Datasets:
dataesr
/
paragraph_classification_eval

Dataset card Data Studio Files
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dataset
10.1103_physrevresearch.4.033101
doi10.1103_physrevresearch.4.033101
Data availability statement No new data were created or analysed in this study.
false
true
false
dataset
10.1186_s12889-023-15561-7
doi10.1186_s12889-023-15561-7
Data Availability The genetic variable information of single nucleotide polymorphisms (SNPs) was obtained from the IEU GWAS database (https://gwas.mrcieu.ac.uk/datasets/), a publicly available GWAS summary database.
false
true
false
dataset
10.1371_journal.pgph.0002821
doi10.1371_journal.pgph.0002821
Data Availability Statement: The data analysed in this study is available upon request only. Indeed, de-identified data cannot be publicly shared, as our study involves sensitive data on human participants, and could be indirectly identifying based on multiple patient characteristics. Individual data requests may be sent to the CorC (secr-CORC@pasteur.fr).
false
true
false
dataset
10.1371_journal.pone.0301207
doi10.1371_journal.pone.0301207
Data Availability Statement: All data are available from the below links: Data base: site: ans.gov.br/images/stories/Materiais_para_pesquisa/Perfil_setor/sala-de-situacao.html and BI where the women by age were selected: ans.gov.br/images/stories/Materiais_para_pesquisa/Perfil_setor/sala-de-situacao.html and Microsoft Power BI.
false
true
false
dataset
10.1186_s12909-023-04345-7
doi10.1186_s12909-023-04345-7
Availability of data and materials The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request.
false
true
false
dataset
10.1093_nar_gkad460
doi10.1093_nar_gkad460
Data AvailabilityAll raw sequencing data generated for this project are submitted to the SRA database under BioProject accession number PRJNA785663.
true
true
false
dataset
10.1371_journal.pmed.1003088
doi10.1371_journal.pmed.1003088
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1155_2021_7179632
doi10.1155_2021_7179632
Data AvailabilityThe data used to support the findings of this study are available from the corresponding author upon request.
true
true
false
dataset
10.1038_s41597-022-01645-3
doi10.1038_s41597-022-01645-3
Code availability Code associated with this manuscript can be found at OSF70.
false
false
true
dataset
10.1073_pnas.2300203120
doi10.1073_pnas.2300203120
Data, Materials, and Software Availability Seeds of the platz1 mutant have been deposited in GRIN-global (PI 702421) (39). All other data used in this study are included in the article and/or SI Appendix.
false
true
true
dataset
10.1371_journal.pone.0300534
doi10.1371_journal.pone.0300534
Data Availability Statement: The novel networks proposed in the manuscript are theoretical. There are no data.
false
true
true
dataset
10.1371_journal.pntd.0012056
doi10.1371_journal.pntd.0012056
Data Availability Statement: All relevant data are within the paper and its supporting information files.
false
true
false
dataset
10.1371_journal.ppat.1010767
doi10.1371_journal.ppat.1010767
Data Availability Statement All relevant data are within the manuscript and its Supporting information files.
false
true
true
dataset
10
doi10
Data Availability Statement: Not applicable.
false
true
false
dataset
10
doi10
DATA AVAILABILITY UK Biobank data are freely available for research purposes by application (https:// www.ukbiobank.ac.uk/enable-your-research/register). Phecode-based outcomes developed for the current study will be returned to the UK Biobank for future research use within 6 months of publication.
false
true
false
dataset
10.1371_journal.pgph.0001427
doi10.1371_journal.pgph.0001427
Data Availability Statement We used anonymised data from the 2016 Australian Census obtained from the Australian Bureau of Statistics (ABS) and the Australian Curriculum and Assessment and Reporting Authority (ACARA). These datasets can be obtained publicly, with the exception of the work travel data which can be obtained from the ABS on request. It should be noted that some of the data needs to be processed using the TableBuilder: https://www.abs.gov.au/websitedbs/censushome.nsf/home/tablebuilder. The actual incidence data are available from the health departments across Australia (state, territories, and national), and at: https://www.covid19data.com.au/. Other source and supplementary data are available at Zenodo (https://doi.org/10.5281/zenodo.7325756). The source code of AMTraC-19 is also available at Zenodo (https://doi.org/10.5281/zenodo.7325675).
false
true
true
dataset
10.1038_s41586-023-05895-y
doi10.1038_s41586-023-05895-y
Data availability PacBio HiFi and ONT data have been deposited into NCBI SRA under the following BioProject IDs: PRJNA850430, PRJNA731524, PRJNA551670, PRJNA540705 and PRJEB36100. PacBio HiFi data for CHM1 are available under the following SRA accessions: SRX10759865 and SRX10759866. Sequencing data for Clint PTR are available on NCBI SRA under the BioProject PRJNA659034. The T2T-CHM13 v1.1 assembly can be found on NCBI (GCA_009914755.3). Cell lines obtained from the NIGMS Human Genetic Cell Repository at the Coriell Institute for Medical Research are listed in Supplementary Table 1. Assemblies of HPRC samples are available on NCBI under the BioProject PRJNA730822. All additional assemblies used in this work (Clint PTR, CHM1, HG00514, NA12878 and HG03125), variant calls, assembly alignments, and other annotation data used in analysis are available on Zenodo (10.5281/zenodo.6792653)71.
