cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14189574.v1
title: Additional file 1 of Stable DNMT3L overexpression in SH-SY5Y neurons recreates a facet of the genome-wide Down syndrome DNA methylation signature

description: Additional file 1: Table 1. Testable background regions and significant DMRs for DNMT3L overexpression in A) growth phase, B) phase 1, and C) phase 3. Table 2. Testable background regions and significant DMRs for DNMT3L overexpression in all 3 cell line replicates for A) growth phase, B) phase 1, and C) phase 3 (XLSX 78248 KB)
DOI: 10.6084/m9.figshare.14189586
title: Additional file 1 of Genome-wide analysis of AP2/ERF superfamily in lotus (Nelumbo nucifera) and the association between NnADAP and rhizome morphology

description: Additional file 1: Table S1. The AP2/ERF family in Nelumbo nucfera. Table S2. The motif sequence of lotus AP2/ERF family. Table S3. The transcriptome data of AP2/ERF family in the temperate lotus and tropical lotus rhizome. Table S4. Primers used in this study. Table S5. Detection and the authentication of SNPs in genome sequencing results through first-generation sequencing. Table S6. The rhizome traits and SNP phenotype of 95 lotus germplasm resources
DOI: 10.6084/m9.figshare.14189586.v1
title: Additional file 1 of Genome-wide analysis of AP2/ERF superfamily in lotus (Nelumbo nucifera) and the association between NnADAP and rhizome morphology

description: Additional file 1: Table S1. The AP2/ERF family in Nelumbo nucfera. Table S2. The motif sequence of lotus AP2/ERF family. Table S3. The transcriptome data of AP2/ERF family in the temperate lotus and tropical lotus rhizome. Table S4. Primers used in this study. Table S5. Detection and the authentication of SNPs in genome sequencing results through first-generation sequencing. Table S6. The rhizome traits and SNP phenotype of 95 lotus germplasm resources
DOI: 10.6084/m9.figshare.13719003
title: Additional file 2 of Synthetic analysis of the efficacy of the S-net system in tsunami forecasting

description: Additional file 2: Table S1. Optimized S-net stations distribution with respect to the specified magnitude ranges.
DOI: 10.6084/m9.figshare.13719003.v1
title: Additional file 2 of Synthetic analysis of the efficacy of the S-net system in tsunami forecasting

description: Additional file 2: Table S1. Optimized S-net stations distribution with respect to the specified magnitude ranges.
DOI: 10.6084/m9.figshare.14189598
title: Additional file 3 of Adaptation of central metabolite pools to variations in growth rate and cultivation conditions in Saccharomyces cerevisiae

description: Additional file 3.
DOI: 10.6084/m9.figshare.14189598.v1
title: Additional file 3 of Adaptation of central metabolite pools to variations in growth rate and cultivation conditions in Saccharomyces cerevisiae

description: Additional file 3.
DOI: 10.6084/m9.figshare.14189601
title: Additional file 4 of Adaptation of central metabolite pools to variations in growth rate and cultivation conditions in Saccharomyces cerevisiae

description: Additional file 4.
DOI: 10.6084/m9.figshare.14189604
title: Additional file 5 of Adaptation of central metabolite pools to variations in growth rate and cultivation conditions in Saccharomyces cerevisiae

description: Additional file 5: Table S8. t-test of pairwise comparisons (paired, 2-tailed) in Panel A-G in Figure 2. Yellow asterix indicate p &lt; 0.05.
DOI: 10.6084/m9.figshare.14189604.v1
title: Additional file 5 of Adaptation of central metabolite pools to variations in growth rate and cultivation conditions in Saccharomyces cerevisiae

description: Additional file 5: Table S8. t-test of pairwise comparisons (paired, 2-tailed) in Panel A-G in Figure 2. Yellow asterix indicate p &lt; 0.05.
DOI: 10.6084/m9.figshare.14189607.v1
title: Additional file 6 of Adaptation of central metabolite pools to variations in growth rate and cultivation conditions in Saccharomyces cerevisiae

description: Additional file 6: Table S9. Correlation between carbon source consumption rate and and other rates and metabolite pools. Color formatting of rates and metabolites mentioned in the main text.
DOI: 10.6084/m9.figshare.14189601.v1
title: Additional file 4 of Adaptation of central metabolite pools to variations in growth rate and cultivation conditions in Saccharomyces cerevisiae

description: Additional file 4.
DOI: 10.6084/m9.figshare.14189607
title: Additional file 6 of Adaptation of central metabolite pools to variations in growth rate and cultivation conditions in Saccharomyces cerevisiae

