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bool 2
classes |
|---|---|---|---|---|---|---|
dataset
|
10.1126_science.adg6518
|
doi10.1126_science.adg6518
|
Data and materials availability: The plasmids used in this study are available through AddGene (depositor: David R. Liu). DNA sequencing files can be accessed using the NCBI SRA (SUB# PRJNA871232). All data are available in the main text or the supplementary materials.
| false
| true
| false
|
dataset
|
10.1371_journal.pone.0286527
|
doi10.1371_journal.pone.0286527
|
Data Availability Statement All relevant data are within the paper and its Supporting information files.
| false
| true
| false
|
dataset
|
10.1371_journal.pone.0255193
|
doi10.1371_journal.pone.0255193
|
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
| false
| true
| true
|
dataset
|
10
|
doi10
|
Data availability The data that support the findings of this study are available from the corresponding authors on reasonable request. Source data are provided with this paper.
| false
| true
| false
|
dataset
|
10.1186_s12985-019-1252-3
|
doi10.1186_s12985-019-1252-3
|
Availability of data and materialsThe datasets used and/or analyzed during the current study are available from the corresponding author on request.
| false
| true
| false
|
dataset
|
10.1186_s12872-021-02125-z
|
doi10.1186_s12872-021-02125-z
|
Availability of data and materials The datasets used and analyzed during the current study are available from the principal investigator of CCC-ACS on reasonable request.
| false
| true
| false
|
dataset
|
10.1001_jamanetworkopen.2023.6431
|
doi10.1001_jamanetworkopen.2023.6431
|
Data Sharing Statement: See Supplement 2.
| false
| true
| false
|
dataset
|
10.1088_1361-6501_ad060f
|
doi10.1088_1361-6501_ad060f
|
Data availability statementThe data cannot be made publicly available upon publication because they contain commercially sensitive information. The data that support the findings of this study are available upon reasonable request from the authors.
| false
| true
| false
|
dataset
|
10.1088_1361-6528_ad0243
|
doi10.1088_1361-6528_ad0243
|
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.2302325120
|
doi10.1073_pnas.2302325120
|
Data, Materials, and Software Availability Cryo-EM density maps and atomic coordinates of the hSlo1 channel in total membrane vesicles (Ca2+-free and EDTA-free), in plasma membrane vesicles, and in digitonin (Ca2+-free and EDTA-free) have been deposited in the Electron Microscopy Data Bank under accession codes EMD-40038 (60), and EMD-40044 (61), EMD-40045 (62) and in the Protein Data Bank under accession codes 8GH9 (63), 8GHF (64), and 8GHG (65), respectively.
| false
| true
| true
|
dataset
|
10.1371_journal.pone.0285841
|
doi10.1371_journal.pone.0285841
|
Data Availability Statement The data underlying the results presented in the study are available from Swedish national dataservice: https://snd.gu.se/en/describe-and-share-data.
| false
| true
| false
|
dataset
|
10.1371_journal.pmed.1002902
|
doi10.1371_journal.pmed.1002902
|
Data Availability Statement Data cannot be shared publicly because consent was not obtained for this. Data are available from the Ethics Review Board in Sweden (https://etikprovningsmyndigheten.se/) for researchers who meet the criteria for access to confidential data.
| false
| true
| false
|
dataset
|
10.1038_s41565-023-01372-9
|
doi10.1038_s41565-023-01372-9
|
Data Availability The Cancer Genome Atlas (http://cancergenome.nih.gov) and Matrisome (http://matrisomeproject.mit.edu/) are open access resources. The datasets and codes generated and analysed during the current study are available in the Zenodo repository (https://zenodo.org/deposit/7686811). All data that support the findings of this study are available within the Article and its Supplementary Information or from the corresponding author upon reasonable request. Source data are provided with this paper.
| false
| true
| true
|
dataset
|
10.1155_2019_1872536
|
doi10.1155_2019_1872536
|
Data AvailabilityThe data used to support the findings of this study are available from the corresponding author upon request.
| true
| true
| false
|
dataset
|
10.1186_s12871-021-01333-6
|
doi10.1186_s12871-021-01333-6
|
Availability of data and materials The datasets used and/or analyzed during the current study are not publicly available due to patient privacy and institutional policy but are available from the corresponding author on reasonable request.