false
true
true
dataset
10.3390_fluids7050173
doi10.3390_fluids7050173
Data Availability Statement: Data files from simulations will be made available by the authors upon request.
false
true
false
dataset
10.1038_s41467-019-13914-8
doi10.1038_s41467-019-13914-8
Data availability The source data underlying Figs. 1c–e, h–j, l, m, 2a, b, d, f, g, 3b, e, 4a–c, e–k, 5a, d–g, 6a–f, h, k, l, 7b–f, h–k, m, 8a–f and Supplementary Figs. 1a–d, 2a, b, d, 3a, b, d, 4a, b, d, 5a, b, d, f, h, i, 6a–p, 7a–e, 8a–j, 9a, c–g, 10a–d, f, h, 11a–d are provided as a Source Data file. Other datasets generated and/or analyzed in the current study are available from the corresponding author upon reasonable request.
false
true
false
dataset
10.1016_j.xcrm.2023.101042
doi10.1016_j.xcrm.2023.101042
Data and code availabilityStandardized WES dataset has been deposited on the dbGaP repository. dbGaP: phs003268.v1.p1.This paper does not report original code.Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.
true
true
true
dataset
10.1371_journal.pone.0236717
doi10.1371_journal.pone.0236717
Data Availability Statement The genotype file is available from the Dryad Digital Repository (https://doi.org/10.5061/dryad.1c2d3).
false
true
false
dataset
10.1007_s00520-023-07818-z
doi10.1007_s00520-023-07818-z
Data availabilityAll raw data is held securely by the research team and access can be requested if required.
true
true
false
dataset
10.1038_s41467-023-37876-0
doi10.1038_s41467-023-37876-0
Data availability FlyBi binary interaction data and all data described in this study are provided without restrictions. These data are provided as Supplementary file 5 and are also available as a table and as a downloadable data file at the FlyBi project webpage ([https://flybi.hms.harvard.edu/]). In addition, these data have been integrated with other datasets at IntAct ([https://www.ebi.ac.uk/intact/])44 and in the Molecular Interaction Search Tool (MIST; [https://fgrtools.hms.harvard.edu/MIST/])33. MAPPIT data is provided as Supplementary Data 6. RNAi data for the autophagy-related network is provided as Supplementary Data 8. Plasmid clones and associated information are available from both the Drosophila Genomics Resource Center (University of Indiana, Bloomington, IN) and the DNASU plasmid repository (Arizona State University, Phoenix, AZ). ORFs in the Gateway donor vector were end-read sequenced (see above, “Generation of a large-scale ORF clone resource”). Sequence data is available at GenBank and at the FlyBi project website (see Genbank Accession columns in the table at [https://flybi.hms.harvard.edu/results.php]). For a subset of 954 ORFs, the end-reads sequence spanned the full ORF. This sequence data is available at NCBI (Project Accession ID PRJNA349744) and a list of these ORFs, along with NCBI IDs, is available at the FlyBi project website (see [https://flybi.hms.harvard.edu/clones.php]). Interaction data was deposited at EBI IntAct (all Drosophila PPIs viewable at [https://www.ebi.ac.uk/intact/query/pubid:IM-28761]) and DroRI PPIs are available at MIST (see DroRI tab at [https://fgrtools.hms.harvard.edu/MIST/]). ChIPseq data is available at NCBI GEO (Accession ID GSE220887). Source data are provided with this paper.
false
true
true
dataset
10.1186_s12913-021-07120-w
doi10.1186_s12913-021-07120-w
Availability of data and materialsThe authors have made available all data and materials in the Supplemental file.
true
true
false
dataset
10.1088_1361-6641_acf608
doi10.1088_1361-6641_acf608
Data availability statementAll data that support the findings of this study are included within the article (and any supplementary files).
false
true
false
dataset
10.1073_pnas.2219624120
doi10.1073_pnas.2219624120
Data, Materials, and Software Availability The coordinates and the structure factors for the reported crystal structures have been deposited in the Protein Data Bank (PDB) under accession codes 8DIZ (54), 8DJ0 (55), and 8DJ1 (56) for NaVAbΔ28 I119T, L123T, and V126T, respectively. All study data are included in the article and/or SI Appendix.
false
true
true
dataset
10.1186_s12920-023-01452-8
doi10.1186_s12920-023-01452-8
Availability of data and materials The datasets generated and analysed during the current study are available from the corresponding author on reasonable request.
false
true
false
dataset
10.1186_s12913-021-06257-y
doi10.1186_s12913-021-06257-y
Availability of data and materialsThe data sets used and/or analysed during the current study are available from the corresponding author on reasonable request.
false
true
false
dataset
10.1371_journal.pstr.0000094
doi10.1371_journal.pstr.0000094
Data Availability Statement: All relevant data are within the paper and its Supporting Information files.
