cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3668806_d6.v1
title: Additional file 3: of An SNP-based saturated genetic map and QTL analysis of fruit-related traits in Zucchini using Genotyping-by-sequencing

description: a) Genetic map developed using the GBS approach with the RIL population derived from the cross Zucchini x Scallop. The genetic and physical position of each of the the 7,718 SNP markers (in the C. pepo genome version 3.2) is indicated and the flanking sequenced of each SNPs is also included. b) Physical position and annotation (in the C. pepo genome version 3.2) of the SNPs that showed statistically significant distorted segregation. Chi-square p-values were corrected for multiple testing using Benjamini and Yekutieli correction [36]. Distorted SNPs are integrated with the 7,718 non-distorted SNPs used for the map construction for which the genetic position is also indicated. c) Main regions with distorted segregation (main genomic blocks with most of the SNPs with distorted segregation). (XLS 4656 kb)
DOI: 10.6084/m9.figshare.c.3668806_d6
title: Additional file 3: of An SNP-based saturated genetic map and QTL analysis of fruit-related traits in Zucchini using Genotyping-by-sequencing

description: a) Genetic map developed using the GBS approach with the RIL population derived from the cross Zucchini x Scallop. The genetic and physical position of each of the the 7,718 SNP markers (in the C. pepo genome version 3.2) is indicated and the flanking sequenced of each SNPs is also included. b) Physical position and annotation (in the C. pepo genome version 3.2) of the SNPs that showed statistically significant distorted segregation. Chi-square p-values were corrected for multiple testing using Benjamini and Yekutieli correction [36]. Distorted SNPs are integrated with the 7,718 non-distorted SNPs used for the map construction for which the genetic position is also indicated. c) Main regions with distorted segregation (main genomic blocks with most of the SNPs with distorted segregation). (XLS 4656 kb)
DOI: 10.6084/m9.figshare.c.3668827_d2
title: Additional file 1: of Effects of Pleistocene sea-level fluctuations on mangrove population dynamics: a lesson from Sonneratia alba

description: Statistics of genetic diversity of the combined chloroplast DNA (cpDNA) and seven nuclear loci in Sonneratia alba at both population and species level. Length of each locus was showed in the parentheses after locus ID. Population abbreviations were defined in TableÂ 1. (XLSX 45Â kb)
DOI: 10.6084/m9.figshare.c.3668827_d2.v1
title: Additional file 1: of Effects of Pleistocene sea-level fluctuations on mangrove population dynamics: a lesson from Sonneratia alba

description: Statistics of genetic diversity of the combined chloroplast DNA (cpDNA) and seven nuclear loci in Sonneratia alba at both population and species level. Length of each locus was showed in the parentheses after locus ID. Population abbreviations were defined in TableÂ 1. (XLSX 45Â kb)
DOI: 10.6084/m9.figshare.c.3668797_d9.v1
title: Additional file 6: Table S6. of Conserved gene expression in sperm reservoirs between birds and mammals in response to mating

description: Differentially expressed genes (multiple condition comparisons) with permutation test in chicken. (XLSX 20Â kb)
DOI: 10.6084/m9.figshare.c.3668839_d2.v1
title: Additional file 2: of SMITE: an R/Bioconductor package that identifies network modules by integrating genomic and epigenomic information

