data Availability Statement VEGF measurements from the GENRES study and all data for the participants of the observational FinnDiane study are not publicly available and available only under restricted access due to ethical and legal reasons and due to the consent provided by the participant at the time of data collection. The data access, which is subject to local regulations, can be obtained upon reasonable request by contacting: Maaria Puupponen (email: maaria.puupponen@helsinki.fi), Research Program Coordinator, Clinical and Molecular Metabolism (CAMM), University of Helsinki. Upon approval, analysis needs to be performed on a user-specific local server (with protected access) and requires the applicant to sign non-disclosure and secrecy agreements. Cell culture experimental data is available as supplementary material.
false
true
true
dataset
10.1186_s12870-023-04198-8
doi10.1186_s12870-023-04198-8
Data AvailabilityThe mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (http://www.ebi.ac.uk/pride) partner repository with the dataset identifier PXD036246 (project accession) and 10.6019/PXD036246 (project DOI).Note: The data is currently private, and can be accessed with reviewer account that has been created (Username: reviewer_pxd036246@ebi.ac.uk; Password: OYD2kgKf). It is only after paper is accepted, the PRIDE is to be notified and data will be public.
true
true
true
dataset
10.1371_journal.pone.0295207
doi10.1371_journal.pone.0295207
Data Availability Statement: All relevant data are within the paper and its Supporting information files.
false
true
false
dataset
10.1080_02699931.2022.2157377
doi10.1080_02699931.2022.2157377
Data availability statement The data that support the findings of this research are openly available in the Open Science Framework (OSF) through this link https://osf.io/upb2h/?view_only=6eb16e9373c642f784254972f42b449c.
false
true
false
dataset
10.15252_embj.2023113578
doi10.15252_embj.2023113578
Data availabilityElectron tomography data were deposited to EMDB (EMD‐15268, http://www.ebi.ac.uk/pdbe/entry/EMD‐15268; EMD‐15244, http://www.ebi.ac.uk/pdbe/entry/EMD‐15244). Additional data and material related to this publication may be obtained upon request. Atomistic molecular dynamics simulations of initial structures and topology files were deposited to Zenodo (https://doi.org/10.5281/zenodo.7652685).
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true
false
dataset
10.1038_s41598-023-32039-z
doi10.1038_s41598-023-32039-z
Data availability The datasets generated during and/or during the current study are available from the corresponding author on reasonable request.
false
true
false
dataset
10.1038_s41467-020-19120-1
doi10.1038_s41467-020-19120-1
Data availability The data that support the findings of this study are available from the corresponding author upon reasonable request. Code availability The codes that support the findings of this study are available from the corresponding author upon reasonable request.
false
true
true
dataset
10.1038_s41477-023-01501-1
doi10.1038_s41477-023-01501-1
Data availabilityThe RNA-seq raw sequencing and analysed data have been deposited in the NCBI Gene Expression Omnibus database under accession GSE218961 and GSE218962. Raw source 16S rRNA gene sequences from this project are available in the Sequence Read Archive database under BioProject PRJNA977816, accession numbers SAMN35534885 to SAMN35534914. QIIME-compatible SILVA 16S rRNA gene reference sequences and taxonomy (release 138) can be downloaded from https://docs.qiime2.org/2022.2/data-resources/. Source data are provided with this paper.Code availabilityThe code used for RNA-seq raw data analysis can be found at https://github.com/rsohrabi/MIP_ms. The entire sequence analysis workflow for 16S amplicon analysis is available at https://github.com/BradCP/A-critical-role-of-a-eubiotic-microbiota-in-gating-proper-immunocompetence-in-Arabidopsis.
false
true
true
dataset
10.1016_j.isci.2023.106902
doi10.1016_j.isci.2023.106902
Data code and availabilityAll information required to reanalyze the data in this report is presented in the Supporting Information or from the lead contact upon request.
false
true
true
dataset
10.1371_journal.pone.0286962
doi10.1371_journal.pone.0286962
Data Availability Statement All relevant data are within the paper and its Supporting Information files.
false
true
false
dataset
10.1371_journal.pbio.3002093
doi10.1371_journal.pbio.3002093
Data Availability Statement: All relevant data are within the paper and its Supporting Information files.
false
true
false
dataset
10.1186_s12884-023-05590-w
doi10.1186_s12884-023-05590-w
Availability of data and materials The current study utilizes a dataset made available through the California Center for Population Research at the University of California. The dataset has not been made publicly available but can be made available upon reasonable request and with permission of Dr. Randall Kuhn. These data will all be entering the public domain in the coming months, upon which we will gladly provide all code for this paper alongside that public release.
false
true
true
dataset
10.1002/clc
doi10.1002/clc
DATA AVAILABILITY STATEMEN TThe authors confirm that all data underlying the findings are fullyavailable without restriction. The repository can be accessed online(https://biolincc.nhlbi.nih.gov/studies/aric/?q=aric).
false
true
false
dataset
10.1038_s41551-023-01026-0
doi10.1038_s41551-023-01026-0
Data availability All data supporting the results of this study are available within the paper and its Supplementary Information. High-throughput sequencing data are available from the NCBI Sequence Read Archive database (PRJNA915048). Key plasmids are available from Addgene (depositor: D.R.L.), or from the corresponding authors on request. Source data for the figures are provided with this paper.
false
true
false
dataset
10.1371_journal.pntd.0008855
doi10.1371_journal.pntd.0008855
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1371_journal.pgen.1010774
doi10.1371_journal.pgen.1010774
Data AvailabilityRaw sequencing data have been deposited at Gene Expression Omnibus with accession number: GSE227356
false
true
false
dataset
10.1186_s12964-020-00677-9
doi10.1186_s12964-020-00677-9
Availability of data and materials The datasets supporting the conclusions of this article are included within the article and its additional files.
false
true
false
dataset
10.1126_sciadv.adg2239
doi10.1126_sciadv.adg2239
Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. Transcriptomic data were deposited to the Gene Expression Omnibus (GEO) database under accession number GSE224626.
true
true
false
dataset
10.1371_journal.pone.0264329
doi10.1371_journal.pone.0264329
Data Availability Statement: All relevant data are within the manuscript and its Supporting Information files.
false
true
true