Datasets:
dataesr
/
paragraph_classification_eval

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dataset
10.1038_s41467-023-37263-9
doi10.1038_s41467-023-37263-9
Data availability Source data of Figs.1a and 6c, and Supplementary Figs. 1a and 11b are provided with this paper. All the high-throughput sequencing data generated in this study are accessible at NCBI’s Gene Expression Omnibus (GEO) via GEO Series accession number GSE204681. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the MassIVE partner repository, and the accession number is MSV000091349. Source data are provided with this paper.
false
true
true
dataset
10.1371_journal.pcbi.1011796
doi10.1371_journal.pcbi.1011796
Data Availability Statement: All data and code used for running experiments and plotting is available on a GitHub repository at https://github.com/kronga/vision-based-collective-model.
false
true
true
dataset
10.1371_journal.pone.0286685
doi10.1371_journal.pone.0286685
Data Availability Statement All relevant data are within the paper and its Supporting Information files.
false
true
false
dataset
10.1088_1751-8121_ad0a71
doi10.1088_1751-8121_ad0a71
Data availability statementThe data that support the findings of this study are available upon reasonable request from the authors.
false
true
false
dataset
10.1038_s41467-023-39332-5
doi10.1038_s41467-023-39332-5
Data availabilityThe data supporting the findings of this study are available within the paper and its supplementary information files. The RNA-sequencing, HTGTS and CRISPR-Cas9 screen data generated in this study have been deposited in NCBI’s Gene Expression Omnibus and are accessible through the GEO Series accession numbers GSE212194, GSE212195, GSE212196, and GSE214643. Source Data for the data presented in graphs are provided with this paper. The uncropped gels and western blots are provided in the Supplementary Information. All data are available from the authors upon request. Source data are provided with this paper.
false
true
true
dataset
10.1016_j.devcel.2023.03.018
doi10.1016_j.devcel.2023.03.018
Data and code availability All data reported in this paper will be shared by the lead contact upon request. No large-scale datasets or original code were generated in this study. 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.0011283
doi10.1371_journal.pntd.0011283
Data Availability Statement All relevant data are within the manuscript and its Supporting information files.
false
true
true
dataset
10.1371_journal.pone.0265395
doi10.1371_journal.pone.0265395
Data Availability Statement Data underlying this study cannot be shared publicly due to Ecuador government regulations that they are requested directly. Direct requests to the Ministry of Public Health can be made by contacting ventanillaunica.msp@msp.gob.ec and to the Ecuadorian Institute of Social Security at https://www.iess.gob.ec/contactos.
false
true
false
dataset
10.3389_fams.2022.830530
doi10.3389_fams.2022.830530
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
10.3390_bioengineering9010002
doi10.3390_bioengineering9010002
Data Availability Statement: The data presented in this study are available on request from the corresponding author.
false
true
false
dataset
10.1186_s12859-023-05169-4
doi10.1186_s12859-023-05169-4
Availability of data and materialsThe documentation and the source code of PSReliP are available at https://github.com/solelena/PSReliP. Detailed instructions on installing the pipeline can be found in the main README file of the PSReliP repository on GitHub. To prepare the datasets on rice varieties and Malawian cichlids used as input data for PSReliP, the raw sequence data in FASTQ format were downloaded from the European Nucleotide Archive (ENA) database by accession number, as listed in Additional file 2: Tables S4 and S5. In these tables, the ‘BioSample accession’ represents the BioSample accession numbers from the BioSample database (https://www.ncbi.nlm.nih.gov/biosample/); the ‘BioProject accession’ represents the BioProject accession numbers from BioProject (https://www.ncbi.nlm.nih.gov/bioproject/); and the ‘Run accession’ represents the SRA accession numbers from the Sequence Read Archive (SRA) based on the source database (SRA, European Bioinformatics Institute (EBI), or DNA Data Bank of Japan (DDBJ)). The SRA run accessions