description: Supplementary Tables. Table S3 Gene symbol and score of the high scoring genes using three different methods: SMITE full model, SMITE reduced model, and FEM. Table S4 Modules discovered using FEM and genes composing the modules with their DNA methylation, expression, and overall statistics. Table S5 Modules discovered using the reduced model of SMITE (SMITE-R) with spin-glass. Table S6 Modules discovered using the full model of SMITE (SMITE-F) with spin-glass. Table S7 Pathways associated with the genes composing the modules discovered by FEM. Table S8 Pathways associated with the genes composing the modules discovered by the reduced model of SMITE (SMITE-R) using spin-glass. Table S9 Pathways associated with the genes composing the modules discovered by the full model of SMITE (SMITE-F) using spin-glass. Table S10 Quantifying the number of times pathways were found to be associated the modules discovered by either FEM, the reduced model of SMITE (SMITE-R) using spin-glass, or the full model of SMITE(SMITE-F) using spin-glass. Table S11 Genes composing the “summary network” found by either the reduced (SMITE-R) or full (SMITE-F) SMITE models using the Heinz algorithm. Table S12 Pathways associated with the genes composing the “summary network” discovered by the reduced model of SMITE(SMITE-R) using the Heinz algorithm. Table S13 Pathways associated with the genes composing the “summary network” discovered by the full model of SMITE (SMITE-F) using the Heinz algorithm. Table S14 Genes composing the “modules” found using no weights instead of weighting by distance. Table S15 Pathways associated with the genes in the modules identified without using distance weighting. (XLSX 269 kb)
DOI: 10.6084/m9.figshare.c.3668839_d2
title: Additional file 2: of SMITE: an R/Bioconductor package that identifies network modules by integrating genomic and epigenomic information

description: Supplementary Tables. Table S3 Gene symbol and score of the high scoring genes using three different methods: SMITE full model, SMITE reduced model, and FEM. Table S4 Modules discovered using FEM and genes composing the modules with their DNA methylation, expression, and overall statistics. Table S5 Modules discovered using the reduced model of SMITE (SMITE-R) with spin-glass. Table S6 Modules discovered using the full model of SMITE (SMITE-F) with spin-glass. Table S7 Pathways associated with the genes composing the modules discovered by FEM. Table S8 Pathways associated with the genes composing the modules discovered by the reduced model of SMITE (SMITE-R) using spin-glass. Table S9 Pathways associated with the genes composing the modules discovered by the full model of SMITE (SMITE-F) using spin-glass. Table S10 Quantifying the number of times pathways were found to be associated the modules discovered by either FEM, the reduced model of SMITE (SMITE-R) using spin-glass, or the full model of SMITE(SMITE-F) using spin-glass. Table S11 Genes composing the “summary network” found by either the reduced (SMITE-R) or full (SMITE-F) SMITE models using the Heinz algorithm. Table S12 Pathways associated with the genes composing the “summary network” discovered by the reduced model of SMITE(SMITE-R) using the Heinz algorithm. Table S13 Pathways associated with the genes composing the “summary network” discovered by the full model of SMITE (SMITE-F) using the Heinz algorithm. Table S14 Genes composing the “modules” found using no weights instead of weighting by distance. Table S15 Pathways associated with the genes in the modules identified without using distance weighting. (XLSX 269 kb)
DOI: 10.6084/m9.figshare.c.3669856_d1.v1
title: MOESM2 of Application of 3D printing to prototype and develop novel plant tissue culture systems

description: Additional file 2: Video S1. Timelapse video for printing culture vessels using AXIOM 3D printers (Airwolf3D, CA, USA).
DOI: 10.6084/m9.figshare.c.3669862_d1.v1
title: Additional file 1: of Stepwise addition of genetic changes correlated with histological change from “well-differentiated” to “sarcomatoid” phenotypes: a case report

description: Table S1.Somatic mutations identified by targeted sequencing (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3669856_d1
title: MOESM2 of Application of 3D printing to prototype and develop novel plant tissue culture systems

description: Additional file 2: Video S1. Timelapse video for printing culture vessels using AXIOM 3D printers (Airwolf3D, CA, USA).
DOI: 10.6084/m9.figshare.c.3669862_d1
title: Additional file 1: of Stepwise addition of genetic changes correlated with histological change from “well-differentiated” to “sarcomatoid” phenotypes: a case report

description: Table S1.Somatic mutations identified by targeted sequencing (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3669889_d2
title: Additional file 1: Table S1. of Towards long-read metagenomics: complete assembly of three novel genomes from bacteria dependent on a diazotrophic cyanobacterium in a freshwater lake co-culture

