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  • image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Authors: Centro Euro-Mediterraneo sui Cambiamenti Climatici (CMCC);

    Project: IPCC Assessment Report 5 and Coupled Model Intercomparison Project data sets - These data belong to two projects: 1) to the Assessment Report No 5 of the International Panel on Climate Change (IPCC-AR5) and 2) to the Coupled Model Intercomparison Project No 5 (CMIP5). CMIP5 is executed by the Program for Climate Model Diagnosis and Intercomparison (PCMDI) on behalf of the World Climate Research Programme (WCRP). Most of the data is replicated between the three data nodes at the World Data Centre for Climate (WDCC), the British Atmospheric Data Centre (BADC), and the PCMDI. The project embraces the simulations with about 30 climate models of about 20 institutes worldwide. Summary: rcp85 is an experiment of the CMIP5 - Coupled Model Intercomparison Project Phase 5 ( http://cmip-pcmdi.llnl.gov/cmip5/ ). CMIP5 is meant to provide a framework for coordinated climate change experiments for the next five years and thus includes simulations for assessment in the AR5 as well as others that extend beyond the AR5. 4.2 rcp85 (4.2 RCP8.5) - Version 1: Future projection (2006-2100) forced by RCP8.5. RCP8.5 is a representative concentration pathway which approximately results in a radiative forcing of 8.5 W m-2 at year 2100, relative to pre-industrial conditions. RCPs are time-dependent, consistent projections of emissions and concentrations of radiatively active gases and particles. Experiment design: http://cmip-pcmdi.llnl.gov/cmip5/docs/Taylor_CMIP5_design.pdf List of output variables: http://cmip-pcmdi.llnl.gov/cmip5/docs/standard_output.pdf Output: time series per variable in model grid spatial resolution in netCDF format Earth System model and the simulation information: CIM repository Entry name/title of data are specified according to the Data Reference Syntax ( http://cmip-pcmdi.llnl.gov/cmip5/docs/cmip5_data_reference_syntax.pdf ) as activity/product/institute/model/experiment/frequency/modeling realm/MIP table/ensemble member/version number/variable name/CMOR filename.nc .

    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao World Data Center fo...arrow_drop_down
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    World Data Center for Climate
    Dataset . 2013
    Data sources: Datacite
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      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao World Data Center fo...arrow_drop_down
      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
      World Data Center for Climate
      Dataset . 2013
      Data sources: Datacite
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  • image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Authors: Vaidehi Krishnan; Florian Schmidt; Zahid Nawaz; Prasanna Nori Venkatesh; +14 Authors