description: Additional file 6: Table S9. Correlation between carbon source consumption rate and and other rates and metabolite pools. Color formatting of rates and metabolites mentioned in the main text.
DOI: 10.6084/m9.figshare.14189735.v1
title: Additional file 3 of Association between body mass index and severe infection in older adults with microscopic polyangiitis: a retrospective cohort in Japan

description: Additional file 3.
DOI: 10.6084/m9.figshare.14189735
title: Additional file 3 of Association between body mass index and severe infection in older adults with microscopic polyangiitis: a retrospective cohort in Japan

description: Additional file 3.
DOI: 10.6084/m9.figshare.14189736.v1
title: Additional file 1 of Determination of wheat spike and spikelet architecture and grain traits using X-ray Computed Tomography imaging

description: Additional file 1: S1. Matlab code for the spikelet identification.
DOI: 10.6084/m9.figshare.14189739
title: Additional file 2 of Determination of wheat spike and spikelet architecture and grain traits using X-ray Computed Tomography imaging

description: Additional file 2: S2. ImageJ macro for the spikelet visualization.
DOI: 10.6084/m9.figshare.14189736
title: Additional file 1 of Determination of wheat spike and spikelet architecture and grain traits using X-ray Computed Tomography imaging

description: Additional file 1: S1. Matlab code for the spikelet identification.
DOI: 10.6084/m9.figshare.14189739.v1
title: Additional file 2 of Determination of wheat spike and spikelet architecture and grain traits using X-ray Computed Tomography imaging

description: Additional file 2: S2. ImageJ macro for the spikelet visualization.
DOI: 10.6084/m9.figshare.14189765.v1
title: Additional file 13 of Dynamic expression of Ralstonia solanacearum virulence factors and metabolism-controlling genes during plant infection

description: Additional file 13: Proportion of reads aligned to R. solanacearum UY031 genome. Total number of reads obtained in each biological replicate for each condition (first column). Total number of reads aligned to R. solanacearum UY031 genome (second column). Proportion of reads aligned to R. solanacearum genome expressed as percentage (third column).
DOI: 10.6084/m9.figshare.14189765
title: Additional file 13 of Dynamic expression of Ralstonia solanacearum virulence factors and metabolism-controlling genes during plant infection

description: Additional file 13: Proportion of reads aligned to R. solanacearum UY031 genome. Total number of reads obtained in each biological replicate for each condition (first column). Total number of reads aligned to R. solanacearum UY031 genome (second column). Proportion of reads aligned to R. solanacearum genome expressed as percentage (third column).
DOI: 10.6084/m9.figshare.14189768.v1
title: Additional file 14 of Dynamic expression of Ralstonia solanacearum virulence factors and metabolism-controlling genes during plant infection

description: Additional file 14: Transcripts Per Million of each gene in rich medium, apoplast, early and late xylem. Reads normalized per Transcripts Per Million for each R. solanacearum gene in every condition: rich medium (philiq1, 2, 3), apoplast (Apo.10, .7, .9), early xylem (Early.D, .E, .G) and late xylem (Xylem.E, .O, Fresh.xylem). (CSV 986 kb)
DOI: 10.6084/m9.figshare.14189768
title: Additional file 14 of Dynamic expression of Ralstonia solanacearum virulence factors and metabolism-controlling genes during plant infection

description: Additional file 14: Transcripts Per Million of each gene in rich medium, apoplast, early and late xylem. Reads normalized per Transcripts Per Million for each R. solanacearum gene in every condition: rich medium (philiq1, 2, 3), apoplast (Apo.10, .7, .9), early xylem (Early.D, .E, .G) and late xylem (Xylem.E, .O, Fresh.xylem). (CSV 986 kb)
DOI: 10.6084/m9.figshare.14189777
title: Additional file 3 of Dynamic expression of Ralstonia solanacearum virulence factors and metabolism-controlling genes during plant infection

description: Additional file 3: DEGs in the three in planta conditions. Differentially expressed genes of R. solanacearum in apoplast, early and late xylem compared to liquid rich medium obtained with DESeq2 (p-adj &gt; 0.01, log2 FC ± 1.5).
DOI: 10.6084/m9.figshare.14189777.v1
title: Additional file 3 of Dynamic expression of Ralstonia solanacearum virulence factors and metabolism-controlling genes during plant infection

description: Additional file 3: DEGs in the three in planta conditions. Differentially expressed genes of R. solanacearum in apoplast, early and late xylem compared to liquid rich medium obtained with DESeq2 (p-adj &gt; 0.01, log2 FC ± 1.5).
DOI: 10.6084/m9.figshare.14189786.v1
title: Additional file 6 of Dynamic expression of Ralstonia solanacearum virulence factors and metabolism-controlling genes during plant infection