description: Taxonomic placement of each novel genome by 16S similarity, composition (PhyloPythiaS+), and multiple marker gene similarities (Phylosift). (CSV 312 bytes)
DOI: 10.6084/m9.figshare.c.3669856_d4.v1
title: MOESM6 of Application of 3D printing to prototype and develop novel plant tissue culture systems

description: Additional file 6. STL (StereoLithography) file was designed for an accessory lid without fan slot using SketchUp or Fusion 360 (Autodesk) software and the STL file was processed using MatterControl 3D printing software and exported as gcode files.
DOI: 10.6084/m9.figshare.c.3669856_d4
title: MOESM6 of Application of 3D printing to prototype and develop novel plant tissue culture systems

description: Additional file 6. STL (StereoLithography) file was designed for an accessory lid without fan slot using SketchUp or Fusion 360 (Autodesk) software and the STL file was processed using MatterControl 3D printing software and exported as gcode files.
DOI: 10.6084/m9.figshare.c.3669889_d3.v1
title: Additional file 3: Figure S1a. of Towards long-read metagenomics: complete assembly of three novel genomes from bacteria dependent on a diazotrophic cyanobacterium in a freshwater lake co-culture

description: Hyphomonadaceae UKL13-1 genome repeats and Illumina breaks. Blue lines signify intragenomic repeats (based on BLASTN with a minimum E-value cutoff of 1E-30), and red bars mark sequences missing from Illumina assemblies. b. Betaproteobacterium UKL13-2 genome repeats and Illumina breaks. c. Bacteroidetes bacterium UKL13-3 genome repeats and Illumina breaks. (ZIP 4776 kb)
DOI: 10.6084/m9.figshare.c.3669889_d3
title: Additional file 3: Figure S1a. of Towards long-read metagenomics: complete assembly of three novel genomes from bacteria dependent on a diazotrophic cyanobacterium in a freshwater lake co-culture

description: Hyphomonadaceae UKL13-1 genome repeats and Illumina breaks. Blue lines signify intragenomic repeats (based on BLASTN with a minimum E-value cutoff of 1E-30), and red bars mark sequences missing from Illumina assemblies. b. Betaproteobacterium UKL13-2 genome repeats and Illumina breaks. c. Bacteroidetes bacterium UKL13-3 genome repeats and Illumina breaks. (ZIP 4776 kb)
DOI: 10.6084/m9.figshare.c.3669901_d1
title: Additional file 2: Table S1. of A fast and robust protocol for metataxonomic analysis using RNAseq data

description: TPR and FDR are averaged across all 36 experiments. (XLSX 57 kb)
DOI: 10.6084/m9.figshare.c.3669889_d4.v1
title: Additional file 5: Table S4. of Towards long-read metagenomics: complete assembly of three novel genomes from bacteria dependent on a diazotrophic cyanobacterium in a freshwater lake co-culture

description: Annotated genes in Betaproteobacterium UKL13-2 Illumina breaks. Genes called and annotated with PROKKA. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.c.3669886_d4.v1
title: Additional file 3: Table S4. of Short oligogalacturonides induce pathogen resistance-associated gene expression in Arabidopsis thaliana

description: GSEA results based on gene expression data from trimer treated plants compared to mock treatment. (XLSX 31 kb)
DOI: 10.6084/m9.figshare.c.3669889_d4
title: Additional file 5: Table S4. of Towards long-read metagenomics: complete assembly of three novel genomes from bacteria dependent on a diazotrophic cyanobacterium in a freshwater lake co-culture

description: Annotated genes in Betaproteobacterium UKL13-2 Illumina breaks. Genes called and annotated with PROKKA. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.c.3669886_d4
title: Additional file 3: Table S4. of Short oligogalacturonides induce pathogen resistance-associated gene expression in Arabidopsis thaliana