    This archive contains data of scRNAseq and CyTOF in form of Seurat objects, txt and csv files as well as R scripts for data analysis and Figure generation. A summary of the content is provided in the following. R scripts Script to run Machine learning models predicting group specific marker genes: CML_Find_Markers_Zenodo.R Script to reproduce the majority of Main and Supplementary Figures shown in the manuscript: CML_Paper_Figures_Zenodo.R Script to run inferCNV analysis: inferCNV_Zenodo.R Script to plot NATMI analysis results:NATMI_CvsA_FC0.32_Updown_Column_plot_Zenodo.R Script to conduct sub-clustering and filtering of NK cells NK_Marker_Detection_Zenodo.R Helper scripts for plotting and DEG calculation:ComputePairWiseDE_v2.R, Seurat_DE_Heatmap_RCA_Style.R RDS files General scRNA-seq Seurat objects: scRNA-seq seurat object after QC, and cell type annotation used for most analysis in the manuscript: DUKE_DataSet_Doublets_Removed_Relabeled.RDS scRNA-seq including findings e.g. from NK analysis used in the shiny app: DUKE_final_for_Shiny_App.rds Neighborhood enrichment score computed for group A across all HSPCs: Enrichment_score_global_groupA.RDS UMAP coordinates used in the article: Layout_2D_nNeighbours_25_Metric_cosine_TCU_removed.RDS SCENIC files: Regulon set used in SCENIC: 2.6_regulons_asGeneSet.Rds AUC values computed for regulons: 3.4_regulonAUC.Rds MetaData used in SCENIC cellInfo.Rds Group specific regulons for LCS: groupSpecificRegulonsBCRAblP.RDS Patient specific regulons for LSC: patientSpecificRegulonsBCRAblP.RDS Patient specificity score for LSC: PatientSpecificRegulonSpecificityScoreBCRAblP.RDS Regulon specificty score for LSC: RegulonSpecificityScoreBCRAblP.RDS BCR-ABL1 inference: HSC with inferred BCR-ABL1 label: HSCs_CML_with_BCR-Abl_label.RDS UMAP for HSC with inferred BCR-ABL1 label: HSCs_CML_with_BCR-Abl_label_UMAP.RDS HSPCs with BCR-ABL1 module scores: HSPC_metacluster_74K_with_modscore_27thmay.RDS NK sub-clustering and filtering: NK object with module scores: NK_8617cells_with_modscore_1stjune.RDS Feature genes for NK cells computed with DubStepR: NK_Cells_DubStepR NK cells Seurat object excluding contaminating T and B cells: NK_cells_T_B_17_removed.RDS NK Seurat object including neighbourhood enrichment score calculations: NK_seurat_object_with_enrichment_labels_V2.RDS txt and csv files: Proportions per cluster calculated from CyTOF: CyTOF_Proportions.txt Correlation between scRNAseq and CyTOF cell type abundance: scRNAseq_Cor_Cytof.txt Correlation between manual gating and FlowSOM clustering: Manual_vs_FlowSOM.txt GSEA results: HSPC, HSC and LSC results: FINAL_GSEA_DATA_For_GGPLOT.txt NK: NK_For_Plotting.txt TFRC and HLA expression: TFRC_and_HLA_Values.txt NATMI result files: UP-regulated_mean.csv DOWN-regulated_mean.csv Gene position file used in inferCNV: inferCNV_gene_positions_hg38.txt Module scores for NK subclusters per cell: NK_Supplementary_Module_Scores.csv Compressed folders: All CyTOF raw data files: CyTOF_Data_raw.zip Results of the patient-based classifier: PatientwiseClassifier.zip Results of the single-cell based classifier: SingleCellClassifierResults.zip For general new data analysis approaches, we recommend the readers to use the Seruat object stored in DUKE_final_for_Shiny_App.rds or to use the shiny app(http://scdbm.ddnetbio.com/) and perform further analysis from there. RAW data is available at EGA upon request using Study ID: EGAS00001005509 Revision The for_CML_manuscript_revision.tar.gz folder contains scripts and data for the paper revision including 1) Detection of the BCR-ABL fusion with long read sequencing; 2) Identification of BCR-ABL junction reads with scRNAseq; 3) Detection of expressed mutations using scRNAseq.

    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao ZENODOarrow_drop_down
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    ZENODO
    Dataset . 2021
    Data sources: Datacite
    ZENODO
    Dataset . 2021
    Data sources: ZENODO
    ZENODO
    Dataset . 2021
    Data sources: ZENODO
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      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao ZENODOarrow_drop_down
      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
      ZENODO
      Dataset . 2021
      Data sources: Datacite
      ZENODO
      Dataset . 2021
      Data sources: ZENODO
      ZENODO
      Dataset . 2021
      Data sources: ZENODO
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  • image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Authors: Pérez Brunius, P; García Carrillo, P; Ronquillo Méndez, A; Rodríguez Outerelo, J; +3 Authors