that were used for to create the dataset of rice varieties: DRR018360, DRR018358, DRR018356–DRR018357, DRR018359, DRR018355, DRR008446–DRR008447, DRR001185, DRR000719–DRR000720, DRR003661, DRR003656–DRR003657, DRR003660, DRR003652, DRR003655, DRR003650–DRR003651, DRR003659, DRR003653–DRR003654, DRR003648–DRR003649, DRR003658, DRR004451–DRR004453, DRR125602, DRR054198, DRR054216, DRR099981–DRR099990, DRR093954–DRR093956, DRR093959, DRR093961–DRR093970, DRR092498, DRR092500, DRR128976–DRR128981, ERR2240123–ERR2240128, ERR2241054–ERR2241058, ERR2241060, ERR2242620–ERR2242626, ERR2245512–ERR2245513, ERR2245515–ERR2245520, ERR2245522–ERR2245525, ERR2245527–ERR2245529, ERR2245533–ERR2245540, ERR2245542–ERR2245544, ERR2245546–ERR2245557, ERR157947, ERR161560, ERR161567–ERR158568, ERR161564, SRR1614244, SRR546420, SRR546695, SRR921498, SRR921505, SRR923809, SRR925387, SRR933669, SRR1016473–SRR1016474, SRR1016489–SRR1016491, SRR3056468, SRR1328207, SRR1328218, SRR1328220, SRR1328233, SRR1328254, SRR1450213–SRR1450215, SRR1450217, SRR1450219, SRR1450197–SRR1450198, SRR1528301, SRR1528330, SRR1528440, SRR1528449, SRR1712585, SRR1712645–SRR1712647, SRR1712649, SRR1712651, SRR1712653, SRR1712656, SRR1712898–SRR1712901, SRR1712903–SRR1712907, SRR1712909–SRR1712910, SRR1712953, SRR1712964–SRR1712970, SRR1712971–SRR1712981, SRR3056114, SRR3056466, SRR3056278, SRR3133641, SRR5880534, SRR6166428. The SRA run accessions that were used for to create the dataset of Malawi cichlids: ERR266450–ERR266461, ERR266464–ERR266485, ERR266488–ERR266493, ERR266496–ERR266498, ERR266502, ERR266505, ERR266508–ERR266509, ERR266511, ERR266513, ERR271651, ERR271655, ERR271658–ERR271659, ERR271663, ERR271666, ERR271669, ERR271670, ERR271672, ERR271674, ERR271677–ERR271678, ERR271680, ERR271682, ERR295124–ERR295132, ERR299198–ERR299215, ERR303339–ERR303340, ERR303342–ERR303343, ERR303345–ERR303346, ERR303348–ERR303349, ERR303351–ERR303352, ERR303354–ERR303355, ERR303357–ERR303358, ERR303360–ERR303361, ERR303363–ERR303364, ERR303366–ERR303367, ERR303369–ERR303370, ERR303372–ERR303373, ERR303375–ERR303376, ERR303378–ERR303379, ERR303381–ERR303382, ERR303384–ERR303385, ERR303387–ERR303388, ERR303390–ERR303391, ERR303393–ERR303394, ERR303396–ERR303397, ERR303399–ERR303400, ERR303402–ERR303403, ERR303405–ERR303406, ERR303408–ERR303409, ERR315227–ERR315228, ERR315230–ERR315231, ERR315233–ERR315234, ERR702304–ERR702307, ERR715499–ERR715501, ERR702308, ERR715502–ERR715504, ERR715506–ERR715513, ERR702309, ERR715476, ERR715514–ERR715515, ERR715477, ERR715516–ERR715519, ERR715521, ERR715523–ERR715524, ERR715478–ERR715487, ERR715530–ERR715540, ERR1081365–ERR1081371, ERR1081373–ERR1081376, ERR1081378–ERR1081388, ERR1081372, ERR3634107–ERR3634110, ERR3634112–ERR3634115.
false
true
true
dataset
10.1186_s12954-023-00771-4
doi10.1186_s12954-023-00771-4
Availability of data and materials All data used during the study are available on reasonable request from the corresponding author.
false
true
false
dataset
10.1038_s41586-023-05836-9
doi10.1038_s41586-023-05836-9
Data availability Structure factors and refined models obtained using X-ray crystallography have been deposited into PDB under accession codes 8DBA (wild-type KaiCRS) and 8DB3 (KaiCRS-∆coil). Cryo-EM maps and refined models have been deposited into the Electron Microscopy Data Bank (EMDB) and PDB, respectively. The composite map and model for the KaiCRS-S413E/S414E dodecamer reconstruction are submitted under entries EMD-29505 and 8FWI, respectively. The composite map and model for the KaiCRS-S413E/S414E–KaiBRS dodecamer reconstruction are submitted under entries EMD-29506 and 8FWJ, respectively. The focused KaiCRS-S413E/S414E hexamer refinement map is available under accession EMD-29507 and the focused KaiCRS-S413E/S414E–KaiBRS hexamer refinement map is available under accession EMD-29508. The full KaiCRS-S413E/S414E dodecamer refinement is available under accession EMD-29509 and the full KaiCRS-S413E/S414E–KaiBRS dodecamer refinement is available under accession EMD-29510. Other datasets used are all publicly available in public community or discipline-specific repositories (for example, PDB identifiers 5JWQ, 1W0J, 1TF7 and 7S65). The accession codes for protein sequences, sequence alignments and phylogeny are listed in Supplementary Datasets 1 and 2.