false
true
false
dataset
10.1093_nar_gkad501
doi10.1093_nar_gkad501
Data AvailabilityThe spacer sequences and accompanying statistics that are discussed in this paper are provided in Supplementary File 1. The original FASTQ files from the NGS experiments have been uploaded to the SRA database [accession # PRJNA972507]. The raw data from this study are available from the corresponding author upon request.Custom python scripts are deposited at Figshare: https://figshare.com/articles/software/kenneyc_etal_code_2023/22970996.
false
true
true
dataset
10.1038_s41598-020-61054-7
doi10.1038_s41598-020-61054-7
Data availability Data will be made available by the corresponding author upon request.
false
true
false
dataset
10.1088_1741-2552_acfe9c
doi10.1088_1741-2552_acfe9c
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
10.1371_journal.pgen.1010503
doi10.1371_journal.pgen.1010503
Data Availability Statement: All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1088_2634-4386_acfbf3
doi10.1088_2634-4386_acfbf3
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
10.7554_elife.85814
doi10.7554_elife.85814
Data availabilitySequencing data have been deposited in GEO under accession code GSE219105.
true
true
true
dataset
10.1002_advs.202300445
doi10.1002_advs.202300445
Data Availability StatementThe data that support the findings of this study are openly available in Gene expression Ominibus (GEO) at https://www.ncbi.nlm.nih.gov/geo, reference number 152431 and Genome Sequence Archieve (GSA) at https://ngdc.cncb.ac.cn/gsa‐human, reference number HRA000372.
false
true
false
dataset
10.1088_1741-2552_acfbfa
doi10.1088_1741-2552_acfbfa
Data availability statementThe datasets generated for this study are available on request to the corresponding author, while the model source code will be made available from the ModelDB (https://senselab.med.yale.edu/modeldb/) upon article publication.
false
true
true
dataset
10.1088_1361-648x_acfc8f
doi10.1088_1361-648x_acfc8f
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.pstr.0000049
doi10.1371_journal.pstr.0000049
Data Availability Statement All underlying data is available from https://cloud.univ-grenoble-alpes.fr/s/yDojHCrPHBdKY8D.
false
true
false
dataset
10.1099_mgen.0.001019
doi10.1099_mgen.0.001019
Data statement: All supporting data, code and protocols have been provided within the article or through supplementary data files.Three supplementary files are available with the online version of this article.
true
true
true
dataset
10.1126_sciimmunol.ade2860
doi10.1126_sciimmunol.ade2860
Data and materials availability: The materials and reagents used are commercially available and nonproprietary, with the exception of the gene-KO or patient-specific cell lines generated by this study. The cell lines generated by this study are available from S.-Y.Z. and J.-L.C upon request under MTAs from the Rockefeller University and the Imagine Institute. The RNA sequencing data generated by this study are available in the NCBI database under the NCBI-SRA project PRJNA937264. All other data needed to support the conclusions of the paper are in the paper or the supplementary materials.
true
true
true
dataset
10.1093_gbe_evad099
doi10.1093_gbe_evad099
Data AvailabilityThe Nextflow pipeline is available from https://github.com/4ment/gradient-benchmark. The versions of the programs used in this study are provided in table 1.
false
true
true
dataset
10.1371_journal.pone.0248476
doi10.1371_journal.pone.0248476
Data Availability Statement Individual level data cannot be shared publicly because of identifiability concerns that could occur with individual level electronic medical record data. We have provided aggregate data in S1 Table. Hospital discharge data are housed at the Arizona Department of Health Services, and may be provided for future analyses upon approval of a Human Subjects Research Board protocol at the discretion of the Arizona Department of Health Services. Researchers wishing to reproduce or build on this study will need to submit a data request to the Arizona Department of Health Services to be approved: https://www.azdhs.gov/documents/director/administrative-counsel-rules/HSRB_NewProductSubmission.pdf.
false
true
false
dataset
10.1242_dev.201085
doi10.1242_dev.201085
Data availability All relevant data can be found within the article and its supplementary information.
false
true
false
dataset
10.1371_journal.pbio.3002375
doi10.1371_journal.pbio.3002375
Data Availability Statement: Data and code to reproduce the main findings of this study can be downloaded from Open Science Framework (OSF, https://doi.org/10.17605/OSF.IO/GDJWH).
false
true
true
dataset
10.1088_2631-8695_ad1216
doi10.1088_2631-8695_ad1216
Data availability statementThe data presented in the work is a part of research work carried out jointly. However. upon reasonable request, the data can be provided from the authors. The data that support the findings of this study are available upon reasonable request from the authors.
true
true
false
dataset
10.1371_journal.pone.0286008
doi10.1371_journal.pone.0286008
Data Availability Statement In order to protect subjects’ confidentiality and privacy, data are only available on request. Interested researchers may contact the Ethics Committee of the Faculty of Sport, Porto University (cefade@fade.up.pt).
