cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7284/135416
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise OC1905A using a Hawaii UHDAS instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7369211
title: Additional file 4 of Large scale study of anti-sense regulation by differential network analysis

description: H experiment â http://www.info.univ-angers.fr/~legeay/AF4_Harvest.zip . Normalized data (without background suppression) of the H (Harvest) experiment. The file contains the normalized expression data of the 126,022 apple genes (rows) of the 22 samples (columns). The normalization method used is the quantile normalization. (TXT 1 kb)
DOI: 10.6084/m9.figshare.7369211.v1
title: Additional file 4 of Large scale study of anti-sense regulation by differential network analysis

description: H experiment â http://www.info.univ-angers.fr/~legeay/AF4_Harvest.zip . Normalized data (without background suppression) of the H (Harvest) experiment. The file contains the normalized expression data of the 126,022 apple genes (rows) of the 22 samples (columns). The normalization method used is the quantile normalization. (TXT 1 kb)
DOI: 10.6084/m9.figshare.7369214.v1
title: Additional file 7: of Comparative genomics analysis to differentiate metabolic and virulence gene potential in gastric versus enterohepatic Helicobacter species

description: Figure S1. A) Genome sizes were plotted against the number of annotated protein coding sequences (CDS) and GC content. For all Helicobacter genomes, a linear relationship existed for genome size versus number of annotated protein CDS (R2 = 0.8939). Three EHS genomes (H. muridarum ST1, H. pametensis ATCC 51478, and H. cholecystus ATCC 700242) and one gastric genome (H. bizzozeronii CCUG 35545) appeared to be outliers and are indicated in the graph. Diamonds (◆), gastric genomes; circles (●) EHS genomes; cross (X), C. jejuni genome. B) Genome sizes were plotted against the additive size of all protein CDS, RNA genes, and non-coding gene sequences. Linear relationships existed for genome size versus size of protein CDS (R2 = 0.9782) and non-coding gene sequences (R2 = 0.8057), but not for RNA gene sequences (R2 = 0.0076). (ZIP 458 kb)
DOI: 10.6084/m9.figshare.7369208
title: Additional file 5: of Denosumab treatment is associated with the absence of circulating tumor cells in patients with breast cancer

description: Table S4. Therapy evaluation in patients with circulating tumor cells. The table shows the types of therapy that patients with and without circulating tumor cells (CTCs) underwent. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7369208.v1
title: Additional file 5: of Denosumab treatment is associated with the absence of circulating tumor cells in patients with breast cancer

description: Table S4. Therapy evaluation in patients with circulating tumor cells. The table shows the types of therapy that patients with and without circulating tumor cells (CTCs) underwent. (XLSX 9 kb)
DOI: 10.7284/135425
title: Anemometer data collected during research cruise OC1905A using a Gill WindObserver II instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7369199
title: Additional file 3 of Large scale study of anti-sense regulation by differential network analysis

description: Functional annotation of change motifs significantly enriched according GO slim classification. For each enriched change motif from Additional file 2, we associate functional keywords from the TAIR annotation. Columns A to D: apple genes, nodes of the change motif. Column E: GO slim category significantly over-represented by the genes present in the change motif. Column F: significant p-value below 0.05 (change motifs are ordered according to this criteria). Column G: Arabidopsis orthologs tagged by the GO slim term associated with the change motif. Columns H to N: Functional keywords from Arabidopsis orthologs (TAIR annotations), keywords consistent with the biological context (fruit ripening in abiotic stress condition) are highlighted in orange. In columns H to N, we use the following abbreviations: ABA: abscissic acid; SA: salicylic acid; JA: jasmonate acid; ROS: reactive oxygen species. The three change motifs described in the manuscript (Fig. 5) are highlighted in blue. (ODS 23 kb)
DOI: 10.6084/m9.figshare.7369196
title: Additional file 9: of Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis

description: Table S7. Table comparing relevant germline alterations, presented here, with other publications. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.7369199.v1
title: Additional file 3 of Large scale study of anti-sense regulation by differential network analysis

description: Functional annotation of change motifs significantly enriched according GO slim classification. For each enriched change motif from Additional file 2, we associate functional keywords from the TAIR annotation. Columns A to D: apple genes, nodes of the change motif. Column E: GO slim category significantly over-represented by the genes present in the change motif. Column F: significant p-value below 0.05 (change motifs are ordered according to this criteria). Column G: Arabidopsis orthologs tagged by the GO slim term associated with the change motif. Columns H to N: Functional keywords from Arabidopsis orthologs (TAIR annotations), keywords consistent with the biological context (fruit ripening in abiotic stress condition) are highlighted in orange. In columns H to N, we use the following abbreviations: ABA: abscissic acid; SA: salicylic acid; JA: jasmonate acid; ROS: reactive oxygen species. The three change motifs described in the manuscript (Fig. 5) are highlighted in blue. (ODS 23 kb)
DOI: 10.7284/135419
title: Fluorometer data collected during research cruise OC1905A using a WET Labs WETStar instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7369196.v1
title: Additional file 9: of Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis

