cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12788914.v1
title: Additional file 4 of ContamLD: estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium

description: Additional file 4: Table S3. ContamLD, ContamMix, and ANGSD Estimates. Excel spreadsheet providing ContamLD, ContamMix, and ANGSD estimates from ancient male individuals with meta-data of the ancient individuals also included.
DOI: 10.6084/m9.figshare.12788917.v1
title: Additional file 5 of ContamLD: estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium

description: Additional file 5: Table S4. Simulation with Damaged Contaminated Reads. Excel spreadsheet providing ContamLD estimates for a simulation where the damaged reads of the contaminant individual were also included in the contamination.
DOI: 10.6084/m9.figshare.12788908.v1
title: Additional file 2 of ContamLD: estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium

description: Additional file 2: Table S1. Ancient Individual Meta-Data. Excel spreadsheet detailing information about the ancient individuals analyzed.
DOI: 10.6084/m9.figshare.12788811
title: Additional file 4 of Cul o 2 specific IgG3/5 antibodies predicted Culicoides hypersensitivity in a group imported Icelandic horses

description: Additional file 4. Original data file.
DOI: 10.6084/m9.figshare.12788803
title: Additional file 1 of The chromosome-level wintersweet (Chimonanthus praecox) genome provides insights into floral scent biosynthesis and flowering in winter

description: Additional file 1: Table S1. Summary of sequencing data of Chimonanthus praecox and Calycanthus chinensis genome. Table S2. Estimation of genome size of Chimonanthus praecox and Calycanthus chinensis using K-mer analysis. Table S3. Statistic of Chimonanthus praecox and Calycanthus chinensis genome assembly. Table S4. Chromosomes length of wintersweet using HiC reads. Table S5. Assembly results of wintersweet using Hi-C. Table S6. Validation of genome assembly using BUSCO and CEGMA method. Table S7. Statistics of predicted protein-coding genes in Chimonanthus praecox and Calycanthus chinensis genome. Table S8. Functional annotation of the wintersweet protein-coding genes. Table S9. Annotation of conserved non-coding RNA genes in the wintersweet genome. Table S10. Wintersweet-specific gene families. Table S11. The list of expansion genes in wintersweet genome. Table S12. Annotation of repeat sequences in the wintersweet genome. Table S13. List of flowering-time and floral organ identity gene candidates in wintersweet. Table S14. The upregulated expressed genes involved in flowering networks in FBS1 stage compared with FBS2 stage. Table S15. Monthly temperatures in Wuhan (March 2017–February 2018). Table S16. Differently expressed genes between FBS6 and FBS7 stage. Table S17. List of Heat stress transcription factors (Hsf) and DEHYDRATION- RESPONSIVE ELEMENT BINDING PROTEIN (DREB) gene candidates identified in the wintersweet genome. Table S18.The candidate genes involved in the terpene synthesis pathways in wintersweet. Table S19. Terpene synthase family in wintersweet. Table S20. The candidate genes involved in the benzenoid/ phenylpropanoid synthesis pathways in wintersweet. Table S21. The list of transcription factor candidates involved in the regulation of VOCs synthesis in wintersweet. Table S22. Primers for CpTPS genes coloning and MADS-box B&C class genes Real-Time PCR. Table S23. Transporter candidates involved in benzenoid/phenylpropanoid synthesis pathways in wintersweet genome. Table S24. Tandem duplicated gene clusters in wintersweet genome.
DOI: 10.6084/m9.figshare.12788811.v1
title: Additional file 4 of Cul o 2 specific IgG3/5 antibodies predicted Culicoides hypersensitivity in a group imported Icelandic horses

description: Additional file 4. Original data file.
DOI: 10.6084/m9.figshare.12788787
title: Additional file 1 of Evolution and development of three highly specialized floral structures of bee-pollinated Phalaenopsis species

description: Additional file 1: Table S1. List of primers used for semi quantitative RT PCR analysis. Table S2. List of Phalaenopsis sequences generated from transcriptome analysis. Table S3. List of sequences used for phylogenetic analyses. Table S4. Results of differential gene expression of MADS-box gene analyses using DESeq in R. Table S5. Results of differential gene expression of MYB and TCP genes analyses using DESeq in R.
DOI: 10.6084/m9.figshare.12788784
title: Additional file 2 of Metagenomics revealing molecular profiling of community structure and metabolic pathways in natural hot springs of the Sikkim Himalaya