    This dataset is comprised of the final processed data collected by 207 surface drifters deployed in the western Gulf of Mexico during the Deep Water Dispersion Experiment (DWDE), as part of the project “Implementación de redes de observación oceanográficas (físicas geoquímicas, ecológicas) para la generación de escenarios ante posibles contingencias relacionadas a la exploración y producción de hidrocarburos en aguas profundas del Golfo de México” of the Gulf de Mexico Research Consortium (CIGoM), funded by CONACYT‐SENER‐Hydrocarbon Fund, Mexico”. The DWDE drifter data is also made available with the GulfDriftersWithDWDE dataset (http://doi.org/10.5281/zenodo.3985916), which is a merged and uniformly processed surface drifter dataset which includes publicly available data from several different drifter experiments. These latter database is the basis for the gridded product GulfFlow (http://doi.org/10.5281/zenodo.3978793). See Lilly and Pérez-Brunius (2021) "A gridded surface current product for the Gulf of Mexico from consolidated drifter measurements" for details. García Carrillo, P., Ronquillo Méndez, A., Rodríguez Outerelo, J., Pérez Brunius, P. 2018. Experimento de Dispersión en Aguas Profundas ( DWDE ). Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California. 253 pp. Pérez-Brunius P., P. García Carrillo, A. Ronquillo Méndez, J. Rodríguez Outerelo, A. Sandoval Rangel, C. Liera Grijalva, X. Flores Vidal (2019). Trayectorias de Derivadores Superficiales en el Oeste del Golfo de México del Experimento de Dispersión en Aguas Profundas. Reg. INDAUTOR, México (03-2019- 120510255600-01, 13 December 2019). The acquisition of the surface drifter data from the DWDE experiment has been financed by the CONACYT-SENER-Hydrocarbons Sector Fund, Mexico (project 201441), developed by the Gulf of Mexico Research Consortium (CIGoM). We recognize PEMEX for promoting to the Fund the specific demand on oil spills and the environment. See database webpage with additional information (https://giola.cicese.mx/database/DWDE) {"references": ["Garc\u00eda Carrillo, P., Ronquillo M\u00e9ndez, A., Rodr\u00edguez Outerelo, J., P\u00e9rez Brunius, P. 2018. Experimento de Dispersi\u00f3n en Aguas Profundas ( DWDE ). Centro de Investigaci\u00f3n Cient\u00edfica y de Educaci\u00f3n Superior de Ensenada, Baja California. 253 pp."]}

    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao ZENODOarrow_drop_down
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    ZENODO
    Dataset . 2021
    Data sources: Datacite
    ZENODO
    Dataset . 2021
    Data sources: ZENODO
    ZENODO
    Dataset . 2020
    Data sources: ZENODO
    ZENODO
    Dataset . 2020
    Data sources: ZENODO
    ZENODO
    Dataset . 2020
    Data sources: ZENODO
    ZENODO
    Dataset . 2021
    Data sources: ZENODO
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      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao ZENODOarrow_drop_down
      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
      ZENODO
      Dataset . 2021
      Data sources: Datacite
      ZENODO
      Dataset . 2021
      Data sources: ZENODO
      ZENODO
      Dataset . 2020
      Data sources: ZENODO
      ZENODO
      Dataset . 2020
      Data sources: ZENODO
      ZENODO
      Dataset . 2020
      Data sources: ZENODO
      ZENODO
      Dataset . 2021
      Data sources: ZENODO
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  • image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao

    EmERGE - WP3 Lisbon data

    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao ZENODOarrow_drop_down
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    ZENODO
    Dataset . 2020
    Data sources: Datacite
    ZENODO
    Dataset . 2020
    Data sources: ZENODO
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      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao ZENODOarrow_drop_down
      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
      ZENODO
      Dataset . 2020
      Data sources: Datacite
      ZENODO
      Dataset . 2020
      Data sources: ZENODO
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  • image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Authors: Hoeber, Heinrich; Kruspe, Gottfried; Brümmer, Burghard; Wetzel, Christian;