description: Table S7. Table comparing relevant germline alterations, presented here, with other publications. (XLSX 26 kb)
DOI: 10.7284/135420
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC1905A using a Furuno GP-90 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7369184
title: Additional file 2 of Large scale study of anti-sense regulation by differential network analysis

description: Change motifs enrichment. Results of the enrichment analysis of the 308 change motifs from the 60DAH experiment. Columns A to D: apple genes, nodes of the change motif. Column E: GO slim category significantly over-represented by the genes present in the change motif (“No enrichment” if there is no significantly over-represented category). Column F: significant p-value below 0.05 (-1 if no enrichment). Column G: Apple genes from the sample tagged with the GO slim category. Column H: Number of apple genes in the genome. Column I: Number of apple genes in the sample. Column J: Number of apple genes from the genome tagged with the GO slim category. Column K: Number of apple genes from the sample tagged with the GO slim category. Columns L to O: Arabidopsis orthologs of the apple genes of the change motif. Column P: Arabidopsis orthologs of the apple genes from the sample tagged with the GO category. (ODS 34 kb)
DOI: 10.6084/m9.figshare.7369184.v1
title: Additional file 2 of Large scale study of anti-sense regulation by differential network analysis

description: Change motifs enrichment. Results of the enrichment analysis of the 308 change motifs from the 60DAH experiment. Columns A to D: apple genes, nodes of the change motif. Column E: GO slim category significantly over-represented by the genes present in the change motif (“No enrichment” if there is no significantly over-represented category). Column F: significant p-value below 0.05 (-1 if no enrichment). Column G: Apple genes from the sample tagged with the GO slim category. Column H: Number of apple genes in the genome. Column I: Number of apple genes in the sample. Column J: Number of apple genes from the genome tagged with the GO slim category. Column K: Number of apple genes from the sample tagged with the GO slim category. Columns L to O: Arabidopsis orthologs of the apple genes of the change motif. Column P: Arabidopsis orthologs of the apple genes from the sample tagged with the GO category. (ODS 34 kb)
DOI: 10.6084/m9.figshare.7369169
title: Additional file 3: of Denosumab treatment is associated with the absence of circulating tumor cells in patients with breast cancer

description: Table S3. Patient characteristics. The table shows the characteristics of the 73 patients included in the study. Abbreviations: ER Estrogen receptor, HER2 Human epidermal growth factor receptor 2, ID Invasive ductal, IL Invasive lobular, NA Not available, PR Progesterone receptor, ECOG Eastern Cooperative Oncology Group (as defined by Oken et al. [24]). (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7369172
title: Additional file 8: of Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis

description: Table S6. Somatic and germline alterations. (XLSX 141 kb)
DOI: 10.7284/135424
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC1905A using a Ashtech ADU5 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7369169.v1
title: Additional file 3: of Denosumab treatment is associated with the absence of circulating tumor cells in patients with breast cancer

description: Table S3. Patient characteristics. The table shows the characteristics of the 73 patients included in the study. Abbreviations: ER Estrogen receptor, HER2 Human epidermal growth factor receptor 2, ID Invasive ductal, IL Invasive lobular, NA Not available, PR Progesterone receptor, ECOG Eastern Cooperative Oncology Group (as defined by Oken et al. [24]). (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7369172.v1
title: Additional file 8: of Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis

description: Table S6. Somatic and germline alterations. (XLSX 141 kb)
DOI: 10.6084/m9.figshare.7369163
title: Additional file 1: of Haploid females in the isomorphic biphasic life-cycle of Gracilaria chilensis excel in survival

description: Gracilaria chilensis raw data. Data comprising the life cycle stage, size and sexual maturity of each Gracilaria chilensis frond at each pool and each census. (ZIP 830Â kb)
DOI: 10.6084/m9.figshare.7369166
title: Additional file 1 of Large scale study of anti-sense regulation by differential network analysis