| false
| true
| false
|
dataset
|
10.1371_journal.pone.0267550
|
doi10.1371_journal.pone.0267550
|
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files. We have clearly described all of the statistical tests used as well as which functions in R were used. Furthermore, we provide supplementary files that include all the raw data from the surveys (S3), all estimates from generalized linear mixed models (S2), and the R scripts used to analyze the data (S4) so that anyone interested can re-run the analyses if they wish.
| false
| true
| true
|
dataset
|
10.1371_journal.pone.0223212
|
doi10.1371_journal.pone.0223212
|
Data Availability Statement Supplementary material for this article is available online. RNA sequencing data are deposited into the GEO database with GEO accession number GSE136234. All other data generated by the authors are presented in the paper.
| true
| true
| false
|
dataset
|
10.1371_journal.pone.0228975
|
doi10.1371_journal.pone.0228975
|
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
| false
| true
| true
|
dataset
|
10
|
doi10
|
Availability of data and materials Links to the datasets generated and/or analysed during the current study can be found in Table 2. Code to replicate and extend this work can be found at https://github.com/AbigailJ32/The-persistent-homology-of-genealogical-networks.
| false
| true
| true
|
dataset
|
10.1088_1361-6382_ad0a19
|
doi10.1088_1361-6382_ad0a19
|
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.pone.0283829
|
doi10.1371_journal.pone.0283829
|
Data Availability Statement The data used for this manuscript are available upon request from the ethics committee of Arsi University College of Health Science and Medicine (pr.arsiu@arsiun.edu.et). Because the dataset file contains personal information, it may not be ethical to publicly deposit the data.
| false
| true
| true
|
dataset
|
10.1088_1748-9326_ad0d3b
|
doi10.1088_1748-9326_ad0d3b
|
Data availability statementThe data that support the findings of this study are openly available at the following URL/DOI: https://doi.org/10.5281/zenodo.8322973.
| false
| true
| false
|
dataset
|
10.1242_jcs.261100
|
doi10.1242_jcs.261100
|
Data availability Mass spectrometry data, as well as spreadsheets with all derived values, are available from ProteomeXchange (http://www.proteomexchange.org) using the accession number PXD038234; information conforming to Minimal Information About a Proteomics Experiment (MIAPE) standards (Taylor et al., 2007) was included in the submission.
| false
| true
| false
|
dataset
|
10.1371_journal.pone.0288068
|
doi10.1371_journal.pone.0288068
|
Data Availability Statement All relevant data are within the paper and its Supporting Information files.
| false
| true
| false
|
dataset
|
10.1186_s40168-023-01517-x
|
doi10.1186_s40168-023-01517-x
|
Availability of data and materials Metagenome, metatranscriptome, and MAG sequence data are available from the European Nucleotide Archive (accession PRJEB52999). Supporting environmental data is also available as Zenodo repository (https://doi.org/10.5281/zenodo.7656261).
| true
| true
| false
|
dataset
|
10.1371_journal.pone.0217131
|
doi10.1371_journal.pone.0217131
|
Data Availability Statement All relevant data are within the paper and its Supporting Information files.
| false
| true
| false
|
dataset
|
10.1088_1402-4896_ad137d
|
doi10.1088_1402-4896_ad137d
|
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.0234902
|
doi10.1371_journal.pone.0234902
|
Data Availability Statement Data is provided with supporting information file. Please refer S1 File. All python source code, trained model, and test images are available on Github web site: https://github.com/climyth/VFbySD-OCT (DOI: 10.5281/zenodo.3757702). The training images are available from the first (climyth@naver.com) or corresponding author (alertlee@naver.com) on reasonable request. The provided data must be used for only research purpose and should not be shared with other unauthorized institutions. Data will be stored in our research NAS (network attached storage) and cloud storage for backup purpose up to December 2022, after which it will be discarded as required by local regulations. Although the authors cannot make their study’s data publicly available at the time of publication, all authors commit to make the data underlying the findings described in this study fully available without restriction to those who request the data, in compliance with the PLOS Data Availability Statement policy. For data sets involving personally identifiable information or other sensitive data, data sharing is contingent on the data being handled appropriately by the data requester and in accordance with all applicable local requirements.
