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  • ZENODO

  • 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: Doña-Reveco, Cristián; Sotomayor, Pablo;

    Encuesta online diseñada y aplicada para el estudio de la integración laboral y social inmigrante en Chile. Se recibieron un total de 4771 respuestas de las cuales se consideraron como válidas 3406. El instrumento consideró como población objetivo o universo de estudio a inmigrantes con permiso de residencia en Chile mayores de 18 años y con correo electrónico válido registrados por el Departamento de Extranjería y Migración, entre los meses de marzo y mayo de 2017. La cantidad de inmigrantes que recibió el cuestionario fue de 35.377, correspondientes al total de inmigrantes con estas características durante ese período. Investigacion financiada por la Comisión Nacional de Ciencia y Tecnologia (CONICYT-CHILE), actualmente Agencia Nacional de Investigación y Desarrollo, bajo el proyecto CONICYT+PAI/ Concurso Nacional Apoyo al Retorno de Investigadores/as desde el Extranjero Convocatoria 2014 + 82140058 (Agosto 2015 – Julio 2017)

    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: De Rose, Fiorenza; Fogliata, Antonella; Franceschini, Davide; Iftode, Cristina Simona; +10 Authors

    This record contains raw data related to article "Hypofractionation with simultaneous boost in breast cancer patients receiving adjuvant chemotherapy A prospective evaluation of a case series and review of the literature" To evaluate acute toxicity and cosmetic outcomes of hypofractionated simultaneous integrated boost (SIB) as adjuvant treatment after breast-conserving surgery and adjuvant chemotherapy and to review the association of chemotherapy and short fractionation with boost. MATERIALS AND METHODS: Patients presenting early-stage breast cancer were enrolled in a phase II trial. All patients received VMAT-SIB technique to the whole breast and tumor bed in 15 fractions, for a total dose of 40.5 and 48 Gy. Acute and late skin toxicities and breast pain were recorded. Cosmetic outcomes were also assessed as excellent/good or fair/poor. RESULTS: Between August 2010 and December 2015, 787 consecutive patients were treated and had at least 2 year follow-up. A subset of 175 patients underwent adjuvant chemotherapy (median age of 55 years) and was analysed. The median follow up was 39 months (range 24-80). At the end of RT treatment, skin toxicity was G1 in 51.1% of patients, G2 in 9.7%. At 2 years of follow up, it was G1 in 13.5% of patients, no cases ≥ G2; cosmetic outcome was excellent in 63.5% and good in 36.5% of the patients. No significant difference compared to the patients without systemic therapy was observed. CONCLUSION: Hypofractionated VMAT-SIB in patients who had undergone adjuvant systemic therapy was safe and well tolerated in terms of acute and early late settings and cosmesis. Our data confirmed the results of other studies published on the association of hypofractionation and chemotherapy or concomitant boost.

    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 . 2019
    Data sources: Datacite
    ZENODO
    Dataset . 2019
    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 . 2019
      Data sources: Datacite
      ZENODO
      Dataset . 2019
      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
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      ZENODO
      Dataset . 2020
      Data sources: Datacite
      ZENODO
      Dataset . 2020
      Data sources: ZENODO
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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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      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/

    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
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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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  • 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: Morcillo, Fabienne; Serret, Julien; Beckers, Antoine; Collin, Myriam; +4 Authors

    Supplementary data for a manuscript entitled "A non-shedding fruit Elaeis oleifera palm reveals perturbations to hormone signaling, ROS homeostasis, and hemicellulose metabolism" submitted to Genes

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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
    ZENODO
    Dataset . 2021
    Data sources: Datacite
    ZENODO
    Dataset . 2021
    Data sources: ZENODO
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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
    Authors: Godmer Alexandre; Aubry Alexandra; Giai Gianetto Quentin; Veziris Nicolas; +1 Authors