description: Additional file 2 Table S1 Domain level classification taxonomic composition in Polok and Reshi. Table S2 Phylum level classification of taxonomic composition in Polok and Reshi. Table S3 Family level classification of taxonomic composition in Polok and Reshi. Table S4 Genus level classification of taxonomic composition in Polok and Reshi. Table S5 Species distribution in Polok and Reshi. Table S6 Psychrophiles, mesophiles, and thermophiles in the metagenome. Table S7 Pearson product moment correlation among the species detected in the metagenome. Table S8 Principle Component analysis at species level. Table S9 Metagenomic ORFs assigned to different COG categories. Table S10 Metagenomic ORFs assigned to different KEGG Categories. Table S11 ORFs associated with nitrogen regulating genes in the metagenome. Table S12 ORFs associated with sulfur metabolism genes in the metagenome. Table S13 ORFs associated with methane metabolism genes in the metagenome. Table S14 Genes associated with antibiotic biosynthesis in the metagenome. Table S15 ORFs associated with antibiotic resistance genes in the metagenome from KEGG and CARD database. Table S16 Putative antibiotics resistance genes and their possible source microbial genera from CARD database. Table S17 Different CAZymes in the metagenome. Table S18 ORFs associated with COG functions.
DOI: 10.6084/m9.figshare.12788784.v1
title: Additional file 2 of Metagenomics revealing molecular profiling of community structure and metabolic pathways in natural hot springs of the Sikkim Himalaya

description: Additional file 2 Table S1 Domain level classification taxonomic composition in Polok and Reshi. Table S2 Phylum level classification of taxonomic composition in Polok and Reshi. Table S3 Family level classification of taxonomic composition in Polok and Reshi. Table S4 Genus level classification of taxonomic composition in Polok and Reshi. Table S5 Species distribution in Polok and Reshi. Table S6 Psychrophiles, mesophiles, and thermophiles in the metagenome. Table S7 Pearson product moment correlation among the species detected in the metagenome. Table S8 Principle Component analysis at species level. Table S9 Metagenomic ORFs assigned to different COG categories. Table S10 Metagenomic ORFs assigned to different KEGG Categories. Table S11 ORFs associated with nitrogen regulating genes in the metagenome. Table S12 ORFs associated with sulfur metabolism genes in the metagenome. Table S13 ORFs associated with methane metabolism genes in the metagenome. Table S14 Genes associated with antibiotic biosynthesis in the metagenome. Table S15 ORFs associated with antibiotic resistance genes in the metagenome from KEGG and CARD database. Table S16 Putative antibiotics resistance genes and their possible source microbial genera from CARD database. Table S17 Different CAZymes in the metagenome. Table S18 ORFs associated with COG functions.
DOI: 10.6084/m9.figshare.12788787.v1
title: Additional file 1 of Evolution and development of three highly specialized floral structures of bee-pollinated Phalaenopsis species

description: Additional file 1: Table S1. List of primers used for semi quantitative RT PCR analysis. Table S2. List of Phalaenopsis sequences generated from transcriptome analysis. Table S3. List of sequences used for phylogenetic analyses. Table S4. Results of differential gene expression of MADS-box gene analyses using DESeq in R. Table S5. Results of differential gene expression of MYB and TCP genes analyses using DESeq in R.
DOI: 10.6084/m9.figshare.12788757
title: Additional file 5 of Biomethanation processes: new insights on the effect of a high H2 partial pressure on microbial communities

description: Additional file 5: The results of the preliminary experiment.
DOI: 10.6084/m9.figshare.12788757.v1
title: Additional file 5 of Biomethanation processes: new insights on the effect of a high H2 partial pressure on microbial communities

description: Additional file 5: The results of the preliminary experiment.
DOI: 10.6084/m9.figshare.12788745
title: Additional file 1 of Biomethanation processes: new insights on the effect of a high H2 partial pressure on microbial communities

description: Additional file 1: The reactors’ performances results and qPCR results.
DOI: 10.6084/m9.figshare.12788745.v1
title: Additional file 1 of Biomethanation processes: new insights on the effect of a high H2 partial pressure on microbial communities

description: Additional file 1: The reactors’ performances results and qPCR results.
DOI: 10.6084/m9.figshare.12788675
title: Table S19. comparison between adjusting and removing overlapped samples.xlsx