false
true
true
dataset
10.1016/j.celrep.2022
doi10.1016/j.celrep.2022
Data and code availability d The data for this study is available upon request from the lead contact. d All original code has been deposited at Zenodo (https://zenodo.org/record/7055600) and is publicly available as of the date of publication. DOIs are listed in the key resources table. 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
10.1088_1402-4896_ad1024
doi10.1088_1402-4896_ad1024
Data availability statementOur university's policy is to share data only upon request to avoid plagiarism and the misuse of data. 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.0284036
doi10.1371_journal.pone.0284036
Data Availability Statement Unfortunately, due to the General Data Protection Regulation (GDPR) of EU and the connected Dutch data protection legislation we are not allowed to share individual patient data even in a pseudonymized format (data contact: University Medical Center Utrecht, WAG/mb/20/016983, mvianen@umcutrecht.nl).
false
true
false
dataset
10.1371_journal.pcbi.1007568
doi10.1371_journal.pcbi.1007568
Data Availability Statement All relevant files are available from https://github.com/look0012/GCNCDA/.
false
true
true
dataset
10.1186_s12931-023-02455-w
doi10.1186_s12931-023-02455-w
Data availability All data generated and analysed during this study are included in this published article.
false
true
false
dataset
10.1186_s13059-023-02939-4
doi10.1186_s13059-023-02939-4
Availability of data and materials Data supporting the findings of this work are available within the paper and its Supplementary Information files. All high-throughput sequencing data generated in this study are accessible at NCBI’s Gene Expression Omnibus (GEO) via GEO Series accession number GSE212801 [42]. The customized codes used in this study are available Github [43], Figshare [44], and is released under the terms of the GNU General Public License (GPL) version 3.0 (https://opensource.org/license/gpl-3-0/). ChIP-seq data from the following studies and accession numbers were used: Liu et al. [26] (GSM2667837 [45]), Liu et al. [46] (GSM4275144 [47], GSM4275146 [48]), Zhu et al. [49] (SRR1509479 [50]), Harris et al. [51] (GSM2897853 [52]), Jégu et al. [53] (GSM2366606 [54]), Chen et al. [55] (GSM2882803 [56]), Lu et al. [57] (GSM3674621 [58]), and Zhong et al. [59] (GSM5684049 [60], GSM5684053 [61], GSM5684057 [62]).
false
true
true
dataset
10.1371_journal.pstr.0000102
doi10.1371_journal.pstr.0000102
Data Availability Statement: The data in this manuscript are available on the Figshare data repository. https://doi.org/10.6084/m9.figshare.24808338.v1.
false
true
true
dataset
10.7554_elife.83529
doi10.7554_elife.83529
Data availability All materials are available through requests to the corresponding authors. All custom code was identical to that reported in Pederick et al., 2021 and can be accessed at https://github.com/dpederick/Reciprocal-repulsions-instruct-the-precise-assembly-of-parallel-hippocampal-networks/tree/1 (Pederick, 2021). All data generated or analyzed during this study are included in the manuscript and supporting file. Source data files have been provided for all figures.
false
true
true
dataset
10.2196_44990
doi10.2196_44990
Data Availability Twitter data were collected using Twitter’s Application Programming Interface for Academic Research. More information on applying for access can be found at [72]. The paper also uses restricted US natality files with geographic identifiers. The files were obtained after submitting a research proposal to and obtaining approval for data access from the National Center for Health Statistics. More information on applying can be found at [73]. We have added example code to run the analyses in Multimedia Appendix 1.
false
true
true
dataset
10.1038_s41467-023-40476-7
doi10.1038_s41467-023-40476-7
Data availabilityHigh-throughput sequencing data have been deposited in the NCBI Sequence Read Archive database under accession code SUB13659056 and Bioproject PRJNA994108. All data supporting the findings described in this manuscript are available in the article and in the Supplementary Information and from the corresponding author upon request. Source data are provided with this paper.
false
true
true
dataset
10.3847_1538-4357_ac721b
doi10.3847_1538-4357_ac721b
Software: astropy (Astropy Collaboration et al. 2013), deeplenstronomy (Morgan et al. 2021), lenstronomy (Birrer & Amara 2018; Birrer et al. 2021), matplotlib (Hunter 2007), numpy (Harris et al. 2020), pandas (McKinney 2010), PlotNeuralNet (Iqbal 2018), PyTorch (Paszke et al. 2019), Scikit-Learn (Pedregosa et al. 2011), scipy (Virtanen et al. 2020).
true
false
true
dataset
10.1371_journal.pdig.0000081
doi10.1371_journal.pdig.0000081
Data Availability Statement Relevant data set is provided in the manuscript and in the supplementary. Further data cannot be shared publicly as they contain potentially identifying patient information. The data are owned by Poriya hospital. For researchers who meet the criteria for access to confidential data, requests for these data sets can be sent to zohar@odmachine.com. The authors had no special access privileges that others would not have.
false
true
true
dataset
10.1371_journal.pone.0285717
doi10.1371_journal.pone.0285717
Data Availability Statement The datasets generated during and/or analysed during the current study are not publicly available due to constraints imposed by the consent form and the IRB committee. However, a request to access the data can be requested from the research ethics committee at JUH hospital (sssaleh@ju.edu.jo).