    Spectral database of the subspecies of the Mycobacterium abscessus complex (MALDI-TOF Mass Spectrometry) This data set originates from a collection of 41 clinical strains of Mycobacterium abscessus complex corresponding to 1001 mass spectra: 25 strains of Mycobacterium abscessus subsp. abscessus (633 mass spectra) 9 strains of Mycobacterium abscessus subsp. massiliense (204 mass spectra) 7 strains of Mycobacterium abscessus subsp. bolletii (164 mass spectra) Each strain has been characterized using molecular method (DNA/DNA hydridation, using GenoType NTM-DR (Hain Lifescience, Nehren, Germany) according to the manufacturer's instructions for identification and analyzed by MALDI-TOF mass spectrometry according MycoEx protocol (Bruker��). The mass spectra spectra were obtained according to the following steps : Each of the 41 strains was cultured in aerobic atmosphere at 37��C for 7 �� 2 days on blood agar (COH, bioMerieux��). Then, one colony was extracted according to the MycoEx protocol (Bruker��). For each of the extracts, 8 technical replicates were realized and analyzed by MALDITOF MS (Bruker��). Dried spots were overlaid with 1��L of MALDI matrix (��-HCCA). Data acquisition was performed using a Microflex LT (Bruker�� Daltonics) mass spectrometer equipped with a N2 laser (�� =377 nm). Instrument parameters used were as follows: a masse range between 200-20000 Da, ion source 1: 20 kV, ion source 2: 18.5 kV, Iens: 8.45 kV, pulsed ion extraction: 330 ns, laser frequency: 20.0 Hz. Spectra were obtained after 500 shots. Each spot was analyzed three times. In total 24 spectra were obtained for each extraction. Spectra acquired for each isolate were visualized and analyzed using Flex Analysis software (Bruker�� Daltonics), and spectra with low quality peaks were removed. A minimum of 15 spectra per extraction was necessary to validate the extraction. This database is only intended for medical research. Please contact: medecine-drv@sorbonne-universite.fr for data access. After access agreement, the three following files will be available : The MABSC_spectra.zip file contains the MS peak list data in a Matlab compatible format. The MABSC_metadata.pdf file contains the molecular identifications of strains. The MABSC_notes.txt file contains informations concerning contains informations on the method of obtaining the data.

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    ZENODO
    Dataset . 2021
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    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
      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: 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
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      Dataset . 2020
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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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      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
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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: Doña-Reveco, Cristián; Sotomayor, Pablo;

    Encuesta online diseñada y aplicada para el estudio de la integración laboral y social inmigrante en Chile. Se recibieron un total de 4771 respuestas de las cuales se consideraron como válidas 3406. El instrumento consideró como población objetivo o universo de estudio a inmigrantes con permiso de residencia en Chile mayores de 18 años y con correo electrónico válido registrados por el Departamento de Extranjería y Migración, entre los meses de marzo y mayo de 2017. La cantidad de inmigrantes que recibió el cuestionario fue de 35.377, correspondientes al total de inmigrantes con estas características durante ese período. Investigacion financiada por la Comisión Nacional de Ciencia y Tecnologia (CONICYT-CHILE), actualmente Agencia Nacional de Investigación y Desarrollo, bajo el proyecto CONICYT+PAI/ Concurso Nacional Apoyo al Retorno de Investigadores/as desde el Extranjero Convocatoria 2014 + 82140058 (Agosto 2015 – Julio 2017)

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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
    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
      ZENODO
      Dataset . 2020
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      ZENODO
      Dataset . 2020
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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: De Rose, Fiorenza; Fogliata, Antonella; Franceschini, Davide; Iftode, Cristina Simona; +10 Authors

    This record contains raw data related to article "Hypofractionation with simultaneous boost in breast cancer patients receiving adjuvant chemotherapy A prospective evaluation of a case series and review of the literature" To evaluate acute toxicity and cosmetic outcomes of hypofractionated simultaneous integrated boost (SIB) as adjuvant treatment after breast-conserving surgery and adjuvant chemotherapy and to review the association of chemotherapy and short fractionation with boost. MATERIALS AND METHODS: Patients presenting early-stage breast cancer were enrolled in a phase II trial. All patients received VMAT-SIB technique to the whole breast and tumor bed in 15 fractions, for a total dose of 40.5 and 48 Gy. Acute and late skin toxicities and breast pain were recorded. Cosmetic outcomes were also assessed as excellent/good or fair/poor. RESULTS: Between August 2010 and December 2015, 787 consecutive patients were treated and had at least 2 year follow-up. A subset of 175 patients underwent adjuvant chemotherapy (median age of 55 years) and was analysed. The median follow up was 39 months (range 24-80). At the end of RT treatment, skin toxicity was G1 in 51.1% of patients, G2 in 9.7%. At 2 years of follow up, it was G1 in 13.5% of patients, no cases ≥ G2; cosmetic outcome was excellent in 63.5% and good in 36.5% of the patients. No significant difference compared to the patients without systemic therapy was observed. CONCLUSION: Hypofractionated VMAT-SIB in patients who had undergone adjuvant systemic therapy was safe and well tolerated in terms of acute and early late settings and cosmesis. Our data confirmed the results of other studies published on the association of hypofractionation and chemotherapy or concomitant boost.

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    ZENODO
    Dataset . 2019
    Data sources: Datacite
    ZENODO
    Dataset . 2019
    Data sources: ZENODO
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