description: List of the GO categories revealed by anti-sense data. List of the 104 revealed-by-AS terms. Column A: Identifier of the GO category. Column B: significant p-value. Column C: significant corrected p-value below 0.05, the correction used is the Benjamini & Hochberg False Discovery Rate (FDR) correction (Revealed-by-AS terms are ordered according to this criteria). Column D: Number of apple genes from the sample tagged with the GO category. Column E: Number of apple genes from the genome tagged with the GO category. Column F: Number of apple genes in the sample. Column G: Number of apple genes in the genome. Column H: Name of the GO category. Column I: Apple genes from the sample tagged with the GO category. Column J: Arabidopsis orthologs of the apple genes from the sample tagged with the GO category; here an Arabidopsis ortholog with an anti-sense apple gene is identified by the “_AS” prefix. (ODS 57 kb)
DOI: 10.7284/135415
title: Gyrocompass data collected during research cruise OC1905A using a Sperry MK-37 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7369163.v1
title: Additional file 1: of Haploid females in the isomorphic biphasic life-cycle of Gracilaria chilensis excel in survival

description: Gracilaria chilensis raw data. Data comprising the life cycle stage, size and sexual maturity of each Gracilaria chilensis frond at each pool and each census. (ZIP 830Â kb)
DOI: 10.6084/m9.figshare.7369166.v1
title: Additional file 1 of Large scale study of anti-sense regulation by differential network analysis

description: List of the GO categories revealed by anti-sense data. List of the 104 revealed-by-AS terms. Column A: Identifier of the GO category. Column B: significant p-value. Column C: significant corrected p-value below 0.05, the correction used is the Benjamini & Hochberg False Discovery Rate (FDR) correction (Revealed-by-AS terms are ordered according to this criteria). Column D: Number of apple genes from the sample tagged with the GO category. Column E: Number of apple genes from the genome tagged with the GO category. Column F: Number of apple genes in the sample. Column G: Number of apple genes in the genome. Column H: Name of the GO category. Column I: Apple genes from the sample tagged with the GO category. Column J: Arabidopsis orthologs of the apple genes from the sample tagged with the GO category; here an Arabidopsis ortholog with an anti-sense apple gene is identified by the “_AS” prefix. (ODS 57 kb)
DOI: 10.7284/135414
title: PTU (Pressure, Temperature, Humidity) data collected during research cruise OC1905A using a Vaisala PTU300 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7369154
title: Additional file 2: of Denosumab treatment is associated with the absence of circulating tumor cells in patients with breast cancer

description: Table S2. Variable classification and statistical test applied. The table shows the type of variable and statistical test used for the analysis of individual clinicopathological parameters. Abbreviations: ER, Estrogen receptor, HER2, Human epidermal growth factor receptor 2, PR Progesterone receptor. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7369154.v1
title: Additional file 2: of Denosumab treatment is associated with the absence of circulating tumor cells in patients with breast cancer

description: Table S2. Variable classification and statistical test applied. The table shows the type of variable and statistical test used for the analysis of individual clinicopathological parameters. Abbreviations: ER, Estrogen receptor, HER2, Human epidermal growth factor receptor 2, PR Progesterone receptor. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7369148
title: Additional file 7: of Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis

description: Table S5. CTC count, ctDNA fraction and line of therapy. (XLSX 27 kb)
DOI: 10.7284/135421
title: Singlebeam Echosounder data collected during research cruise OC1905A using a Knudsen 3260 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7369148.v1
title: Additional file 7: of Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis

description: Table S5. CTC count, ctDNA fraction and line of therapy. (XLSX 27 kb)
DOI: 10.7284/135417
title: Water Temperature data collected during research cruise OC1905A using a Sea-Bird SBE-48 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7369133
title: Additional file 1: of Denosumab treatment is associated with the absence of circulating tumor cells in patients with breast cancer

description: Table S1. Drug classification. The table shows the drug classification used for the analysis, grouping drugs into targeted therapy, chemotherapy, hormone therapy and immunotherapy. Abbreviations: cbx6 ChromoboxÂ 6, CDK4 Cyclin-dependent kinase 4, CDK6 Cyclin-dependent kinase 6, EGFR Epidermal growth factor receptor, Her2 Human epidermal growth factor receptor 2, mTOR Mechanistic target of rapamycin, PD-L1 Programmed cell death 1 ligand 1, VEGF Vascular endothelial growth factor. (XLSX 10 kb)
DOI: 10.7284/135423
title: Water Temperature data collected during research cruise OC1905A using a Sea-Bird SBE-38 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7369133.v1
title: Additional file 1: of Denosumab treatment is associated with the absence of circulating tumor cells in patients with breast cancer

description: Table S1. Drug classification. The table shows the drug classification used for the analysis, grouping drugs into targeted therapy, chemotherapy, hormone therapy and immunotherapy. Abbreviations: cbx6 ChromoboxÂ 6, CDK4 Cyclin-dependent kinase 4, CDK6 Cyclin-dependent kinase 6, EGFR Epidermal growth factor receptor, Her2 Human epidermal growth factor receptor 2, mTOR Mechanistic target of rapamycin, PD-L1 Programmed cell death 1 ligand 1, VEGF Vascular endothelial growth factor. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7369124
title: Additional file 10: of Denosumab treatment is associated with the absence of circulating tumor cells in patients with breast cancer