description: Table S19. comparison between adjusting and removing overlapped samples.xlsx
DOI: 10.6084/m9.figshare.12788665
title: Additional file 8 of ImmunoGlobe: enabling systems immunology with a manually curated intercellular immune interaction network

description: Additional file 8: File S1. Interactive ImmunoGlobe network as Cytoscape file
DOI: 10.6084/m9.figshare.12788675.v1
title: Table S19. comparison between adjusting and removing overlapped samples.xlsx

description: Table S19. comparison between adjusting and removing overlapped samples.xlsx
DOI: 10.6084/m9.figshare.12788668
title: Additional file 9 of ImmunoGlobe: enabling systems immunology with a manually curated intercellular immune interaction network

description: Additional file 9: File S2. ImmunoGlobe ontology XML file
DOI: 10.6084/m9.figshare.12788668.v1
title: Additional file 9 of ImmunoGlobe: enabling systems immunology with a manually curated intercellular immune interaction network

description: Additional file 9: File S2. ImmunoGlobe ontology XML file
DOI: 10.6084/m9.figshare.12788659
title: Additional file 6 of ImmunoGlobe: enabling systems immunology with a manually curated intercellular immune interaction network

description: Additional file 6: Table S5. Search terms used to generate immuneXpresso comparison network
DOI: 10.6084/m9.figshare.12788662
title: Additional file 7 of ImmunoGlobe: enabling systems immunology with a manually curated intercellular immune interaction network

description: Additional file 7: Table S6. Multiple edge types between pairs of nodes
DOI: 10.6084/m9.figshare.12788662.v1
title: Additional file 7 of ImmunoGlobe: enabling systems immunology with a manually curated intercellular immune interaction network

description: Additional file 7: Table S6. Multiple edge types between pairs of nodes
DOI: 10.6084/m9.figshare.12788665.v1
title: Additional file 8 of ImmunoGlobe: enabling systems immunology with a manually curated intercellular immune interaction network

description: Additional file 8: File S1. Interactive ImmunoGlobe network as Cytoscape file
DOI: 10.6084/m9.figshare.12788647
title: Additional file 2 of ImmunoGlobe: enabling systems immunology with a manually curated intercellular immune interaction network

description: Additional file 2: Table S1. Complete immune interaction table.
DOI: 10.6084/m9.figshare.12788650
title: Additional file 3 of ImmunoGlobe: enabling systems immunology with a manually curated intercellular immune interaction network

description: Additional file 3: Table S2. Node Attributes table.
DOI: 10.6084/m9.figshare.12788653
title: Additional file 4 of ImmunoGlobe: enabling systems immunology with a manually curated intercellular immune interaction network

description: Additional file 4: Table S3. Final Edge List used to generate ImmunoGlobe network.
DOI: 10.6084/m9.figshare.12788656
title: Additional file 5 of ImmunoGlobe: enabling systems immunology with a manually curated intercellular immune interaction network

description: Additional file 5: Table S4. Catalog of differences between mouse and human immune systems.
DOI: 10.6084/m9.figshare.12788650.v1
title: Additional file 3 of ImmunoGlobe: enabling systems immunology with a manually curated intercellular immune interaction network

description: Additional file 3: Table S2. Node Attributes table.
DOI: 10.6084/m9.figshare.12788656.v1
title: Additional file 5 of ImmunoGlobe: enabling systems immunology with a manually curated intercellular immune interaction network

description: Additional file 5: Table S4. Catalog of differences between mouse and human immune systems.
DOI: 10.6084/m9.figshare.12788659.v1
title: Additional file 6 of ImmunoGlobe: enabling systems immunology with a manually curated intercellular immune interaction network

description: Additional file 6: Table S5. Search terms used to generate immuneXpresso comparison network
DOI: 10.6084/m9.figshare.12788653.v1
title: Additional file 4 of ImmunoGlobe: enabling systems immunology with a manually curated intercellular immune interaction network

description: Additional file 4: Table S3. Final Edge List used to generate ImmunoGlobe network.
DOI: 10.6084/m9.figshare.12788647.v1
title: Additional file 2 of ImmunoGlobe: enabling systems immunology with a manually curated intercellular immune interaction network

description: Additional file 2: Table S1. Complete immune interaction table.
DOI: 10.6084/m9.figshare.12788571
title: Additional file 2 of An evolutionary driver of interspersed segmental duplications in primates