description: GSEA results based on gene expression data from trimer treated plants compared to mock treatment. (XLSX 31 kb)
DOI: 10.6084/m9.figshare.c.3669856_d6.v1
title: MOESM4 of Application of 3D printing to prototype and develop novel plant tissue culture systems

description: Additional file 4. STL (StereoLithography) file was designed for culture vessel's lid using SketchUp or Fusion 360 (Autodesk) software and the STL file was processed using MatterControl 3D printing software and exported as gcode files.
DOI: 10.6084/m9.figshare.c.3669856_d6
title: MOESM4 of Application of 3D printing to prototype and develop novel plant tissue culture systems

description: Additional file 4. STL (StereoLithography) file was designed for culture vessel's lid using SketchUp or Fusion 360 (Autodesk) software and the STL file was processed using MatterControl 3D printing software and exported as gcode files.
DOI: 10.6084/m9.figshare.c.3669919_d1
title: Additional file 4: of The interaction between vaginal microbiota, cervical length, and vaginal progesterone treatment for preterm birth risk

description: Patient metadata for cross-sectional cohort.
DOI: 10.6084/m9.figshare.c.3669889_d8
title: Additional file 8: Table S6. of Towards long-read metagenomics: complete assembly of three novel genomes from bacteria dependent on a diazotrophic cyanobacterium in a freshwater lake co-culture

description: Predicted significant genes identified in the novel genomes. Identified by PGAP annotation, PROKKA annotation, or whole-genome alignment to reference genomes with Mauve. Locus names correspond with PGAP gene calls. (XLSX 36 kb)
DOI: 10.6084/m9.figshare.c.3669922_d1.v1
title: Additional file 1: Table S1. of The respiratory microbiome in bronchial mucosa and secretions from severe IgE-mediated asthma patients

description: Relative abundance (median, IQR) of all genera detected in BB and BA samples. (XLSX 32 kb)
DOI: 10.6084/m9.figshare.c.3669922_d1
title: Additional file 1: Table S1. of The respiratory microbiome in bronchial mucosa and secretions from severe IgE-mediated asthma patients

description: Relative abundance (median, IQR) of all genera detected in BB and BA samples. (XLSX 32 kb)
DOI: 10.6084/m9.figshare.c.3669886_d8.v1
title: Additional file 7: Table S8. of Short oligogalacturonides induce pathogen resistance-associated gene expression in Arabidopsis thaliana

description: GSEA results based on gene expression data of long OGs at 3Â h (Denoux et al. 2008) disregarding genesets also affected by trimers. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.c.3669886_d8
title: Additional file 7: Table S8. of Short oligogalacturonides induce pathogen resistance-associated gene expression in Arabidopsis thaliana

description: GSEA results based on gene expression data of long OGs at 3Â h (Denoux et al. 2008) disregarding genesets also affected by trimers. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.c.3669901_d8.v1
title: Additional file 3: Table S2. of A fast and robust protocol for metataxonomic analysis using RNAseq data

description: The new counting and original IMSA counting methods. (XLSX 59 kb)
DOI: 10.6084/m9.figshare.c.3669901_d8
title: Additional file 3: Table S2. of A fast and robust protocol for metataxonomic analysis using RNAseq data

description: The new counting and original IMSA counting methods. (XLSX 59 kb)
DOI: 10.6084/m9.figshare.c.3669925_d2.v1
title: MOESM11 of Identification and characterization of the glucose dual-affinity transport system in Neurospora crassa: pleiotropic roles in nutrient transport, signaling, and carbon catabolite repression

description: Additional file 11: Table S5. Hierarchical clustering and functional category analysis of differentially expressed genes in Î 2hgt vs. the WT. Sheet 1: expression clustering and functional annotation of the 629 genes upregulated in Î 2hgt vs. the WT; sheet 2: functional category analysis of genes up/downregulated in Î 2hgt vs. the WT; sheet 3: expression profile and functional annotation of the major documented genes in the conidiation process of N. crassa.
DOI: 10.6084/m9.figshare.c.3669925_d2
title: MOESM11 of Identification and characterization of the glucose dual-affinity transport system in Neurospora crassa: pleiotropic roles in nutrient transport, signaling, and carbon catabolite repression