description: Additional file 6: “Virulence and parasitic fitness” manually defined category. Genes belonging to specific virulence categories (T3SS & T3Es, Motility, ROS scavenging enzymes, phytohormone biosynthesis, EPS, nitrogen metabolism, cell wall degrading enzymes) of R. solanacearum are listed showing information related to: UY031 NCBI locus tag (first column), gene name (second column), gene description (third column), category, (forth column), reference (fifth column).
DOI: 10.6084/m9.figshare.14189789.v1
title: Additional file 7 of Dynamic expression of Ralstonia solanacearum virulence factors and metabolism-controlling genes during plant infection

description: Additional file 7: List of genes included in each of the six expression profiles.
DOI: 10.6084/m9.figshare.14189786
title: Additional file 6 of Dynamic expression of Ralstonia solanacearum virulence factors and metabolism-controlling genes during plant infection

description: Additional file 6: “Virulence and parasitic fitness” manually defined category. Genes belonging to specific virulence categories (T3SS & T3Es, Motility, ROS scavenging enzymes, phytohormone biosynthesis, EPS, nitrogen metabolism, cell wall degrading enzymes) of R. solanacearum are listed showing information related to: UY031 NCBI locus tag (first column), gene name (second column), gene description (third column), category, (forth column), reference (fifth column).
DOI: 10.6084/m9.figshare.14189789
title: Additional file 7 of Dynamic expression of Ralstonia solanacearum virulence factors and metabolism-controlling genes during plant infection

description: Additional file 7: List of genes included in each of the six expression profiles.
DOI: 10.6084/m9.figshare.14189802
title: Additional file 1 of Phenomic characterization of Crotalaria germplasm for crop improvement

description: Additional file 1: Table S1. Summary information of the different samples used to study phenomic diversity of Crotalaria species in Kenya.
DOI: 10.6084/m9.figshare.14189802.v1
title: Additional file 1 of Phenomic characterization of Crotalaria germplasm for crop improvement

description: Additional file 1: Table S1. Summary information of the different samples used to study phenomic diversity of Crotalaria species in Kenya.
DOI: 10.6084/m9.figshare.14189817
title: Additional file 5 of Phenomic characterization of Crotalaria germplasm for crop improvement

description: Additional file 5: Table S5. Cluster wise means and range values for the different traits used to study phenomic diversity of Crotalaria species in Kenya.
DOI: 10.6084/m9.figshare.14189817.v1
title: Additional file 5 of Phenomic characterization of Crotalaria germplasm for crop improvement

description: Additional file 5: Table S5. Cluster wise means and range values for the different traits used to study phenomic diversity of Crotalaria species in Kenya.
DOI: 10.6084/m9.figshare.14189873
title: Additional file 6 of A first insight into the genome of Prototheca wickerhamii, a major causative agent of human protothecosis

description: Additional file 6: Supplementary Materials.
DOI: 10.6084/m9.figshare.14189873.v1
title: Additional file 6 of A first insight into the genome of Prototheca wickerhamii, a major causative agent of human protothecosis

description: Additional file 6: Supplementary Materials.
DOI: 10.6084/m9.figshare.14189876.v1
title: Additional file 1 of Discrete choice experiment for eliciting preference for health services for patients with ALS and their informal caregivers

description: Additional file1: Supplementary Tables. This file includes additional analyses of subgroup data. Table 1. Results of Random effects probit model for patient DCE – Gender and Site of Onset subgroup analysis. Table 2. Results of Random effects probit model for patient DCE – Time since diagnosis and King’s Staging subgroup analysis. Table 3. Results of Random effects probit model for caregiver DCE – Sex and Relationship to patient subgroup analysis.
DOI: 10.6084/m9.figshare.14189876
title: Additional file 1 of Discrete choice experiment for eliciting preference for health services for patients with ALS and their informal caregivers

description: Additional file1: Supplementary Tables. This file includes additional analyses of subgroup data. Table 1. Results of Random effects probit model for patient DCE – Gender and Site of Onset subgroup analysis. Table 2. Results of Random effects probit model for patient DCE – Time since diagnosis and King’s Staging subgroup analysis. Table 3. Results of Random effects probit model for caregiver DCE – Sex and Relationship to patient subgroup analysis.
DOI: 10.6084/m9.figshare.14189927.v1
title: Additional file 2 of Genome-wide analysis of DNA methylation in Hirschsprung enteric precursor cells: unraveling the epigenetic landscape of enteric nervous system development