false
true
false
dataset
10.2196_43965
doi10.2196_43965
Data Availability The data sets generated and analyzed during this study are available from the corresponding author on reasonable request. Interested parties will be required to complete an institutional Data Use Agreement, and data will be made available via Secure Data transfer.
false
true
true
dataset
10.1371_journal.pone.0266065
doi10.1371_journal.pone.0266065
Data Availability Statement All relevant data is available within the paper.
false
true
false
dataset
10.1021_acscentsci.3c00160
doi10.1021_acscentsci.3c00160
Data Availability Statement The authors declare that the data supporting the findings of this study are available within the paper and its Supporting Information files, and at Mendeley Data, V1, doi: 10.17632/dn37cj6z5m.1, as well as from the corresponding author upon reasonable request.
true
true
false
dataset
10.1371_journal.pone.0283908
doi10.1371_journal.pone.0283908
Data Availability Statement All relevant data are within the paper and are shown in the Supporting Information, S6 Fig.
false
true
false
dataset
10.1088_1361-6463_acffd7
doi10.1088_1361-6463_acffd7
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.0254520
doi10.1371_journal.pone.0254520
Data Availability Statement All relevant data are within the manuscript and its S1 Appendix files.
false
true
true
dataset
10.1186_s40168-023-01493-2
doi10.1186_s40168-023-01493-2
Availability of data and materials The datasets supporting the conclusions of this article are available in the National Center for Biotechnology Information repository, under BioProject number PRJNA763533. The previously published, free-living raw sequencing reads and corresponding MAGs are available at the National Center for Biotechnology Information under BioProject PRJNA454888.
true
true
false
dataset
10.1073_pnas.2220159120
doi10.1073_pnas.2220159120
Data, Materials, and Software Availability. ATAC sequencing data have been submitted to the NCBI Sequence Read Archive, accession number: BioProject PRJNA887449. All study data are included in the article and/or SI Appendix.
true
true
true
dataset
10.1186_s13073-023-01173-8
doi10.1186_s13073-023-01173-8
Availability of data and materials Data supporting the findings of this study are available within the manuscript and supplemental files. The whole-genome sequencing data of anonymized patients recruited through the National Institutes of Health (NIH) and sequenced at the National Institute of Allergy and Infectious Diseases (NIAID) through the Uniformed Services University of the Health Sciences (USUHS)/the American Genome Center (TAGC) are available under dbGaP submission phs002245.v1. Other patients were not consented to share the raw WES/WGS data files beyond the research and clinical teams.
false
true
true
dataset
10.1038_s41593-023-01345-0
doi10.1038_s41593-023-01345-0
Data availability All source data are provided with this paper. Raw electrophysiology and imaging datasets are available from the corresponding authors upon reasonable request. Plasmids for our newly generated viral constructs have been deposited at https://www.addgene.org/plasmids/articles/28225278/. Source data are provided with this paper.
false
true
false
dataset
10.1371_journal.pgen.1010655
doi10.1371_journal.pgen.1010655
Data Availability Mutant lines were deposited in the National Small Grains Collection under ID numbers PI 701905 (Kronos-PS, introgression of photoperiod sensitive allele Ppd-A1b), PI 701906 (Kronos elf3 phyB combined knock-outs), and PI 701907 (Kronos elf3 ppd1). Additional information about these accessions and/or seed requests can be done at GRIN-Global https://npgsweb.ars-grin.gov/gringlobal/search. All other relevant data are within the paper and its Supporting Information files.
false
true
false
dataset
10.1186_s40359-021-00605-7
doi10.1186_s40359-021-00605-7
Availability of data and materialsAll data generated or analysed during this study are included in this published article.
false
true
false
dataset
10.1172_jci.insight.166698
doi10.1172_jci.insight.166698
Data availability.RNA-Seq data can be accessed in the NCBI GEO via GSE197571 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE197571).
false
true
false
dataset
10.1099_mgen.0.000977
doi10.1099_mgen.0.000977
All sequence data are available online. The assembled sequencing reads generated in the present study are publicly available at the National Center for Biotechnology Information (NCBI), BioProject Number: PRJNA851747 and PRJNA659865. The authors confirm that all supporting data, code and protocols have been provided within the article or through supplementary data files. All new multilocus sequence typing (MLST) sequences generated were deposited onto the respective databases available on PubMLST (https://pubmlst.org/organisms/Acinetobacter-baumannii). Additional A. baumannii genomes used in this study are available and can be downloaded from GenBank (accession numbers available in File S2).
false
true
true
dataset
10.1016_j.pocean.2023.102995
doi10.1016_j.pocean.2023.102995
Data availability Data has been made available on GitHub: https://github.com/Kenhasteandersen/FirstPrinciplesPlankton. Research data for this article Dryad Dryad Digital Repository Scientific and medical research data Data associated with the article: Body size, light intensity and nutrient supply determine plankton stoichiometry in mixotrophic plankton food webs
false
true
true
dataset
10.1371_journal.pone.0285449
doi10.1371_journal.pone.0285449
Data AvailabilityThe aligned sequences are available through the European Nucleotide Archive under accession number PRJEB61755. Otherwise, all data generated or analyzed during this study are included in this published article and its Supporting Information files.