false
true
false
dataset
10.1007_s00285-023-01885-w
doi10.1007_s00285-023-01885-w
Data and CodeTime series simulations were performed numerically with MATLAB. The analysis for the reproduction number was computed with Mathematica. The parameter sensitivity was computed using the statistical package in Matlab. The codes can be accessed upon request.
false
true
true
dataset
10.1038_s41594-023-00948-2
doi10.1038_s41594-023-00948-2
Data availability The atomic coordinates and cryo-EM maps from this study are deposited in the Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) under PDB codes 8FVR (EC) and 8FVW (EC + ppGpp), and EMDB entries EMD-29491 (EC) and EMD-29494 (EC + ppGpp), respectively. All other data are available in the manuscript or supplementary materials. Requests for strains or plasmids will be fulfilled by the lead contact author (E.N.) upon request.
true
true
true
dataset
10.1186_s12920-023-01484-0
doi10.1186_s12920-023-01484-0
Data availability The datasets generated and/or analyzed during the current study are not publicly available due Mashhad University of Medical Sciences research council rules, but are available from the corresponding author on reasonable request.
false
true
false
dataset
10.1088_1748-9326_ad0dda
doi10.1088_1748-9326_ad0dda
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.pmed.1004146
doi10.1371_journal.pmed.1004146
Data Availability Statement All 42 files are available from the Dataverse Repository database (accession number(s) https://doi.org/10.7910/DVN/PMV0TG) https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/PMV0TG.
false
true
false
dataset
10.1088_1361-6501_ad0999
doi10.1088_1361-6501_ad0999
Data availability statementThe data that support the findings of this study are openly available at the following URL/DOI: https://csegroups.case.edu/bearingdatacenter/pages/download-data-file/ https://github.com/ClarkGableWang/JNU-Bearing-Dataset.
false
true
true
dataset
10.1088_1361-6560_ad0357
doi10.1088_1361-6560_ad0357
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
10.1192_j.eurpsy.2023.2418
doi10.1192_j.eurpsy.2023.2418
Data availability statement We believe that knowledge sharing increases the quantity and quality of scientific results. Sharing of relevant data will be discussed within the study group upon reasonable request.
false
true
false
dataset
10.1371_journal.pmed.1004341
doi10.1371_journal.pmed.1004341
Data Availability Statement: All mortality data used in our study were obtained from a collaborative research network under a data sharing agreement and the authors are not permitted to directly share the third-party raw data used in the analyses. For information on data access, readers are asked to contact Dr Sharon Harrison (sharon.harrison@monash.edu) for information on each country’s data providers. Annual gridded population was obtained from the Global Carbon Project (https://www.cger.nies.go.jp/gcp/population-and-gdp.html). Historical information on the temporal dynamics of cyclone events across the globe was collected from the IBTrACS data (https://www.ncei.noaa.gov/products/international-best-track-archive).
false
true
false
dataset
10.1088_1367-2630_ad091e
doi10.1088_1367-2630_ad091e
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.0258711
doi10.1371_journal.pone.0258711
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1002_nop2.1112
doi10.1002_nop2.1112
DATA AVAILABILITY STATEMENTResearchers allow this article to be used by anyone interested. All data generated during this study are included in this published article.
false
true
false
dataset
10.1371_journal.pone.0264346
doi10.1371_journal.pone.0264346
Data Availability Statement The model and sample codes are freely available at the GitHub repository (http://github.com/sangsoopark1739/pedaling_DC_OpenSim).
false
true
true
dataset
10.1088_1361-6463_ad098b
doi10.1088_1361-6463_ad098b
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_s41593-023-01382-9
doi10.1038_s41593-023-01382-9
Data availabilityThe MNIST65, CIFAR-10 (ref. 66) and Tiny ImageNet67 datasets (used in Supplementary Fig. 5) are publicly available from http://yann.lecun.com/exdb/mnist/, https://www.cs.toronto.edu/~kriz/cifar.html and https://www.kaggle.com/c/tiny-imagenet, respectively.Code availabilityCode reproducing the results is available at GitHub (https://github.com/neuroai/Go-CLS_v2) and archived at Zenodo (10.5281/zenodo.7941122).
false
true
true
dataset
10.1038_s41467-020-14670-w
doi10.1038_s41467-020-14670-w
Data availabilityThe RNA-seq and single-cell RNA seq raw reads have been deposited in the SRA database under accession PRJNA556211. The VRC01 KI mouse immunoglobulin VDJ sequence reads have been deposited in the SRA database under accession PRJNA603102. Source data for Figs. 1B, 1C, 1F–I, 2A–D, 4B–I, 5B–D, 5E, 6A–F, and Supplementary Figs. 1A–C, 1E–H. 2A–D, and 6E are provided as a source data file.
false
true
true
dataset
10.1371_journal.pone.0287750
doi10.1371_journal.pone.0287750
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files. the GitHub in .csv format, and its URL is: https://github.com/XAUT-WangLin/Summary-table-of-evaluation-index.