description: Additional file 11: Table S5. Hierarchical clustering and functional category analysis of differentially expressed genes in Î 2hgt vs. the WT. Sheet 1: expression clustering and functional annotation of the 629 genes upregulated in Î 2hgt vs. the WT; sheet 2: functional category analysis of genes up/downregulated in Î 2hgt vs. the WT; sheet 3: expression profile and functional annotation of the major documented genes in the conidiation process of N. crassa.
DOI: 10.6084/m9.figshare.c.3669919_d3.v1
title: Additional file 9: of The interaction between vaginal microbiota, cervical length, and vaginal progesterone treatment for preterm birth risk

description: Linear mixed-effects model assessing the impact of relative species abundance at 16Â weeks on subsequent gestation at birth.
DOI: 10.6084/m9.figshare.c.3669919_d3
title: Additional file 9: of The interaction between vaginal microbiota, cervical length, and vaginal progesterone treatment for preterm birth risk

description: Linear mixed-effects model assessing the impact of relative species abundance at 16Â weeks on subsequent gestation at birth.
DOI: 10.6084/m9.figshare.28050011
title: Parkinsonia aculeata raw GC-MS files

description: Metabolite extraction from Parkinsonia aculeata seeds
DOI: 10.6084/m9.figshare.28050011.v1
title: Parkinsonia aculeata raw GC-MS files

description: Metabolite extraction from Parkinsonia aculeata seeds
DOI: 10.6084/m9.figshare.c.3669919_d6.v1
title: Additional file 14: of The interaction between vaginal microbiota, cervical length, and vaginal progesterone treatment for preterm birth risk

description: Mixed-effects model assessing the impact of progesterone treatment on CST profile at longitudinal sampling, incorporating potential contributing confounders (gestational age at sample, maternal age, BMI, and ethnicity).
DOI: 10.6084/m9.figshare.c.3669886_d12.v1
title: Additional file 1: Table S2. of Short oligogalacturonides induce pathogen resistance-associated gene expression in Arabidopsis thaliana

description: RNA-sequencing gene expression data of plants treated by trimers compared to plants treated by a mock. Corresponding data is presented from plants treated with microarray results from long OG treatment at 1 h (long OGs 1 h - Denoux et al. 2008), 3 h (long OGs 3 h - Denoux et al. 2008) and 2 h (long OGs 2 h, cell culture - Moscatiello et al. 2006). #N/A = not significantly affected in expression. (XLSX 242 kb)
DOI: 10.6084/m9.figshare.c.3669919_d6
title: Additional file 14: of The interaction between vaginal microbiota, cervical length, and vaginal progesterone treatment for preterm birth risk

description: Mixed-effects model assessing the impact of progesterone treatment on CST profile at longitudinal sampling, incorporating potential contributing confounders (gestational age at sample, maternal age, BMI, and ethnicity).
DOI: 10.6084/m9.figshare.c.3669886_d12
title: Additional file 1: Table S2. of Short oligogalacturonides induce pathogen resistance-associated gene expression in Arabidopsis thaliana

description: RNA-sequencing gene expression data of plants treated by trimers compared to plants treated by a mock. Corresponding data is presented from plants treated with microarray results from long OG treatment at 1 h (long OGs 1 h - Denoux et al. 2008), 3 h (long OGs 3 h - Denoux et al. 2008) and 2 h (long OGs 2 h, cell culture - Moscatiello et al. 2006). #N/A = not significantly affected in expression. (XLSX 242 kb)
DOI: 10.6084/m9.figshare.c.3669919_d7.v1
title: Additional file 8: of The interaction between vaginal microbiota, cervical length, and vaginal progesterone treatment for preterm birth risk