description: Additional file 2: Table S1. List of large-insert clones from OWM, NWM and prosimian lineages. Table S2. List of LCR16a positive clones from apes. Table S3. Sequence contigs generated using large-insert BAC clones. Table S4. Characteristics of LCR16a-associated duplications. Table S5. dN/dS ratio analysis (synonymous/nonsynonymous) for individual NPIP exons. Table S6. Primer sequences for BAC hybridization probes. Table S7. Primer sequences for RT-PCR expression experiments. Table S8. Oligonucleotide capture probes used for Iso-Seq analysis.
DOI: 10.6084/m9.figshare.12788571.v1
title: Additional file 2 of An evolutionary driver of interspersed segmental duplications in primates

description: Additional file 2: Table S1. List of large-insert clones from OWM, NWM and prosimian lineages. Table S2. List of LCR16a positive clones from apes. Table S3. Sequence contigs generated using large-insert BAC clones. Table S4. Characteristics of LCR16a-associated duplications. Table S5. dN/dS ratio analysis (synonymous/nonsynonymous) for individual NPIP exons. Table S6. Primer sequences for BAC hybridization probes. Table S7. Primer sequences for RT-PCR expression experiments. Table S8. Oligonucleotide capture probes used for Iso-Seq analysis.
DOI: 10.6084/m9.figshare.12788550
title: Additional file 1 of Intra- and inter-rater reliability of thoracic spine mobility and posture assessments in subjects with thoracic spine pain

description: Additional file 1. Additional Figure. 1–7. Bland–Altman plot for agreement of posture inspection in standing (1A and 1B), posture inspection in sitting (2A and 2B), segmental mobility into flexion (3A and 3B), segmental mobility into extension (4A and 4B), posterior to anterior pressure (5A and 5B), inclination of T1–6 in standing (6A and 6B), inclination of T6–12 in standing (7A and 7B), inclination of T1–12 in standing (8A and 8B), inclination of T1–6 in sitting (9A and 9B), inclination of T6–12 in sitting (10A and 10B), inclination of T1–12 in sitting (11A and 11B), C7–T5 flexion mobility (12A and 12B), Schober in neutral (13A and 13B), Schober in flexion (14A and 14B), Schober in extension (15A and 15B), flexion mobility of the T1–6 in sitting (16A and 16B), flexion mobility of the T6–12 in sitting (17A and 17B), flexion mobility of the T1–12 in sitting (18A and 18B), extension mobility of the T1–6 in sitting (19A and 19B), extension mobility of the T6–12 in sitting (20A and 20B) and extension mobility of the T1–12 in sitting (21A and 21B) between raters (A) and within rater (B). The red lines depict the mean difference between raters and dotted green lines depict 95% limits of agreement in the Bland–Altman plot.
DOI: 10.6084/m9.figshare.12788550.v1
title: Additional file 1 of Intra- and inter-rater reliability of thoracic spine mobility and posture assessments in subjects with thoracic spine pain

description: Additional file 1. Additional Figure. 1–7. Bland–Altman plot for agreement of posture inspection in standing (1A and 1B), posture inspection in sitting (2A and 2B), segmental mobility into flexion (3A and 3B), segmental mobility into extension (4A and 4B), posterior to anterior pressure (5A and 5B), inclination of T1–6 in standing (6A and 6B), inclination of T6–12 in standing (7A and 7B), inclination of T1–12 in standing (8A and 8B), inclination of T1–6 in sitting (9A and 9B), inclination of T6–12 in sitting (10A and 10B), inclination of T1–12 in sitting (11A and 11B), C7–T5 flexion mobility (12A and 12B), Schober in neutral (13A and 13B), Schober in flexion (14A and 14B), Schober in extension (15A and 15B), flexion mobility of the T1–6 in sitting (16A and 16B), flexion mobility of the T6–12 in sitting (17A and 17B), flexion mobility of the T1–12 in sitting (18A and 18B), extension mobility of the T1–6 in sitting (19A and 19B), extension mobility of the T6–12 in sitting (20A and 20B) and extension mobility of the T1–12 in sitting (21A and 21B) between raters (A) and within rater (B). The red lines depict the mean difference between raters and dotted green lines depict 95% limits of agreement in the Bland–Altman plot.
DOI: 10.6084/m9.figshare.12788508
title: Additional file 1 of SILEX: a fast and inexpensive high-quality DNA extraction method suitable for multiple sequencing platforms and recalcitrant plant species