false
true
false
dataset
10.1371_journal.pntd.0007125
doi10.1371_journal.pntd.0007125
Data Availability Statement It is a systematic review, all the included papers are published online and can be found in the references of the paper.
false
true
false
dataset
10.1371_journal.pbio.3002483
doi10.1371_journal.pbio.3002483
Data Availability Statement: All datasets are publicly available: Figs 1–8: dx.doi.org/10.5281/zenodo.10386854. S1–S4 Figs: dx.doi.org/10.5281/zenodo.10387118. R code for graphical outputs and statistical analyses of Figs 1–4: dx.doi.org/10.5281/zenodo.10386496. Modelling code and R code to recreate all modelling figures dx.doi.org/10.5281/zenodo.10162264.
true
true
true
dataset
10.1515_anona-2022-0288
doi10.1515_anona-2022-0288
Data availability statement: The datasets generated during and/or analysed during the current study are available from the corresponding author on reasonable request.
false
true
false
dataset
10.1038_s42003-023-04898-9
doi10.1038_s42003-023-04898-9
Data availability RNA sequencing data that support the findings of this study have been deposited in GEO with the accession code GSE216060. Data can be downloaded by going to ncbi.nlm.nih.gov/geo and searching for the accession code. The source data for the main figures are given in Supplementary Data 1 and 2, and any remaining information can be obtained from the corresponding author upon reasonable request.
false
true
true
dataset
10.1371_journal.pgph.0002529
doi10.1371_journal.pgph.0002529
Data Availability Statement: All datasets underlying this study are freely available at the public repository https://osf.io/7ysb9/.
false
true
false
dataset
10.7554_elife.85145
doi10.7554_elife.85145
Data availability The current manuscript is a computational study, so no data have been generated for this manuscript. Code is available on GitHub (copy archived at Russell et al., 2022a). Numerical data used to generate figures is available as source data for Figures 3, 4, 5, 6, and 7. The following previously published datasets were used: EmersonRODeWittWSVignaliMGravleyJOsborneEJDesmaraisCKlingerMCarlsonCSHansenJARiederMRobinsHSHuJK2017Immunosequencing identifies signatures of cytomegalovirus exposure history and HLA mediated effects on the T cell repertoireImmuneACCESS10.21417/B7001Z RussellMLSouquetteALevineDMAllenEKKuanGSimonNBalmasedaAGordonAThomasPGMatsenFABradleyP2022Combining genotypes and T cell receptor distributions to infer genetic loci determining V(D)J recombination probabilitiesNCBI BioProjectPRJNA762269 RobinsHPearsonO2015Normal Human PBMC Deep Sequencing TCRB versus TCRG comparisonImmuneACCESSTCRB-TCRG-comparison BrineyBInderbitzinAJoyceCBurtonDR2019Commonality despite exceptional diversity in the baseline human antibody repertoireNCBI BioProjectPRJNA406949 JaffeDBShahiPAdamsBAChrismanAMFinneganPMRamanNRoyallAETsaiFVollbrechtTReyesDSMcDonnellWJ2022Functional antibodies exhibit light chain coherenceFigshare10.25452/figshare.plus.20338177 MartinPJLevineDMStorerBENelsonSCDongXHansenJA2020Recipient and donor genetic variants associated with mortality after allogeneic hematopoietic cell transplantationNCBI dbGaPphs001918
false
true
true
dataset
10.1073_pnas.2221652120
doi10.1073_pnas.2221652120
Data, Materials, and Software Availability All study data are included in the article and/or SI Appendix.
true
true
true
dataset
10.1186_s12891-023-06370-5
doi10.1186_s12891-023-06370-5
Availability of data and materials The data used in the present study are publicly available through the Inter-University Consortium for Political and Social Research (ICPSR): www.icpsr.umich.edu/web/ICPSR/studies/29282.
false
true
false
dataset
10.1371_journal.pmed.1004257
doi10.1371_journal.pmed.1004257
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1088_2515-7620_ad028c
doi10.1088_2515-7620_ad028c
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_s41467-023-39248-0
doi10.1038_s41467-023-39248-0
Data availabilityControl genomic data can be requested from the Scottish Family Health Study (Generations Scotland) by email to access@generationscotland.org. Details of the application procedure can be found at https://www.ed.ac.uk/generation-scotland/for-researchers/access. Patient data can be requested from ian.tomlinson@oncology.ox.ac.uk, with response expected within four weeks. All data are protected by formal agreements in order to preserve patient anonymity and privacy, and to comply with ethical permissions. Data will be released to researchers subject to formal compliance with these conditions of anonymity and existing ethical permissions, as incorporated into a data transfer agreement based on the standard models used by the host institutions concerned.