description: Linear mixed-effects model of cross-sectional data assessing the correlation between CST, gestational age at sample, maternal age, and BMI on pregnancy outcome.
DOI: 10.6084/m9.figshare.c.3669919_d7
title: Additional file 8: of The interaction between vaginal microbiota, cervical length, and vaginal progesterone treatment for preterm birth risk

description: Linear mixed-effects model of cross-sectional data assessing the correlation between CST, gestational age at sample, maternal age, and BMI on pregnancy outcome.
DOI: 10.6084/m9.figshare.c.3669925_d8.v1
title: MOESM2 of Identification and characterization of the glucose dual-affinity transport system in Neurospora crassa: pleiotropic roles in nutrient transport, signaling, and carbon catabolite repression

description: Additional file 2: Table S1. Gene expression profiling and differential analysis of transcriptional responses to a glucose gradient in N. crassa. For each gene, RPKM, log2 fold change, and P values are given for each level of glucose vs. 2.0% glucose.
DOI: 10.6084/m9.figshare.c.3669949_d1.v1
title: Additional file 1: of Ecotone response to climatic variability depends on stress gradient interactions

description: The Netlogo code for the size gradient model. The Netlogo system can be downloaded at https://ccl.northwestern.edu/netlogo/ . (NLOGO 22 kb)
DOI: 10.6084/m9.figshare.c.3669925_d8
title: MOESM2 of Identification and characterization of the glucose dual-affinity transport system in Neurospora crassa: pleiotropic roles in nutrient transport, signaling, and carbon catabolite repression

description: Additional file 2: Table S1. Gene expression profiling and differential analysis of transcriptional responses to a glucose gradient in N. crassa. For each gene, RPKM, log2 fold change, and P values are given for each level of glucose vs. 2.0% glucose.
DOI: 10.6084/m9.figshare.c.3669925_d12.v1
title: MOESM3 of Identification and characterization of the glucose dual-affinity transport system in Neurospora crassa: pleiotropic roles in nutrient transport, signaling, and carbon catabolite repression

description: Additional file 3: Table S2. Functional category analysis (FunCat) of up/downregulated genes at each level of glucose vs. 2.0% glucose. Sheet 1: functional category analysis of upregulated genes; sheet 2: functional category analysis of downregulated genes; sheet 3: gene expression dynamics and annotation of pioneer responses to glucose depletion (no-carbon or glc_0.05% vs. glc_2.0%).
DOI: 10.6084/m9.figshare.c.3669955_d3.v1
title: Additional file 3: of Emergency obstetric and neonatal care availability, use, and quality: a cross-sectional study in the city of Lubumbashi, Democratic Republic of the Congo, 2011

description: Statistics on deliveries, maternal complications and EmONC signal functions between January and March 2011 in the surveyed health care facilities of Lubumbashi. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.c.3669919_d11.v1
title: Additional file 3: of The interaction between vaginal microbiota, cervical length, and vaginal progesterone treatment for preterm birth risk

description: Species read count data for cross-sectional cohort.
DOI: 10.6084/m9.figshare.c.3669925_d12
title: MOESM3 of Identification and characterization of the glucose dual-affinity transport system in Neurospora crassa: pleiotropic roles in nutrient transport, signaling, and carbon catabolite repression

description: Additional file 3: Table S2. Functional category analysis (FunCat) of up/downregulated genes at each level of glucose vs. 2.0% glucose. Sheet 1: functional category analysis of upregulated genes; sheet 2: functional category analysis of downregulated genes; sheet 3: gene expression dynamics and annotation of pioneer responses to glucose depletion (no-carbon or glc_0.05% vs. glc_2.0%).
DOI: 10.6084/m9.figshare.c.3669955_d3
title: Additional file 3: of Emergency obstetric and neonatal care availability, use, and quality: a cross-sectional study in the city of Lubumbashi, Democratic Republic of the Congo, 2011

description: Statistics on deliveries, maternal complications and EmONC signal functions between January and March 2011 in the surveyed health care facilities of Lubumbashi. (XLSX 19 kb)