description: Additional file 2 Table S2 DMRs identified in HSCR patients versus controls.
DOI: 10.6084/m9.figshare.14189927
title: Additional file 2 of Genome-wide analysis of DNA methylation in Hirschsprung enteric precursor cells: unraveling the epigenetic landscape of enteric nervous system development

description: Additional file 2 Table S2 DMRs identified in HSCR patients versus controls.
DOI: 10.6084/m9.figshare.14189933
title: Additional file 4 of Genome-wide analysis of DNA methylation in Hirschsprung enteric precursor cells: unraveling the epigenetic landscape of enteric nervous system development

description: Additional file 4 Table S4 Differentially methylated genes in HSCR patients versus controls.
DOI: 10.6084/m9.figshare.14189933.v1
title: Additional file 4 of Genome-wide analysis of DNA methylation in Hirschsprung enteric precursor cells: unraveling the epigenetic landscape of enteric nervous system development

description: Additional file 4 Table S4 Differentially methylated genes in HSCR patients versus controls.
DOI: 10.6084/m9.figshare.14189936
title: Additional file 5 of Genome-wide analysis of DNA methylation in Hirschsprung enteric precursor cells: unraveling the epigenetic landscape of enteric nervous system development

description: Additional file 5 Table S5 Genes considered as promising candidates according to their biological processes. Genes in green were detected by GO analysis into the main enriched ontology clusters and previously described their involvement in HSCR. Genes in gray were detected by GO analysis into the main enriched ontology clusters and previously described their involvement in ENS.
DOI: 10.6084/m9.figshare.14189936.v1
title: Additional file 5 of Genome-wide analysis of DNA methylation in Hirschsprung enteric precursor cells: unraveling the epigenetic landscape of enteric nervous system development

description: Additional file 5 Table S5 Genes considered as promising candidates according to their biological processes. Genes in green were detected by GO analysis into the main enriched ontology clusters and previously described their involvement in HSCR. Genes in gray were detected by GO analysis into the main enriched ontology clusters and previously described their involvement in ENS.
DOI: 10.6084/m9.figshare.14189952.v1
title: Additional file 1 of Dog breeds and body conformations with predisposition to osteosarcoma in the UK: a case-control study

description: Additional file 1: Table 1 from the main article in excel format. Table 2 from the article in excel format. Table 3 from the article in excel format. Supplementary Data S1 – cases and non-cases split by breed. Supplementary Data S2 - results from multivariable main breed model with all breeds included if associated with at least 1 case. Supplementary Data S3 - full list of breed terms derived from VeNom terms. Supplementary Data S4 - List of chondrodystrophic breeds. Supplementary Data S5 - VIF scores and area under the ROC curve. Supplementary Data S6 – List of breeds by skull shape.
DOI: 10.6084/m9.figshare.14189960.v1
title: Additional file 2 of mtDNAcombine: tools to combine sequences from multiple studies

description: Additional file 2. Input files needed to recreate the plots in this paper: Tracer output files for three species.
DOI: 10.6084/m9.figshare.14189952
title: Additional file 1 of Dog breeds and body conformations with predisposition to osteosarcoma in the UK: a case-control study

description: Additional file 1: Table 1 from the main article in excel format. Table 2 from the article in excel format. Table 3 from the article in excel format. Supplementary Data S1 – cases and non-cases split by breed. Supplementary Data S2 - results from multivariable main breed model with all breeds included if associated with at least 1 case. Supplementary Data S3 - full list of breed terms derived from VeNom terms. Supplementary Data S4 - List of chondrodystrophic breeds. Supplementary Data S5 - VIF scores and area under the ROC curve. Supplementary Data S6 – List of breeds by skull shape.
DOI: 10.6084/m9.figshare.14189963
title: Additional file 3 of mtDNAcombine: tools to combine sequences from multiple studies

description: Additional file 3. Input files needed to recreate the plots in this paper: raw sequence data for alignment.
DOI: 10.6084/m9.figshare.14189969
title: Additional file 4 of mtDNAcombine: tools to combine sequences from multiple studies

description: Additional file 4. Code to create the plots in this paper presented as a R markdown file.
DOI: 10.6084/m9.figshare.14189969.v1
title: Additional file 4 of mtDNAcombine: tools to combine sequences from multiple studies

description: Additional file 4. Code to create the plots in this paper presented as a R markdown file.
DOI: 10.6084/m9.figshare.14189963.v1
title: Additional file 3 of mtDNAcombine: tools to combine sequences from multiple studies