| false
| true
| true
|
dataset
|
10
|
doi10
|
Data availability The authors declare that all data supporting the findings of this study are available from the corresponding authors upon request. The source data within the article, and its Supplementary Data Files, are provided as a Source Data File accompanied with this article. Individual raw data is included on all statistically relevant figures and within the accompanying Source Data File. Source data are provided with this paper. Code availability Capmeter code information is detailed in the Reporting summary linked to this article and available at https://sites.google.com/site/capmeter/.
| false
| true
| true
|
dataset
|
10.1126_science.abn5856
|
doi10.1126_science.abn5856
|
Data and materials availability: The data presented in this paper are detailed in supplementary materials. Summary data and analysis scripts are available at https://github.com/LaMariposa/zoonomia_biodiversity. NCBI accession numbers for sequence data used in analyses are given in table S1.
| false
| true
| true
|
dataset
|
10.1371_journal.pntd.0007109
|
doi10.1371_journal.pntd.0007109
|
Data Availability Statement All relevant data are within the paper and its Supporting Information files.
| false
| true
| false
|
dataset
|
10.1371_journal.pstr.0000077
|
doi10.1371_journal.pstr.0000077
|
Data Availability Statement: The data may be found here: https://urldefense.com/v3/__https://doi.org/10.7924/r4qf8x909__;!!OToaGQ!oUvItyVLC6NVRttkwI0Z8a1Y3GENeXatmIOtoVlI8ZDWdKW05-OzWFbqyHjpSkwfVrNIyaPTQKR9vzhQFw$.
| false
| true
| false
|
dataset
|
10.1371_journal.pone.0286828
|
doi10.1371_journal.pone.0286828
|
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
| false
| true
| true
|
dataset
|
10.1038_s41586-023-06362-4
|
doi10.1038_s41586-023-06362-4
|
Data availabilityAll data will be made freely available upon reasonable request. Single-cell RNA-sequencing data for intestinal immune cells during food allergy in BALB/cJ mice (Extended Data Fig. 7g) can be accessed at the National Center for Biotechnology Information Gene Expression Omnibus, accession number GSE124880 (ref. 73). Alternatively, processed single-cell RNA-sequencing data for this same study can be found at https://portals.broadinstitute.org/single_cell/study/fasi-immune-mouse-small-intestine. Allen Mouse Brain Atlas reference atlas is available from https://atlas.brain-map.org. ClearMap 2.0 with WobblyStitcher, TubeMap and CellMap is available at https://github/ChristophKirst/ClearMap2 (refs. 68,74). Source data are provided with this paper.
| false
| true
| true
|
dataset
|
10.1371_journal.pgph.0002011
|
doi10.1371_journal.pgph.0002011
|
Data Availability Statement All data in Supporting information files.
| false
| true
| false
|
dataset
|
10.1088_1361-648x_ad0c77
|
doi10.1088_1361-648x_ad0c77
|
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
|
10.1007_s00382-022-06544-2
|
doi10.1007_s00382-022-06544-2
|
Data availability The data that support the findings of this study are available from the corresponding author upon request.
| false
| true
| false
|
dataset
|
10.1371_journal.pone.0234905
|
doi10.1371_journal.pone.0234905
|
Data Availability Statement All relevant data are within the paper and its Supporting Information files.
| false
| true
| false
|
dataset
|
10.1038_s41467-023-40821-w
|
doi10.1038_s41467-023-40821-w
|
Data availabilityThe V2-IgG/KRASG12V-HLA-A*03:01 ternary complex data generated in this study have been deposited in the wwPBD database under accession code 7STF and Electron Microscopy Data Bank under accession code EMD-25427. The KRASWT-HLA-A*03:01 complex data generated in this study have been deposited in the wwPDB database under accession code 8DVG. The PDB ID 6O9B was used as the search model for the KRASWT-HLA-A*03:01 structure determination. The coordinates of the KRASWT-HLA-A*03:01 monomer (determined in this paper) PDB ID 8DVG and PDB entry 7KGU (2Q1-Fab) was used as a search model for the V2-IgG/KRASG12V-HLA-A*03:01 complex. Source data are provided with this paper. The SDS-PAGE gels, SPR sensorgrams, co-culture experiments and DSF data generated in this study are provided in the Supplementary Information/Source Data file. Source data are provided with this paper.
