cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26985616.v1
title: Additional file 1 of Dynamic changes in whole genome DNA methylation, chromatin and gene expression during mouse lens differentiation

description: Additional file 1: Table S1. Genic annotations, binomial rank, and binomial p-values of UMRs and LMRs associated with GO biological process terms shown in Fig. 4A. Mean RPKM of associated gene (data from [43]).
DOI: 10.6084/m9.figshare.26985619
title: Additional file 2 of Dynamic changes in whole genome DNA methylation, chromatin and gene expression during mouse lens differentiation

description: Additional file 2: Table S2. Complete GREAT gene ontology analysis output of reproducible demethylated regions in lens cells.
DOI: 10.6084/m9.figshare.26985619.v1
title: Additional file 2 of Dynamic changes in whole genome DNA methylation, chromatin and gene expression during mouse lens differentiation

description: Additional file 2: Table S2. Complete GREAT gene ontology analysis output of reproducible demethylated regions in lens cells.
DOI: 10.6084/m9.figshare.26985622
title: Additional file 3 of Dynamic changes in whole genome DNA methylation, chromatin and gene expression during mouse lens differentiation

description: Additional file 3: Table S3. Complete GREAT gene ontology analysis output of DMRs.
DOI: 10.6084/m9.figshare.26985622.v1
title: Additional file 3 of Dynamic changes in whole genome DNA methylation, chromatin and gene expression during mouse lens differentiation

description: Additional file 3: Table S3. Complete GREAT gene ontology analysis output of DMRs.
DOI: 10.6084/m9.figshare.26985625
title: Additional file 4 of Dynamic changes in whole genome DNA methylation, chromatin and gene expression during mouse lens differentiation

description: Additional file 4: Table S4. Complete GREAT gene ontology analysis output of H3.3 peaks.
DOI: 10.6084/m9.figshare.26985625.v1
title: Additional file 4 of Dynamic changes in whole genome DNA methylation, chromatin and gene expression during mouse lens differentiation

description: Additional file 4: Table S4. Complete GREAT gene ontology analysis output of H3.3 peaks.
DOI: 10.6084/m9.figshare.26985628
title: Additional file 5 of Dynamic changes in whole genome DNA methylation, chromatin and gene expression during mouse lens differentiation

description: Additional file 5: Table S5. Annotation including associated gene and genomic feature of intersections between DMRs and histone H3.3 peaks.
DOI: 10.6084/m9.figshare.26985628.v1
title: Additional file 5 of Dynamic changes in whole genome DNA methylation, chromatin and gene expression during mouse lens differentiation

description: Additional file 5: Table S5. Annotation including associated gene and genomic feature of intersections between DMRs and histone H3.3 peaks.
DOI: 10.6084/m9.figshare.26985637
title: Additional file 8 of Dynamic changes in whole genome DNA methylation, chromatin and gene expression during mouse lens differentiation

description: Additional file 8: Table S6. Complete lists of differentially methylated-accessible regions associated with DEGs for each of Epi(dif), EpiFiber(dif), Fiber(dif) and Epi(E14.5)Fiber (P0.5)(dif) path showing genomic feature and direction of change of methylation, chromatin accessibility, and gene expression.
DOI: 10.6084/m9.figshare.26985637.v1
title: Additional file 8 of Dynamic changes in whole genome DNA methylation, chromatin and gene expression during mouse lens differentiation

description: Additional file 8: Table S6. Complete lists of differentially methylated-accessible regions associated with DEGs for each of Epi(dif), EpiFiber(dif), Fiber(dif) and Epi(E14.5)Fiber (P0.5)(dif) path showing genomic feature and direction of change of methylation, chromatin accessibility, and gene expression.
DOI: 10.6084/m9.figshare.26985640
title: Additional file 9 of Dynamic changes in whole genome DNA methylation, chromatin and gene expression during mouse lens differentiation

description: Additional file 9: Table S7. Complete output of HOMER de novo motif search of path Epi(E14.5)Fiber (P0.5)(dif) hypomethylated DMRs.
DOI: 10.6084/m9.figshare.26985640.v1
title: Additional file 9 of Dynamic changes in whole genome DNA methylation, chromatin and gene expression during mouse lens differentiation

description: Additional file 9: Table S7. Complete output of HOMER de novo motif search of path Epi(E14.5)Fiber (P0.5)(dif) hypomethylated DMRs.
DOI: 10.6084/m9.figshare.26985652
title: Additional file 2 of High-resolution metagenomic reconstruction of the freshwater spring bloom