description: Additional file 3. Input files needed to recreate the plots in this paper: raw sequence data for alignment.
DOI: 10.6084/m9.figshare.14189960
title: Additional file 2 of mtDNAcombine: tools to combine sequences from multiple studies

description: Additional file 2. Input files needed to recreate the plots in this paper: Tracer output files for three species.
DOI: 10.6084/m9.figshare.14189975.v1
title: Additional file 1 of Rust expression browser: an open source database for simultaneous analysis of host and pathogen gene expression profiles with expVIP

description: Additional file 1: Supplementary Table S1. Metadata for the Pst samples used in this study.
DOI: 10.6084/m9.figshare.14189975
title: Additional file 1 of Rust expression browser: an open source database for simultaneous analysis of host and pathogen gene expression profiles with expVIP

description: Additional file 1: Supplementary Table S1. Metadata for the Pst samples used in this study.
DOI: 10.6084/m9.figshare.14189991
title: Additional file 3 of Genome-wide analysis of spatiotemporal expression patterns during rice leaf development

description: Additional file 3:. Three-dimensional model of Supplemental Figure 4. A three-dimensional model of PCA score plot of samples based on the original principal components. The proportions of the total variance explained by PC1, PC2, and PC3 are shown in parentheses. Samples collected at the same stage are shown in the same color. Samples with different tissue identities are indicated by different symbols: shoot apex, square; P3 leaf, circle; blade, triangle; blade-sheath boundary, diamond; sheath, inverted triangle. Red arrows represent the directions of the modified principal components (mPC1, mPC2, and mPC3) shown in Fig. 2.
DOI: 10.6084/m9.figshare.14189994
title: Additional file 4 of Genome-wide analysis of spatiotemporal expression patterns during rice leaf development

description: Additional file 4:. Three-dimensional model of Fig. 2. A three-dimensional model of PCA score plot of samples based on the modified principal components. The proportions of the total variance explained by PC1, PC2, and PC3 are shown in parentheses. Samples collected at the same stage are shown in the same color. Samples with different tissue identities are indicated by different symbols: shoot apex, square; P3 leaf, circle; blade, triangle; blade-sheath boundary, diamond; sheath, inverted triangle. Red arrows represent the directions of the original principal components (PC1, PC2, and PC3) shown in Supplemental Figure 4.
DOI: 10.6084/m9.figshare.14189994.v1
title: Additional file 4 of Genome-wide analysis of spatiotemporal expression patterns during rice leaf development

description: Additional file 4:. Three-dimensional model of Fig. 2. A three-dimensional model of PCA score plot of samples based on the modified principal components. The proportions of the total variance explained by PC1, PC2, and PC3 are shown in parentheses. Samples collected at the same stage are shown in the same color. Samples with different tissue identities are indicated by different symbols: shoot apex, square; P3 leaf, circle; blade, triangle; blade-sheath boundary, diamond; sheath, inverted triangle. Red arrows represent the directions of the original principal components (PC1, PC2, and PC3) shown in Supplemental Figure 4.
DOI: 10.6084/m9.figshare.14189997
title: Additional file 5 of Genome-wide analysis of spatiotemporal expression patterns during rice leaf development

description: Additional file 5: Supplemental Table S1. The list of genes categorized into 28 clusters by K-means analysis.
DOI: 10.6084/m9.figshare.14190000
title: Additional file 6 of Genome-wide analysis of spatiotemporal expression patterns during rice leaf development

description: Additional file 6: Supplemental Table S3. The list of full-length cDNA clones and cloning primers used for preparation of probes for in situ hybridization.
DOI: 10.6084/m9.figshare.14189997.v1
title: Additional file 5 of Genome-wide analysis of spatiotemporal expression patterns during rice leaf development

description: Additional file 5: Supplemental Table S1. The list of genes categorized into 28 clusters by K-means analysis.
DOI: 10.6084/m9.figshare.14190000.v1
title: Additional file 6 of Genome-wide analysis of spatiotemporal expression patterns during rice leaf development

description: Additional file 6: Supplemental Table S3. The list of full-length cDNA clones and cloning primers used for preparation of probes for in situ hybridization.
DOI: 10.6084/m9.figshare.14190003
title: Additional file 7 of Genome-wide analysis of spatiotemporal expression patterns during rice leaf development

description: Additional file 7: Supplemental Table S4. The list of primers and TaqMan probes used for real-time RT-PCR analysis.
DOI: 10.6084/m9.figshare.14190003.v1
title: Additional file 7 of Genome-wide analysis of spatiotemporal expression patterns during rice leaf development

description: Additional file 7: Supplemental Table S4. The list of primers and TaqMan probes used for real-time RT-PCR analysis.