false
true
false
dataset
10.1371_journal.pone.0252732
doi10.1371_journal.pone.0252732
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1038_s41586-023-05754-w
doi10.1038_s41586-023-05754-w
Data availability Bam files of aligned reads for the 80 newly published ancient individuals can be obtained from the European Nucleotide Archive (accession no. PRJEB58698). SNP array genotype data for 122 newly reported modern individuals can be obtained from a permanent link at the Dataverse repository at (10.7910/DVN/NC28XW). The data for 103 of these individuals can be downloaded without registering, whereas the informed consent for 19 individuals from Madagascar is not consistent with unmediated public posting of data, and may be downloaded after filling out a form with an email address and institutional or professional affiliation, and including an affirmation of the following statements: (a) I will not distribute the data outside my collaboration; (b) I will not post the data publicly; (c) I will make no attempt to connect the genetic data to personal identifiers for the samples; (d) I will use the data only for studies of population history; and (e) I will not use the data for commercial purposes.
false
true
false
dataset
10.1371_journal.pone.0226644
doi10.1371_journal.pone.0226644
Data Availability Statement All relevant data are within the paper and its Supporting Information files.
false
true
false
dataset
10.1088_2053-1591_ad135b
doi10.1088_2053-1591_ad135b
Data availability statementThere is no data related to this manuscript that needs to be shared with the public. The data that support the findings of this study are available upon reasonable request from the authors.
false
true
true
dataset
10.1038_s41467-023-39038-8
doi10.1038_s41467-023-39038-8
Data availabilityRNA-seq datasets analyzed in this study were previously published and are publicly available, and they were obtained from the GEO repository using accession numbers GSE116124, GSE152768, GSE120306. This study also accessed the following databases: Ensembl release 100 (https://www.ensembl.org/info/website/archives/index.html?redirect=no), the Human Transcription Factors database (http://humantfs.ccbr.utoronto.ca/), the HumanTFDB portal (http://bioinfo.life.hust.edu.cn/AnimalTFDB/), the TF2DNA database (https://www.fiserlab.org/tf2dna_db/), QuickGO (https://www.ebi.ac.uk/QuickGO/), GSEA (https://www.gsea-msigdb.org/gsea/index.jsp), Biocarta (https://maayanlab.cloud/Harmonizome/dataset/Biocarta+Pathways), KEGG (https://www.genome.jp/kegg/). Source data are provided with this paper.Code availabilityCustom code generated to analyze the RNA-seq data is available at: https://github.com/ArnaudDroitLab/de_rus_jacquet_2023.
false
true
true
dataset
10.1515_culture-2022-0170
doi10.1515_culture-2022-0170
Data availability statement: All data generated or analysed during this study are included in this published article.
false
true
false
dataset
10.1371_journal.pone.0212259
doi10.1371_journal.pone.0212259
Data Availability Statement According to Danish legislation, the authors' own approvals to use the Danish data sources for the current study do not allow them to distribute or make patient data directly available to other parties. Up-to-date information on data access is available online (http://sundhedsdatastyrelsen.dk/da/forskerservice). Access to data from the Danish Health Data Authority requires approval from the Danish Data Protection Agency (https://www.datatilsynet.dk/english/the-danish-data-protection-agency/introduction-to-the-danish-data-protection-agency/). The authors do not have special access privileges to these data.
true
true
false
dataset
10.1126_science.adh1720
doi10.1126_science.adh1720
Data and materials availability: Diffraction images have been deposited at the SBGrid databank. Protein structures and reflection files for LL1 and LL2 complex structures have been deposited at the RCSB Protein Databank with PDB IDs 8DA3, 8DA4, 8DA5, 8DA6, 8DA7, 8DA8, 8DA9, 8DAA, 8DAB, and 8DAC. NGS data is deposited at DRYAD (46). Data and code for MI, coevolution analysis, and deep learning model are available at https://github.com/akds/CoevolveML and archived at Zenodo (47).
true
true
true
dataset
10.1155_2019_6891831
doi10.1155_2019_6891831
Data Availability The data used to support the findings of this study have not been made available because they are restricted by the The Health Care Service Human Research Ethics Committee (Helsinki approval No. 2009087), as well as the Israeli Ministry of Education (No. 506/7902) in order to protect patient privacy. Data are available from Dr. Tsofia Deutsch-Castel, deutsh_t@mac.org.il for researchers who meet the criteria for access to confidential data.
false
true
false
dataset
10.1073_pnas.2221613120
doi10.1073_pnas.2221613120
Data, Materials, and Software Availability All study data are included in the article and/or SI Appendix.
true
true
true
dataset
10.1186_s12889-019-7608-1
doi10.1186_s12889-019-7608-1
Availability of data and materialsThe datasets generated and/or analysed during the current study are not publicly available due [reasons below] but are available from the corresponding author on reasonable request.