description: Table S8. Complete blood counts in patients with single circulating tumor cells and circulating tumor cell clusters. The table shows complete blood counts in patients in whom only single circulating tumor cells (single CTC) or also clustered circulating tumor cells (CTC clusters) were found. Abbreviations: CA 15-3 Cancer antigen 15-3, CRP C-reactive protein, HCT Hematocrit, HGB Hemoglobin, LDH Lactate dehydrogenase, LUC Large unstained cells, MCH Mean corpuscular hemoglobin, MCHC Mean corpuscular hemoglobin concentration, MCV Mean corpuscular volume, MPV Mean platelet volume, PLT Platelets, RBC Red blood cells, WBC White blood cells. (XLSX 10 kb)
DOI: 10.7284/135422
title: Timeserver data collected during research cruise OC1905A using a Microsemi SyncServer S350 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7369124.v1
title: Additional file 10: of Denosumab treatment is associated with the absence of circulating tumor cells in patients with breast cancer

description: Table S8. Complete blood counts in patients with single circulating tumor cells and circulating tumor cell clusters. The table shows complete blood counts in patients in whom only single circulating tumor cells (single CTC) or also clustered circulating tumor cells (CTC clusters) were found. Abbreviations: CA 15-3 Cancer antigen 15-3, CRP C-reactive protein, HCT Hematocrit, HGB Hemoglobin, LDH Lactate dehydrogenase, LUC Large unstained cells, MCH Mean corpuscular hemoglobin, MCHC Mean corpuscular hemoglobin concentration, MCV Mean corpuscular volume, MPV Mean platelet volume, PLT Platelets, RBC Red blood cells, WBC White blood cells. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7369115
title: Additional file 5: of Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis

description: Table S4. Overview of the number of samples per described analysis. (XLSX 12 kb)
DOI: 10.7284/135444
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise OC1905C using a Hawaii UHDAS instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7369115.v1
title: Additional file 5: of Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis

description: Table S4. Overview of the number of samples per described analysis. (XLSX 12 kb)
DOI: 10.7284/135453
title: Anemometer data collected during research cruise OC1905C using a Gill WindObserver II instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7369100
title: Additional file 1: of Comparative genomics analysis to differentiate metabolic and virulence gene potential in gastric versus enterohepatic Helicobacter species

description: Table S1. Average Nucleotide Identity. Table S2. Genome Annotations. Table S3. Gastric and EHS Clade Orthogroups. Table S4. H. mustelae Orthogroups. Table S5. KEGG Heatmap. Table S6. Genome Metadata and Characteristics. Table S7. Metabolism Pathways per Genome. Table S8. Virulence Factor BLAST Results. Table S9. Virulence Factor Heatmap. Table S10. H. pylori T4SS. Table S11 H. hepaticus T6SS. Table S12. H. pylori Outer Membrane Proteins. Table S13. Other Outer Membrane Proteins. Table S14. Novel Membrane-Associated Proteins. Table S15. LPS Biosynthesis. (XLSX 147858 kb)
DOI: 10.7284/135447
title: Fluorometer data collected during research cruise OC1905C using a WET Labs WETStar instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7369094
title: Additional file 4: of Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis

description: Table S3. Overview of which samples that were sequenced with which capture design. (XLSX 123 kb)
DOI: 10.6084/m9.figshare.7369100.v1
title: Additional file 1: of Comparative genomics analysis to differentiate metabolic and virulence gene potential in gastric versus enterohepatic Helicobacter species

description: Table S1. Average Nucleotide Identity. Table S2. Genome Annotations. Table S3. Gastric and EHS Clade Orthogroups. Table S4. H. mustelae Orthogroups. Table S5. KEGG Heatmap. Table S6. Genome Metadata and Characteristics. Table S7. Metabolism Pathways per Genome. Table S8. Virulence Factor BLAST Results. Table S9. Virulence Factor Heatmap. Table S10. H. pylori T4SS. Table S11 H. hepaticus T6SS. Table S12. H. pylori Outer Membrane Proteins. Table S13. Other Outer Membrane Proteins. Table S14. Novel Membrane-Associated Proteins. Table S15. LPS Biosynthesis. (XLSX 147858 kb)
DOI: 10.6084/m9.figshare.7369094.v1
title: Additional file 4: of Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis

description: Table S3. Overview of which samples that were sequenced with which capture design. (XLSX 123 kb)
DOI: 10.7284/135448
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC1905C using a Furuno GP-90 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/135452
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC1905C using a Ashtech ADU5 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7369079
title: Additional file 3: of Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis

description: Table S2. Summary of bioinformatic tools and settings. (XLSX 13 kb)