| false
| true
| true
|
dataset
|
10.1093_gbe_evad100
|
doi10.1093_gbe_evad100
|
Data Availability All data described here are available from the NCBI Umbrella BioProject PRJNA386376. All cicada bacteriome metatranscritpome and metagenome sequencing libraries were deposited in the Sequence Read Archive (SRA) database under BioProject PRJNA923375. Newly generated genome assemblies for endosymbionts of D. near semicincta, T. ulnaria, T. limbata, and O. oregona, as well as the corresponding SRA experiments (containing the raw reads), are available under BioProjects PRJNA923375, PRJNA512238, PRJNA246493, and PRJNA385844, respectively.
| false
| true
| true
|
dataset
|
10.1186_s12884-020-03256-5
|
doi10.1186_s12884-020-03256-5
|
Availability of data and materials All data generated or analyzed during this study are included in this published article.
| false
| true
| false
|
dataset
|
10.1007_s00006-022-01207-1
|
doi10.1007_s00006-022-01207-1
|
Data availability The periods of all the few monomial quartics that we have been able to compute are available on our Dropbox repository. We also in- cluded our Picard lattice computations in that repository. Code availability The software package developed for this project is avail- able at github: period graph. This software depends on the custom package PeriodSuite. These packages are written to work in an environment running SageMath [9] and Magma [3].
| false
| true
| true
|
dataset
|
10.3389/fmicb.2021
|
doi10.3389/fmicb.2021
|
DATA AVAILABILITY STATEMENT Whole genomes and Genbank submissions can be found on NCBI accession number PRJNA649544 and MZ773212– MZ77322, respectively. Kbase with the workflow of the metagenomic analysis can be found on permanent links: WGS: https://narrative.kbase.us/narrative/83182 MISEQ; https: //narrative.kbase.us/narrative/56628.
| false
| true
| false
|
dataset
|
10
|
doi10
|
Data availability The data generated/analyzed during this study are available from the corresponding author on reasonable request.
| false
| true
| false
|
dataset
|
10.1371_journal.pdig.0000438
|
doi10.1371_journal.pdig.0000438
|
Data Availability Statement: All data generated or analyzed during the study are included in the published paper.
| false
| true
| false
|
dataset
|
10.1126_science.adf4721
|
doi10.1126_science.adf4721
|
Data and materials availability: Single-cell RNA-seq data have been deposited at GEO: GSE212230 and can be visualized through an interactive browser at https://shiny.mdc-berlin.de/ARVEX/. All data are available in the manuscript, the supplementary material or deposited at Zenodo (83, 84).
| true
| true
| true
|
dataset
|
10
|
doi10
|
Availability of data and materials The code generated during the current study are available at github.com/ shaharavin/BrainEvolutionSimulator [73].
| false
| true
| true
|
dataset
|
10.1073_pnas.2221175120
|
doi10.1073_pnas.2221175120
|
Data, Materials, and Software Availability All study data are included in the article and/or SI Appendix. RNA-seq and ATAC-seq data have been deposited in the National Center for Biotechnology Information (NCBI)- Gene Expression Omnibus (GEO) under GSE229454 (56).
| true
| true
| true
|
dataset
|
10.1371_journal.pone.0282086
|
doi10.1371_journal.pone.0282086
|
Data Availability Statement All data files are available from the Open Science Framework at https://osf.io/wmr3d/ (DOI: 10.17605/OSF.IO/WMR3D).
| true
| true
| false
|
dataset
|
10.1038_s41467-023-41078-z
|
doi10.1038_s41467-023-41078-z
|
Data availabilityThe reagents and data generated in this study are available without restriction. RNA-sequencing data have been deposited in the Gene Expression Omnibus (GEO) repository with accession number: GSE169392. The accession code for the mouse genome used for the RNA-seq is GRCm38, available at https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001635.20/. The scRNAseq database from ref. 86 can be found at http://dropviz.org/. Source data are provided with this paper.Code availabilityThe scripts generated in this study are available without restriction. Please visit https://github.com/ErogluLab/CellCounts, https://github.com/UlloaSeverinoLab to access the custom codes used in this manuscript. We recommend getting in touch with the corresponding authors to have further information.
| false
| true
| true
|
dataset
|
10.1155_2019_8320316
|
doi10.1155_2019_8320316
|
Data Availability The SWDA data used to support the findings of this study have been deposited in http://compprag.christopherpotts.net/swda.html.
| false
| true
| false
|
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