description: Additional file 1. Detailed cost per sample extracted for all solutions, reagents and consumables used for SILEX workflow.
DOI: 10.6084/m9.figshare.12788508.v1
title: Additional file 1 of SILEX: a fast and inexpensive high-quality DNA extraction method suitable for multiple sequencing platforms and recalcitrant plant species

description: Additional file 1. Detailed cost per sample extracted for all solutions, reagents and consumables used for SILEX workflow.
DOI: 10.6084/m9.figshare.12788476
title: Additional file 2 of Climate and tree seed production predict the abundance of the European Lyme disease vector over a 15-year period

description: Additional file 2: Table S1. Raw data used for all statistical analyses.
DOI: 10.6084/m9.figshare.12788476.v1
title: Additional file 2 of Climate and tree seed production predict the abundance of the European Lyme disease vector over a 15-year period

description: Additional file 2: Table S1. Raw data used for all statistical analyses.
DOI: 10.6084/m9.figshare.12788467
title: Additional file 9 of A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex

description: Additional file 9: Table S8. SnpEff annotation for derived alleles in LUND1.
DOI: 10.6084/m9.figshare.12788458
title: Additional file 6 of A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex

description: Additional file 6: Table S5. List of genomes included in the L4 dataset, with respective publications, accession numbers, lineages, dates, and percentage of total SNPs called as heterozygous.
DOI: 10.6084/m9.figshare.12788461
title: Additional file 7 of A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex

description: Additional file 7: Table S6. List of sites excluded from the full MTBC dataset in GFF format.
DOI: 10.6084/m9.figshare.12788464
title: Additional file 8 of A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex

description: Additional file 8: Table S7. List of sites excluded from the L4 dataset in GFF format.
DOI: 10.6084/m9.figshare.12788467.v1
title: Additional file 9 of A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex

description: Additional file 9: Table S8. SnpEff annotation for derived alleles in LUND1.
DOI: 10.6084/m9.figshare.12788452
title: Additional file 4 of A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex

description: Additional file 4: Table S3. Full EAGER pipeline results for negative controls processed with LUND1, mapped to the reconstructed TB ancestor genome.
DOI: 10.6084/m9.figshare.12788455
title: Additional file 5 of A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex

description: Additional file 5: Table S4. List of genomes included in the full MTBC dataset, with respective publications, accession numbers, lineages, and dates (when applicable).
DOI: 10.6084/m9.figshare.12788452.v1
title: Additional file 4 of A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex

description: Additional file 4: Table S3. Full EAGER pipeline results for negative controls processed with LUND1, mapped to the reconstructed TB ancestor genome.
DOI: 10.6084/m9.figshare.12788455.v1
title: Additional file 5 of A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex

description: Additional file 5: Table S4. List of genomes included in the full MTBC dataset, with respective publications, accession numbers, lineages, and dates (when applicable).
DOI: 10.6084/m9.figshare.12788461.v1
title: Additional file 7 of A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex

description: Additional file 7: Table S6. List of sites excluded from the full MTBC dataset in GFF format.
DOI: 10.6084/m9.figshare.12788464.v1
title: Additional file 8 of A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex

description: Additional file 8: Table S7. List of sites excluded from the L4 dataset in GFF format.
DOI: 10.6084/m9.figshare.12788446
title: Additional file 2 of A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex

description: Additional file 2: Table S2. Full EAGER pipeline results for LUND1 shotgun sequencing data when mapped to HG19 human reference genome and TB ancestor genome, the non-UDG-treated enriched LUND1 data when mapped to the TB ancestor genome, and the UDG-treated enriched LUND1 data when mapped to the TB ancestor genome.
DOI: 10.6084/m9.figshare.12788458.v1
title: Additional file 6 of A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex

description: Additional file 6: Table S5. List of genomes included in the L4 dataset, with respective publications, accession numbers, lineages, dates, and percentage of total SNPs called as heterozygous.
DOI: 10.6084/m9.figshare.12788443
title: Additional file 1 of A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex

description: Additional file 1: Table S1. Assigned reads from all taxonomic levels represented in the metagenomic LUND1 library prior to in-solution capture for MTBC DNA.