    Project: Field Data of the Meteorological Institute, University of Hamburg - The Physical Meteorology Division of the Meteorological Institute is regularly conducting or taking part in field experiments with strong focus on high latitudes. Measurements are performed by aircraft, radiosondes or buoys and at land, ship and ice stations. Published data sets incorporate aircraft measurements of turbulent fluxes and standard meteorological parameters of high temporal and spatial resolution. These measurements are supported by frequent radiosonde ascents and station and ship data in the according region. Another group of data sets consists of measurements by autonomous buoys of different complexity on sea ice and ocean. Summary: The Convection and Turbulence Experiment (KonTur) was conducted in the southeastern part of the North Sea from 14 September to 21 October 1981 (with a break from 4 to 8 October). KONTUR aimed at two main scientific objectives. First, to observe the formation and time variation of regularly organized convection in the lower troposphere as a function of the mean atmospheric flow and the lower boundary condition and to quantify the dependence of the vertical transports of momentum, heat and water mass on various scales of motion in order to test existing convection models and to provide an observational background for the extension of theoretical concepts. Second goal was to determine the mean and turbulent quantities within the marine atmospheric boundary layer (ABL), including the large scale horizontal and vertical advection of momentum, heat and water vapour, cloud microphysics and the radiation field, in order to assemble a comprehensive data set for boundary layer modelling with first and second order closure methods. The experiment covered an area in the southeastern part of the North Sea (German Bight), roughly between latitudes 53¿N and 56¿N and longitudes 6¿E and 9¿E. Both the convection and the turbulence programme made use of the same experimental tools which can be subdivided in the following four groups: the central station occupied by the research vessel Meteor, the aerological network (Borkumriff, RV Meteor, RV Gauss/Poseidon, Research Platform Nordsee, Elbe 1), two aircraft (Hercules C-130, Falcon 20) and supporting observations, such as satellite images, cloud photography, surface and upper air large-scale fields from routine data. KONTUR 1981 was followed by the experiments KONTROL 1984 and KONTROL 1985.

    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao World Data Center fo...arrow_drop_down
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    World Data Center for Climate
    Dataset . 2012
    Data sources: Datacite
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      World Data Center for Climate
      Dataset . 2012
      Data sources: Datacite
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    Authors: Guleria, Abhay; Sumedha, Chakma;

    This database contains an "excel sheet" and ".docx" files having input parameters and health risk metrics generated from a Simplistic Unsaturated Zone Leaching Model-based Probabilistic Human Health Risk Assessment Framework for Ariyamangalam dumping site.

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    ZENODO
    Dataset . 2021
    Data sources: Datacite
    ZENODO
    Dataset . 2021
    Data sources: ZENODO
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      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao ZENODOarrow_drop_down
      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
      ZENODO
      Dataset . 2021
      Data sources: Datacite
      ZENODO
      Dataset . 2021
      Data sources: ZENODO
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  • image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Authors: Zioulis, Nikolaos; Karakottas, Antonis; Zarpalas, Dimitrios; Daras, Petros;

    Modern 3D vision advancements rely on data driven methods and thus, task specific annotated datasets. Especially for geometric inference tasks like depth and surface estimation, the collection of high quality data is very challenging, expensive and laborious. While considerable efforts have been made for traditional pinhole cameras, the same cannot be said for omnidirectional ones. 3D60 is a collective dataset generated in the context of various 360o vision research works. It comprises multi-modal omnidirectional stereo renders of scenes from realistic and synthetic large-scale 3D datasets (Matterport3D, Stanford2D3D and SunCG). Our dataset fills a very important gap in data-driven spherical 3D vision and, more specifically, for the monocular and stereo dense depth and surface estimation tasks. We originate by exploiting the efforts made in providing synthetic and real scanned 3D datasets of interior spaces and re-using them via ray-tracing in order to generate high quality, densely annotated spherical panoramas. Instructions, code and data splits available @ https://vcl3d.github.io/3D60/

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    ZENODO
    Dataset . 2019
    Data sources: Datacite
    ZENODO
    Dataset . 2019
    Data sources: ZENODO
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      ZENODO
      Dataset . 2019
      Data sources: Datacite
      ZENODO
      Dataset . 2019
      Data sources: ZENODO
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    Authors: Shevchuk, Ivan; Rabin, Ira; Bonnerot, Olivier; Delhey, Martin;