false
true
false
dataset
10.1084_jem.20230661
doi10.1084_jem.20230661
Data availabilityAll data supporting the findings of this study are available within the main text and supplemental material and from the corresponding authors upon request.
true
true
false
dataset
10.1007_s40993-022-00409-7
doi10.1007_s40993-022-00409-7
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
doi10
Data Availability Statement: Data is contained within the article or Supplementary Material. The data presented in this study are available in this article and related Supplementary Material.
false
true
false
dataset
10.1371_journal.pone.0242533
doi10.1371_journal.pone.0242533
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1371_journal.pone.0292082
doi10.1371_journal.pone.0292082
Data Availability Statement: The dataset, code and models are publicly available at https://github.com/donghaibing2005001481/YOLOv5s.
false
true
true
dataset
10.1371_journal.pone.0239694
doi10.1371_journal.pone.0239694
Data Availability Statement All of the data used in this research is publically available at http://ClinicalTrials.gov. All of the reports generated from this research can be found at http://CovidResearchTrials.com.
false
true
false
dataset
10.1371_journal.pntd.0011975
doi10.1371_journal.pntd.0011975
Data Availability Statement: All relevant data are within the paper and its Supporting Information files. The study protocol is available at: http://dx.doi.org/10.1136/bmjopen-2017-021372.
false
true
false
dataset
10.1126_science.abn5887
doi10.1126_science.abn5887
Data and materials availability: Raw sequencing reads for Balto and Alaskan sled dogs have been deposited to the NCBI Sequence Read Archive under BioProject accession PRJNA786530.
true
true
false
dataset
10.1371_journal.pone.0243709
doi10.1371_journal.pone.0243709
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1371_journal.pone.0262786
doi10.1371_journal.pone.0262786
Data Availability Statement All relevant data are within the paper and its Supporting information files.
false
true
false
dataset
10.1242_dev.201186
doi10.1242_dev.201186
All relevant data can be found within the article and its supplementary information.
false
true
false
dataset
10.3390_math10030452
doi10.3390_math10030452
Data Availability Statement: Not applicable.
false
true
false
dataset
10.1371_journal.pone.0251372
doi10.1371_journal.pone.0251372
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.7554/eLife
doi10.7554/eLife
Data availability Due to the size of the dataset, raw electrophysiology traces are available on request to the corresponding author. All information has been extracted from the raw electrophysiological traces and is available to download as source data files. All the codes or software used in analyzing the data and their sources are listed in the Key Resources Table.
false
true
true
dataset
10.1186_s12885-021-08130-x
doi10.1186_s12885-021-08130-x
Availability of data and materialsThe datasets generated during the current study are not publicly available due to concerns regarding patient confidentiality and proprietary information but are available upon reasonable request from the corresponding author.
false
true
false
dataset
10.1371_journal.pgen.1010809
doi10.1371_journal.pgen.1010809
Data AvailabilityThe authors confirm that all data underlying the findings are fully available without restriction. All relevant data are within the paper and its Supporting Information files. Data points used to make plots, raw RNA-sequencing data, and unprocessed gels and blots used in this study are available as Data S1, S2, and S3, respectively.
false
true
true
dataset
10.1007_s00220-023-04656-2
doi10.1007_s00220-023-04656-2
Data Availability Statement Data sharing not applicable to this article as no datasets were generated or analysed during the current study.
false
true
false
dataset
10.1088_1741-2552_acfe3a
doi10.1088_1741-2552_acfe3a
Data availability statementThe data that support the findings of this study are openly available at the following URL/DOI: https://github.com/hasanzan/FullSleepNet.
false
true
true
dataset
10.1371_journal.pone.0237585
doi10.1371_journal.pone.0237585
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1021_acs.inorgchem.2c03737
doi10.1021_acs.inorgchem.2c03737
Data Availability Statement CCDC deposition numbers 2195856−2195858 contain the supplementary crystallographic data for this paper.
false
true
false
dataset
10.1088_2752-5295_acf4b6
doi10.1088_2752-5295_acf4b6
Data availability statementThe data that support the findings of this study are openly available at the following URL/DOI: https://climexp.knmi.nl/HeatwaveIndiaPakistan2022.cgi.
false
true
false
dataset
10.7554_elife.85413
doi10.7554_elife.85413
GEO GSE214714 is the accession number for the ChIP-seq data reported in this manuscript. The following dataset was generated: Author(s) Year Dataset title Dataset URL Database and Identifier Yang Q, Lo T, Brejc K, Schartner CM, Ralston EJ, Lapidus DM, Meyer BJ 2022 Caenorhabditis briggsae SDC-2 and DPY-27 ChIP- seq https://www.ncbi. nlm.nih.gov/geo/ query/acc.cgi?acc= GSE214714 NCBI Gene Expression Omnibus, GSE214714
false
true
false
dataset
10.1016_j.cub.2019.01.077
doi10.1016_j.cub.2019.01.077
Data and Software Availability Code will be made available at https://github.com/bicanski
false
true
true
dataset
10.1371_journal.pone.0265361
doi10.1371_journal.pone.0265361
Data Availability Statement Data deposited in the Dryad Digital Repository: https://doi.org/10.5061/dryad.jdfn2z3d0.