false
true
true
dataset
10.1073_pnas.2217096120
doi10.1073_pnas.2217096120
Data, Materials, and Software Availability X-ray structure data have been deposited in Protein Data Bank (8E0P, 8E0R, and 8E0W) for eMBP-APCDD1, APCDD1 crystal-form I and form II, respectively (84–86).
false
true
true
dataset
10.1371_journal.pbio.3000532
doi10.1371_journal.pbio.3000532
Data Availability Statement All relevant data are within the paper and its Supporting Information files.
false
true
false
dataset
10.1128_mSphere.00700-18
doi10.1128_mSphere.00700-18
Accession number(s). The final RNA-Seq data have been deposited in the Gene Expression Omnibus (GEO) database under accession no. GSE113880.
true
true
false
dataset
10.1088_1361-6528_acfd31
doi10.1088_1361-6528_acfd31
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.0198449
doi10.1371_journal.pone.0198449
Data Availability Statement Data are from the NASBOD study whose authors may be contacted at www.ncdrc.info. This study was an attempt to estimate 167 mortality causes in Iran form 1990 to 2015 by 2 sex and 19 age groups. The cirrhosis is one of the 167 causes in the NASBOD. The comprehensive data used in this research was gathered from Ministry of Health and Medical Education of Iran(MOHME); therefore, we are not permitted to publish the data set as it belongs to MOHME. For access to the NASBOD study data sets, interested and qualified researchers may contact Ministry of Health and Medical Education of Iran. The list of all data sets are mentioned in the paper NASBOD 2013: Design, Definitions, and Metrics, Archives of Iranian Medicine. 2014. 17(1). 7-15. DOI: 0141701/AIM.004. The authors of this paper had no special access privileges to the data sets.
false
true
false
dataset
10.1371_journal.ppat.1012129
doi10.1371_journal.ppat.1012129
Data Availability Statement: All relevant data are within the manuscript and its Supporting information files.
false
true
true
dataset
10.1016_j.jbc.2023.105046
doi10.1016_j.jbc.2023.105046
Data availabilityAll data supporting the findings of this study are available within this manuscript. Any further information and requests for resources and reagents should be directed to and will be fulfilled by the Lead Contact, Peter Tsvetkov (ptsvetko@broadinstitute.org).
false
true
false
dataset
10.7554_elife.86130
doi10.7554_elife.86130
Data availabilitySequencing data have been deposited in GEO.The following datasets were generated:WangJRattnerANathansJ2022Bacterial meningitis in the early postnatal mouse studied at single-cell resolutionNCBI Gene Expression OmnibusGSE221678WangJRattnerANathansJ2022snRNAseq_JW19_meninges_control_RP1NCBI Gene Expression OmnibusGSM6892910WangJRattnerANathansJ2022snRNAseq_JW20_meninges_control_RP2NCBI Gene Expression OmnibusGSM6892911WangJRattnerANathansJ2022snRNAseq_JW21_meninges_infected_RP1NCBI Gene Expression OmnibusGSM6892912WangJRattnerANathansJ2022snRNAseq_JW22_meninges_infected_RP2NCBI Gene Expression OmnibusGSM6892913WangJRattnerANathansJ2022snRNAseq_JW23_meninges_infected_RP3NCBI Gene Expression OmnibusGSM6892914
false
true
false
dataset
10.1088_1361-6463_acfb1a
doi10.1088_1361-6463_acfb1a
Data availability statementAll data that support the findings of this study are included within the article (and any supplementary files).
false
true
false
dataset
10.3390_math10234485
doi10.3390_math10234485
Data Availability Statement: Not applicable.
false
true
false
dataset
10.3390_ijms24010865
doi10.3390_ijms24010865
Data Availability Statement- All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. Additional data related to this paper may be requested from the authors.
true
true
false
dataset
10.2196_44326
doi10.2196_44326
Data Availability The data sets generated and analyzed during this study are available from the corresponding author on request.
false
true
false
dataset
10.1371_journal.pone.0238029
doi10.1371_journal.pone.0238029
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1038_s41467-023-38623-1
doi10.1038_s41467-023-38623-1
Data availabilityAll FASTQ files generated in this study have been deposited in the SRA database under accession code “PRJNA966800”. The processed data generated in this study are provided in the Supplementary Information/Source Data file. The structures used in this study can be found under the accession codes “4E8M”, “5A2Q” and “6AHR”. Source data are provided with this paper.Code availabilityAll source codes used in this study are available at a GitHub repository: https://github.com/pylelab/Tb-seq.
false
true
true
dataset
10.1371_journal.pone.0284821
doi10.1371_journal.pone.0284821
Data Availability Statement The data is openly available for all at: https://mics.unicef.org/surveys.
false
true
false
dataset
10.1371_journal.pgph.0002740
doi10.1371_journal.pgph.0002740
Data Availability Statement: All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1371_journal.pone.0234219
doi10.1371_journal.pone.0234219
Data Availability Statement All relevant data are within the paper and its Supporting information files.
false
true
false
dataset
10.1371_journal.pone.0229417
doi10.1371_journal.pone.0229417
Data Availability Statement All relevant data are within the paper and its Supporting Information files.