    The research for project C01 was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) within the Sonderforschungsbereich 950 (SFB 950). The research was conducted within the scope of the Centre for the Study of Manuscript Cultures (CSMC) at Universität Hamburg. In collaboration with Bundesanstalt für Materialforschung und -prüfung Multispectral imaging data. Imaging was performed to recover damaged writing at the Royal Asiatic Society in London XRF Measurements (ARTAX) and reflectography (DInoLite) for ink composition analysis was performed. Link to dataset is included in related identifier. {"references": ["https://twitter.com/CSMC_Hamburg/status/1259815042343723014", "https://royalasiaticsociety.org/new-light-on-old-problems-multi-spectral-imaging-of-sanskrit-manuscripts/"]}

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    ZFDM repository
    Dataset . 2020
    Data sources: B2FIND
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      ZFDM repository
      Dataset . 2020
      Data sources: B2FIND
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    Authors: Spyridon N. Papageorgiou; Raphael Tilen; Vaska Vandevska-Radunovic; Theodore Eliades;

    Dataset for all analyses

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    ZENODO
    Dataset . 2020
    Data sources: Datacite
    ZENODO
    Dataset . 2020
    Data sources: ZENODO
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      ZENODO
      Dataset . 2020
      Data sources: Datacite
      ZENODO
      Dataset . 2020
      Data sources: ZENODO
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    Authors: NASA-GISS;

    Project: IPCC Assessment Report 5 and Coupled Model Intercomparison Project data sets - These data belong to two projects: 1) to the Assessment Report No 5 of the International Panel on Climate Change (IPCC-AR5) and 2) to the Coupled Model Intercomparison Project No 5 (CMIP5). CMIP5 is executed by the Program for Climate Model Diagnosis and Intercomparison (PCMDI) on behalf of the World Climate Research Programme (WCRP). Most of the data is replicated between the three data nodes at the World Data Centre for Climate (WDCC), the British Atmospheric Data Centre (BADC), and the PCMDI. The project embraces the simulations with about 30 climate models of about 20 institutes worldwide. Summary: not filled

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2,950 Research products
  • image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Authors: Centro Euro-Mediterraneo sui Cambiamenti Climatici (CMCC);

    Project: IPCC Assessment Report 5 and Coupled Model Intercomparison Project data sets - These data belong to two projects: 1) to the Assessment Report No 5 of the International Panel on Climate Change (IPCC-AR5) and 2) to the Coupled Model Intercomparison Project No 5 (CMIP5). CMIP5 is executed by the Program for Climate Model Diagnosis and Intercomparison (PCMDI) on behalf of the World Climate Research Programme (WCRP). Most of the data is replicated between the three data nodes at the World Data Centre for Climate (WDCC), the British Atmospheric Data Centre (BADC), and the PCMDI. The project embraces the simulations with about 30 climate models of about 20 institutes worldwide. Summary: rcp85 is an experiment of the CMIP5 - Coupled Model Intercomparison Project Phase 5 ( http://cmip-pcmdi.llnl.gov/cmip5/ ). CMIP5 is meant to provide a framework for coordinated climate change experiments for the next five years and thus includes simulations for assessment in the AR5 as well as others that extend beyond the AR5. 4.2 rcp85 (4.2 RCP8.5) - Version 1: Future projection (2006-2100) forced by RCP8.5. RCP8.5 is a representative concentration pathway which approximately results in a radiative forcing of 8.5 W m-2 at year 2100, relative to pre-industrial conditions. RCPs are time-dependent, consistent projections of emissions and concentrations of radiatively active gases and particles. Experiment design: http://cmip-pcmdi.llnl.gov/cmip5/docs/Taylor_CMIP5_design.pdf List of output variables: http://cmip-pcmdi.llnl.gov/cmip5/docs/standard_output.pdf Output: time series per variable in model grid spatial resolution in netCDF format Earth System model and the simulation information: CIM repository Entry name/title of data are specified according to the Data Reference Syntax ( http://cmip-pcmdi.llnl.gov/cmip5/docs/cmip5_data_reference_syntax.pdf ) as activity/product/institute/model/experiment/frequency/modeling realm/MIP table/ensemble member/version number/variable name/CMOR filename.nc .