false
true
false
dataset
10.1371_journal.pgph.0001991
doi10.1371_journal.pgph.0001991
Data Availability Statement All data underlying the study findings have been uploaded as supporting information.
false
true
false
dataset
10.1038_s41588-023-01366-2
doi10.1038_s41588-023-01366-2
Data availability The raw sequencing files generated during this study are available on the Gene Expression Omnibus (accession number GSE205904); corresponding processed data are available on Zenodo70. TF-binding motifs were obtained from HOCOMOCO v11 (https://hocomoco11.autosome.org/). Gene Ontology assignments were obtained from AmiGO (http://amigo.geneontology.org/amigo). All analyses were carried out on human genome version hg38, except for PRS endophenotype GWAS (hg19). The raw source data for the facial phenotypes—the three-dimensional facial surface models in.obj format—are available through the FaceBase Consortium (https://www.facebase.org). Access to these three-dimensional facial surface models requires proper institutional ethics approval and approval from the FaceBase data access committee. Facial scans from patients with PRS (used to define the PRS endophenotype) are available through the FaceBase Consortium (https://www.facebase.org FB00000861) under controlled access. The participants making up the US dataset of healthy individuals used for PRS endophenotype GWAS were not collected with broad data sharing consent. Given the highly identifiable nature of both facial and genomic information and unresolved issues regarding risks to participants of inherent reidentification, participants were not consented for inclusion in public repositories or the posting of individual data. This restriction is not because of any personal or commercial interests. Further information about access to the raw three-dimensional facial images and/or genomic data can be obtained from the PSU IRB (IRB-ORP@psu.edu, and the IUPUI IRB (irb@iu.edu). The ALSPAC (UK) data will be made available to bona fide researchers on application to the ALSPAC Executive Committee (https://www.bristol.ac.uk/alspac/researchers/access/). Summary statistics from the PRS endophenotype GWAS are available on the GWAS Catalog (GCP000517). Plasmids generated in this study have been deposited in Addgene (plasmid no. 194971). All other reagents are available upon request to J.W. Source data are provided with this paper.
false
true
true
dataset
10.1371_journal.pone.0258709
doi10.1371_journal.pone.0258709
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.3390_vision7010010
doi10.3390_vision7010010
Data Availability Statement: Not applicable.
false
true
false
dataset
10.1371_journal.pone.0285953
doi10.1371_journal.pone.0285953
Data Availability Statement The informed consent forms for this study indicated that participants' data would be shared only in aggregate, so we are unable to share an individual-level dataset. The aggregated data are available in the manuscript tables and figures. If researchers are interested in obtaining the data in this manuscript aggregated in a different way, they can reach out to MVPDB inquiries (mvpdb@cdc.gov) to discuss potential data access. A data use agreement may be required.
false
true
true
dataset
10.1016_j.puhe.2020.04.029
doi10.1016_j.puhe.2020.04.029
Availability of data and materialsUnderstanding Society - The UK Household Longitudinal Study (UKHLS) data are available from the UK Data Service https://discover.ukdataservice.ac.uk/catalogue/?sn = 6614. Data documentation is available from the Understanding Society website https://www.understandingsociety.ac.uk/documentation.
false
true
false
dataset
10.1371_journal.pone.0208971
doi10.1371_journal.pone.0208971
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
false
true
true
dataset
10.1084_jem.20221816
doi10.1084_jem.20221816
Data availability scRNAseq data of intestinal CD4+ T cells from GF or Oligo-MM12 mice fed AA, AA + OVA, or chow diet, and SPF iSellTomato mice in the OVA feeding, tolerance, or allergy protocols are publicly available under Gene Expression Omnibus accession number GSE231351. Other data are available in the published article and online supplemental material.
false
true
false
dataset
10.1126_sciadv.aat9488
doi10.1126_sciadv.aat9488
Data and materials availability: 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
10.1186_s12943-023-01788-w
doi10.1186_s12943-023-01788-w
Availability of data and materials The datasets generated and/or analysed during the current study are available through the referenced publications or at GEO website as described in the Methods section.
false
true
false
dataset
10.1038_s41398-020-00953-9
doi10.1038_s41398-020-00953-9
Data availability Summary statistics are available at https://bitbucket.org/steinlabunc/ spark_asd_sumstats. Code availability Code is available at https://github.com/thewonlab/GWAS_ASD_SPARK.
false
true
true
dataset
10.1371_journal.pone.0299456
doi10.1371_journal.pone.0299456
Data Availability Statement: The code supporting this study is available from https://zenodo.org/records/10542753.
false
true
true