false
true
false
dataset
10.1371_journal.pstr.0000081
doi10.1371_journal.pstr.0000081
Data Availability Statement: The methods used to implement workshop activities are described in this paper. Qualitative data from focus group discussions and notes from workshops are not publicly available due to institutional restrictions on the sharing data that includes potentially identifying information. The Institute for Sustainable Futures Ethics Committee may be contacted with inquiries about the data at ISF-Ethics@uts.edu.au.
false
true
false
dataset
10.1371_journal.pntd.0011919
doi10.1371_journal.pntd.0011919
Data Availability Statement: Base layers for each map are publicly available from the U.S. census (https://www.census.gov/geographies/mapping-files/time-series/geo/carto-boundary-file.html). Environmental spatial data used in environmental niche modeling were collected from EarthExplorer (http://earthexplorer.usgs.gov) and EarthData (http://earthdata.nasa.gov/). Tick encounter data can be accessed at Dryad (https://doi.org/10.5061/dryad.v41ns1s3n).
false
true
false
dataset
10.7554_elife.87146
doi10.7554_elife.87146
Data availabilityThe sequencing data reported in this paper have been deposited in the NCBI Gene expression omnibus https://www.ncbi.nlm.nih.gov/geo/ (accession code, GSE240200).
false
true
false
dataset
10
doi10
Data availability The RNA-seq data for this study is available from the Gene Expression Omnibus (GEO; GSE133278. The metabolic and other gene expression data generated in this study are provided in the Supplementary Information or Source Data files, both provided with this paper. The raw data from human participants (beyond what is shown) are protected and not available due to data privacy considerations. Source data are provided with this paper.
false
true
false
dataset
10.1038_s41467-022-35233-1
doi10.1038_s41467-022-35233-1
Data availability All datasets used in this work are publicly available from the fol- lowing sources: The STARmap PLUS data was obtained from Zeng et al.4 and is available at https://singlecell.broadinstitute.org/ single_cell/study/SCP1375/integrative-in-situ-mapping-of-single- cell-transcriptional-states-and-tissue-histopathology-in-an- alzheimer-disease-model as well as on Zenodo at: https://doi.org/ 10.5281/zenodo.733209177. The reference gene expression used for cell type classification of the predicted gene expression is available from the Allen Brain Map53: https://portal.brain-map. org/atlases-and-data/rnaseq/mouse-whole-cortex-and- hippocampus-10x. The 10x Visium dataset is available at https:// www.10xgenomics.com/resources/datasets/multiomic- integration-neuroscience-application-note-visium-for-ffpe-plus- immunofluorescence-alzheimers-disease-mouse-model-brain- coronal-sections-from-one-hemisphere-over-a-time-course-1- standard. A Source Data file is provided and contains statistics of differential expression reported in Fig. 5b and Supplementary Fig. 29, including p-values and log fold changes. Source data are provided with this paper. Code availability Our code and a list of required open-source software packages are available at https://github.com/uhlerlab/STACI and on Zenodo: https://zenodo.org/record/7300119#.Y2k0VS-B35g78.
false
true
true
dataset
10.1016_j.ejca.2022.10.026
doi10.1016_j.ejca.2022.10.026
Data sharing The study protocol and aggregated and anonymised data that underlie the results reported in this article will be available immediately following publication with no end date to researchers who provide a methodologically- sound proposal to achieve aims related to the approved proposal. Proposals should be submitted to www.eortc. be/services/forms/erp/request.aspx. To gain access, data requestors will need to sign a data access agreement.
false
true
false
dataset
10.1371_journal.ppat.1012094
doi10.1371_journal.ppat.1012094
Data Availability Statement: All data are available in the article and supporting information.
false
true
false
dataset
10.1371_journal.pone.0295062
doi10.1371_journal.pone.0295062
Data Availability Statement: All relevant data are within the paper and its Supporting Information files.
false
true
false
dataset
10.1371_journal.pone.0240029
doi10.1371_journal.pone.0240029
Data Availability Statement All relevant data are uploaded to the CIMMYT repository and publicly accessible via the following URL: http://hdl.handle.net/11529/10714 (Hdl/11529/10714).
false
true
false
dataset
10.1371_journal.pdig.0000181
doi10.1371_journal.pdig.0000181
Data Availability Statement: All relevant data are within the manuscript.
false
true
false
dataset
10
doi10
Availability of data and materials UMG detection code is available at https://github.com/gersteinlab/UMG [51] and https://doi.org/10.5281/zenodo. 5500467 [52]. Results in the paper are in whole or part based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga. MC3 high-quality somatic mutation dataset is obtained from [53]. STRING v11 [54] and HumanNet v2 [55] functional network (FN) are respectively downloaded from https://string-db.org/ and https://www. inetbio.org/humannet. Gene expression data corrected for batch effect and study-specific bias are downloaded from RNAseqDB [56] at https://github.com/mskcc/RNAseqDB. Variant annotations are based on RefSeq hg19 provided via ANNOVAR 2018b [57], and gene length values are provided via the bioMart Bioconductor package [58]. Genetic dependency data from the Cancer Dependency Map [30] (for both CRISPR and RNAi experiments) are downloaded from https://depmap.org/portal/download/, MutSig2CV [45] data across cancer types from http://gdac.broadinstitute.org, COSMIC v90 census gene list from https://cancer.sanger.ac.uk/cosmic, and CancerMine v24 [59] gene lists from http:// bionlp.bcgsc.ca/cancermine.