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    World Data Center for Climate
    Dataset . 2013
    Data sources: Datacite
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      World Data Center for Climate
      Dataset . 2013
      Data sources: Datacite
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  • image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Authors: Vaidehi Krishnan; Florian Schmidt; Zahid Nawaz; Prasanna Nori Venkatesh; +14 Authors

    This archive contains data of scRNAseq and CyTOF in form of Seurat objects, txt and csv files as well as R scripts for data analysis and Figure generation. A summary of the content is provided in the following. R scripts Script to run Machine learning models predicting group specific marker genes: CML_Find_Markers_Zenodo.R Script to reproduce the majority of Main and Supplementary Figures shown in the manuscript: CML_Paper_Figures_Zenodo.R Script to run inferCNV analysis: inferCNV_Zenodo.R Script to plot NATMI analysis results:NATMI_CvsA_FC0.32_Updown_Column_plot_Zenodo.R Script to conduct sub-clustering and filtering of NK cells NK_Marker_Detection_Zenodo.R Helper scripts for plotting and DEG calculation:ComputePairWiseDE_v2.R, Seurat_DE_Heatmap_RCA_Style.R RDS files General scRNA-seq Seurat objects: scRNA-seq seurat object after QC, and cell type annotation used for most analysis in the manuscript: DUKE_DataSet_Doublets_Removed_Relabeled.RDS scRNA-seq including findings e.g. from NK analysis used in the shiny app: DUKE_final_for_Shiny_App.rds Neighborhood enrichment score computed for group A across all HSPCs: Enrichment_score_global_groupA.RDS UMAP coordinates used in the article: Layout_2D_nNeighbours_25_Metric_cosine_TCU_removed.RDS SCENIC files: Regulon set used in SCENIC: 2.6_regulons_asGeneSet.Rds AUC values computed for regulons: 3.4_regulonAUC.Rds MetaData used in SCENIC cellInfo.Rds Group specific regulons for LCS: groupSpecificRegulonsBCRAblP.RDS Patient specific regulons for LSC: patientSpecificRegulonsBCRAblP.RDS Patient specificity score for LSC: PatientSpecificRegulonSpecificityScoreBCRAblP.RDS Regulon specificty score for LSC: RegulonSpecificityScoreBCRAblP.RDS BCR-ABL1 inference: HSC with inferred BCR-ABL1 label: HSCs_CML_with_BCR-Abl_label.RDS UMAP for HSC with inferred BCR-ABL1 label: HSCs_CML_with_BCR-Abl_label_UMAP.RDS HSPCs with BCR-ABL1 module scores: HSPC_metacluster_74K_with_modscore_27thmay.RDS NK sub-clustering and filtering: NK object with module scores: NK_8617cells_with_modscore_1stjune.RDS Feature genes for NK cells computed with DubStepR: NK_Cells_DubStepR NK cells Seurat object excluding contaminating T and B cells: NK_cells_T_B_17_removed.RDS NK Seurat object including neighbourhood enrichment score calculations: NK_seurat_object_with_enrichment_labels_V2.RDS txt and csv files: Proportions per cluster calculated from CyTOF: CyTOF_Proportions.txt Correlation between scRNAseq and CyTOF cell type abundance: scRNAseq_Cor_Cytof.txt Correlation between manual gating and FlowSOM clustering: Manual_vs_FlowSOM.txt GSEA results: HSPC, HSC and LSC results: FINAL_GSEA_DATA_For_GGPLOT.txt NK: NK_For_Plotting.txt TFRC and HLA expression: TFRC_and_HLA_Values.txt NATMI result files: UP-regulated_mean.csv DOWN-regulated_mean.csv Gene position file used in inferCNV: inferCNV_gene_positions_hg38.txt Module scores for NK subclusters per cell: NK_Supplementary_Module_Scores.csv Compressed folders: All CyTOF raw data files: CyTOF_Data_raw.zip Results of the patient-based classifier: PatientwiseClassifier.zip Results of the single-cell based classifier: SingleCellClassifierResults.zip For general new data analysis approaches, we recommend the readers to use the Seruat object stored in DUKE_final_for_Shiny_App.rds or to use the shiny app(http://scdbm.ddnetbio.com/) and perform further analysis from there. RAW data is available at EGA upon request using Study ID: EGAS00001005509 Revision The for_CML_manuscript_revision.tar.gz folder contains scripts and data for the paper revision including 1) Detection of the BCR-ABL fusion with long read sequencing; 2) Identification of BCR-ABL junction reads with scRNAseq; 3) Detection of expressed mutations using scRNAseq.