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true
true
dataset
10.1186_s12879-023-08392-9
doi10.1186_s12879-023-08392-9
Availability of data and materialsThe datasets generated and/or analysed during the current study are not publicly available due to ethical and data access agreements with individual country ethical boards but are available from the corresponding author on reasonable request.
false
true
false
dataset
10.1038_s41467-023-38573-8
doi10.1038_s41467-023-38573-8
Data availability The data that support this study are available in the article and its Supplementary files or from the corresponding authors upon request. All structural data have been deposited in the Protein Data Bank (https://www.rcsb.org), with PDB codes: 7R7V7R7W, 7R7X, 7R7Y, 7R7Z, 7R80. Sequence data have been deposited in GenBank BankIt. The accession numbers for the C3 TCRαβ sequence are OQ858871 and OQ858872, the accession numbers for B57-specific TCRβs are OQ858873, OQ858874, OQ858875, OQ858876, OQ858877, and the accession numbers for B53-specific TCRβs are OQ858878, OQ858879, OQ858880, OQ858881.The source data underlying Figs. 1d–g, 2g, 4b, 4d–f, 6i, 7a, b, f are provided in the Source Data file. Source data are provided with this paper.
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true
dataset
10.1371_journal.pone.0212566
doi10.1371_journal.pone.0212566
Data Availability Statement All relevant data are within the paper and its Supporting Information Files.
false
true
false
dataset
10.1038_s43016-022-00594-9
doi10.1038_s43016-022-00594-9
Data availability The modelled estimates of individual food and nutrient intakes by population subgroup, country, region and globe in 1990 and 2018 are available for download from the GDD (https://www.globaldietarydatabase.org/). Survey-level information and original data download weblinks are also provided for all public surveys; survey-level microdata or stratum-level aggregate data are provided for direct download for all non-public surveys granted consent for public sharing by the data owner. The modelled dietary quality scores are available for download from (https://github.com/victoriaemiller/GDD-Diet-Quality).
false
true
true
dataset
10.1371_journal.pbio.3000447
doi10.1371_journal.pbio.3000447
Data Availability Statement All relevant data are within the paper and its supporting information files.
false
true
false
dataset
10.1038_s41586-023-06426-5
doi10.1038_s41586-023-06426-5
Data availabilityIn terms of data processed or generated as part of this study, we provide per-population mtDNA heteroplasmic and homoplasmic allele frequencies and counts in UKB and AoU (Supplementary Tables 5 and 6), genetic association statistics for LD-independent lead SNPs and fine-mapped variants in UKB in addition to colocalization results (Supplementary Tables 2–4) and gene-based RVAS association statistics for genes at GWS for the Cauchy test (Supplementary Table 7). All GWAS sample sizes for each genetic ancestry group, meta-analysis and phenotype can be found in Supplementary Table 1. All GWAS summary statistics from UKB cross-ancestry meta-analyses (used here in discovery analyses) have been deposited in the GWAS Catalog (ID: GCP000614). Summary statistics containing all per-ancestry association statistics as well as cross-ancestry meta-analyses can be accessed through the Google Cloud Platform (bucket: gs://mito-wgs-public-2023). Full GWAS summary statistics from AoU (used here as a replication cohort) have been deposited in a workspace available on the AoU workbench (titled ‘Nuclear genetic control of mtDNA copy number and heteroplasmy in humans’; https://workbench.researchallofus.org/workspaces/aou-rw-3273c7f0/nucleargeneticcontrolofmtdnacopynumberandheteroplasmyinhumans/data). Individual-level data generated as part of UKB (mtCN and mtDNA variant calls) have been returned to UKB to enable utilization of the full individual-level data by the broader scientific community through the UKB data showcase. Individual-level data generated as part of AoU have been deposited in the same workspace containing summary statistics on the AoU Research Workbench. Please see our GitHub repository (https://github.com/rahulg603/mtSwirl) for more information on accessing these data. At the time of publication, access to the AoU workbench controlled tier is restricted to US-based academic institutions, government entities, health care institutions and non-profit organizations. Please also note that as of the time of publication, the only method to gain access to the AoU workspace containing the data generated here is to contact us to be added to the workspace. For information about access to the Researcher Workbench as a registered researcher, please visit https://www.researchallofus.org. In terms of external data used in this study, we leveraged GWAS summary statistics, and ancestry-specific LD-matrices, and a curated list of 29 common, high-quality disease phenotypes generated as part of the Pan UKBB project61. Paths for these summary statistics (https://pan.ukbb.broadinstitute.org/docs/per-phenotype-files) and LD-matrices (https://pan.ukbb.broadinstitute.org/docs/ld) can be found on the Pan UKBB project website (https://pan.ukbb.broadinstitute.org); these were accessed through the Google Cloud Platform as part of this study. UKB phenotype and whole-genome sequencing data can be accessed through the UKB Research Analysis Platform after completing a UKB access application (https://ukbiobank.dnanexus.com/landing). AoU phenotype and genotype data can be accessed through the Controlled Tier v6 on the AoU researcher workbench (https://workbench.researchallofus.org). gnomAD v.3.1.2 (https://gnomad.broadinstitute.org) WGS was accessed through a custom Terra workspace (titled ‘gnomad_subsampled_mitopipeline_head_to_head’). High-coverage WGS data from 1000G were accessed using the public ‘1000G-high-coverage-2019’ workspace in Terra. Published mtscATAC-seq data used for chrM:302 analysis can be obtained with dbGaP approval. Gene-sets for enrichment analyses can be obtained using COMPARTMENTS (https://compartments.jensenlab.org) and MitoCarta 2.0 (https://www.broadinstitute.org/files/shared/metabolism/mitocarta/human.mitocarta2.0.html) as described previously24. The GRCh37 and GRCh38 reference genomes as well as other standard reference data are available through the GATK resource bundle (https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle). Annotations for the baseline v.1.1 and BaselineLD v.2.2 models for S-LDSC as well certain other relevant reference data, including the HapMap3 SNP list, can be obtained from https://alkesgroup.broadinstitute.org/LDSCORE/. Known reference and polymorphic NUMTs were obtained from supplemental data as provided in published work51,85–87. Code availabilityWe release the full WDL pipelines and associated input files for mtDNA analysis from whole-genome sequencing data on GitHub (https://github.com/rahulg603/mtSwirl; 10.5281/zenodo.8067503). We also provide the code we used to run the pipeline on the UKB Research Analysis Platform, AoU and Terra; consolidate all data; perform mtDNA sample and variant QC; and run GWAS. See the Methods and the README in the GitHub repository for more information on how to use the pipeline. Several tools were used as part of mtSwirl, including GATK v.4.2.6.0 (https://gatk.broadinstitute.org/), samtools v.1.9 (https://github.com/samtools/samtools) and bcftools v.1.16 (https://github.com/samtools/bcftools), Haplochecker 0124 https://github.com/genepi/haplocheck), R v.3.1.1 (https://r-project.org), Hail v.0.2.84 (https://hail.is) and UCSC kent tools source v.430 (genome-source.soe.ucsc.edu/kent.git and https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/). We used several published tools and scripts to perform downstream analysis of the mtDNA call-set in this study. All data wrangling, statistical analysis and figure generation was performed using Hail v.0.2.98 (https://hail.is), python v.3.7.10 (https://www.python.org) or R v.4.2.1 (https://r-project.org). Parallelization of tasks in UKB was performed using Hail Batch (in Hail v.0.2.98) (https://batch.hail.is) and in AoU using Cromwell v.77 (https://cromwell.readthedocs.io). GWAS was performed in UKB using SAIGE v.1.1.5 (https://saigegit.github.io). For scaling of UKB GWAS, a custom modification of the GWAS pipeline from the Pan UKBB pan-ancestry GWAS was implemented (https://github.com/atgu/ukbb_pan_ancestry). Linear regression GWAS was performed in AoU using Hail. We release the code used for GWAS on both UKB and AoU on GitHub (https://github.com/rahulg603/mtSwirl). mtDNA PCA was performed in R using the irlba v.2.3.5.1 package (https://cran.r-project.org/web/packages/irlba/index.html). Multinomial models were trained using the nnet v.7.3-17 package in R (https://cran.r-project.org/web/packages/nnet/index.html). Circos plots were made using the circlize package v.0.4.15 in R (https://jokergoo.github.io/circlize_book/book/). For analysis of chrM:302 in single-cell data, we used BedTools v.2.29.2 (https://bedtools.readthedocs.io). LD clumping was performed using Plink v.1.90 (https://www.cog-genomics.org/plink/). Fine-mapping was performed using FINEMAP-inf v.1.3 and SuSiE-inf v.1.2 (https://github.com/FinucaneLab/fine-mapping-inf). eQTL data were obtained from GTEx v.8 (https://gtexportal.org) and the eQTL catalogue release 4 (https://www.ebi.ac.uk/eqtl/). For replication analysis effect size comparisons, the deming v.1.4 package was used in R (https://cran.r-project.org/web/packages/deming/index.html). Heritability estimates and enrichment analyses were performed using stratified LD-score regression (https://github.com/bulik/ldsc). BLASTn v.2.13.0 was used as available from the NCBI (https://blast.ncbi.nlm.nih.gov/Blast.cgi). MUSCLE v.3.8.31 was used for protein sequence alignment (https://drive5.com/muscle/downloads_v3.htm).
false
true
true
dataset
10.3390_sym14091793
doi10.3390_sym14091793
Data Availability Statement: Not applicable.
false
true
false