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    ZENODO
    Dataset . 2021
    Data sources: Datacite
    ZENODO
    Dataset . 2021
    Data sources: ZENODO
    ZENODO
    Dataset . 2021
    Data sources: ZENODO
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      ZENODO
      Dataset . 2021
      Data sources: Datacite
      ZENODO
      Dataset . 2021
      Data sources: ZENODO
      ZENODO
      Dataset . 2021
      Data sources: ZENODO
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  • image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Authors: Pérez Brunius, P; García Carrillo, P; Ronquillo Méndez, A; Rodríguez Outerelo, J; +3 Authors

    This dataset is comprised of the final processed data collected by 207 surface drifters deployed in the western Gulf of Mexico during the Deep Water Dispersion Experiment (DWDE), as part of the project “Implementación de redes de observación oceanográficas (físicas geoquímicas, ecológicas) para la generación de escenarios ante posibles contingencias relacionadas a la exploración y producción de hidrocarburos en aguas profundas del Golfo de México” of the Gulf de Mexico Research Consortium (CIGoM), funded by CONACYT‐SENER‐Hydrocarbon Fund, Mexico”. The DWDE drifter data is also made available with the GulfDriftersWithDWDE dataset (http://doi.org/10.5281/zenodo.3985916), which is a merged and uniformly processed surface drifter dataset which includes publicly available data from several different drifter experiments. These latter database is the basis for the gridded product GulfFlow (http://doi.org/10.5281/zenodo.3978793). See Lilly and Pérez-Brunius (2021) "A gridded surface current product for the Gulf of Mexico from consolidated drifter measurements" for details. García Carrillo, P., Ronquillo Méndez, A., Rodríguez Outerelo, J., Pérez Brunius, P. 2018. Experimento de Dispersión en Aguas Profundas ( DWDE ). Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California. 253 pp. Pérez-Brunius P., P. García Carrillo, A. Ronquillo Méndez, J. Rodríguez Outerelo, A. Sandoval Rangel, C. Liera Grijalva, X. Flores Vidal (2019). Trayectorias de Derivadores Superficiales en el Oeste del Golfo de México del Experimento de Dispersión en Aguas Profundas. Reg. INDAUTOR, México (03-2019- 120510255600-01, 13 December 2019). The acquisition of the surface drifter data from the DWDE experiment has been financed by the CONACYT-SENER-Hydrocarbons Sector Fund, Mexico (project 201441), developed by the Gulf of Mexico Research Consortium (CIGoM). We recognize PEMEX for promoting to the Fund the specific demand on oil spills and the environment. See database webpage with additional information (https://giola.cicese.mx/database/DWDE) {"references": ["Garc\u00eda Carrillo, P., Ronquillo M\u00e9ndez, A., Rodr\u00edguez Outerelo, J., P\u00e9rez Brunius, P. 2018. Experimento de Dispersi\u00f3n en Aguas Profundas ( DWDE ). Centro de Investigaci\u00f3n Cient\u00edfica y de Educaci\u00f3n Superior de Ensenada, Baja California. 253 pp."]}

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    ZENODO
    Dataset . 2021
    Data sources: Datacite
    ZENODO
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      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao ZENODOarrow_drop_down
      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
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      Dataset . 2021
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      Dataset . 2020
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