description: Additional file 2: Table S1. Microscopy data - Phytoplankton counts.
DOI: 10.6084/m9.figshare.26985652.v1
title: Additional file 2 of High-resolution metagenomic reconstruction of the freshwater spring bloom

description: Additional file 2: Table S1. Microscopy data - Phytoplankton counts.
DOI: 10.6084/m9.figshare.26985655
title: Additional file 3 of High-resolution metagenomic reconstruction of the freshwater spring bloom

description: Additional file 3: Table S2. General statistics and information about the bacterial MAGs.
DOI: 10.6084/m9.figshare.26985655.v1
title: Additional file 3 of High-resolution metagenomic reconstruction of the freshwater spring bloom

description: Additional file 3: Table S2. General statistics and information about the bacterial MAGs.
DOI: 10.6084/m9.figshare.26985658
title: Additional file 4 of High-resolution metagenomic reconstruction of the freshwater spring bloom

description: Additional file 4: Table S3. MAGs containing rhodopsins.
DOI: 10.6084/m9.figshare.26985658.v1
title: Additional file 4 of High-resolution metagenomic reconstruction of the freshwater spring bloom

description: Additional file 4: Table S3. MAGs containing rhodopsins.
DOI: 10.6084/m9.figshare.26985664
title: Additional file 5 of High-resolution metagenomic reconstruction of the freshwater spring bloom

description: Additional file 5: Table S4. Bacteriophage general information.
DOI: 10.6084/m9.figshare.26985664.v1
title: Additional file 5 of High-resolution metagenomic reconstruction of the freshwater spring bloom

description: Additional file 5: Table S4. Bacteriophage general information.
DOI: 10.6084/m9.figshare.26985667
title: Additional file 6 of High-resolution metagenomic reconstruction of the freshwater spring bloom

description: Additional file 6:Table S5. FISH counts in epilimnion and hypolimnion.
DOI: 10.6084/m9.figshare.26985667.v1
title: Additional file 6 of High-resolution metagenomic reconstruction of the freshwater spring bloom

description: Additional file 6:Table S5. FISH counts in epilimnion and hypolimnion.
DOI: 10.6084/m9.figshare.26985670
title: Additional file 7 of High-resolution metagenomic reconstruction of the freshwater spring bloom

description: Additional file 7: Table S6. Eukaryotic MAGs information.
DOI: 10.6084/m9.figshare.26985670.v1
title: Additional file 7 of High-resolution metagenomic reconstruction of the freshwater spring bloom

description: Additional file 7: Table S6. Eukaryotic MAGs information.
DOI: 10.6084/m9.figshare.26985673
title: Additional file 8 of High-resolution metagenomic reconstruction of the freshwater spring bloom

description: Additional file 8: Table S7. NCLDV abundances and general information.
DOI: 10.6084/m9.figshare.26985673.v1
title: Additional file 8 of High-resolution metagenomic reconstruction of the freshwater spring bloom

description: Additional file 8: Table S7. NCLDV abundances and general information.
DOI: 10.6084/m9.figshare.26985676
title: Additional file 9 of High-resolution metagenomic reconstruction of the freshwater spring bloom

description: Additional file 9: Table S8. Details of organellar genomes recovered.
DOI: 10.6084/m9.figshare.26985676.v1
title: Additional file 9 of High-resolution metagenomic reconstruction of the freshwater spring bloom

description: Additional file 9: Table S8. Details of organellar genomes recovered.
DOI: 10.6084/m9.figshare.26985679
title: Additional file 10 of High-resolution metagenomic reconstruction of the freshwater spring bloom

description: Additional file 10:Table S9. Characteristics of phylogenomic trees constructed using IQTREE2.
DOI: 10.6084/m9.figshare.26985679.v1
title: Additional file 10 of High-resolution metagenomic reconstruction of the freshwater spring bloom

description: Additional file 10:Table S9. Characteristics of phylogenomic trees constructed using IQTREE2.
DOI: 10.6084/m9.figshare.26985682
title: Additional file 11 of High-resolution metagenomic reconstruction of the freshwater spring bloom

description: Additional file 11: Table S10. Public datasets used in Fig. 4, pane D.
DOI: 10.6084/m9.figshare.26985682.v1
title: Additional file 11 of High-resolution metagenomic reconstruction of the freshwater spring bloom

description: Additional file 11: Table S10. Public datasets used in Fig. 4, pane D.
DOI: 10.6084/m9.figshare.26985685
title: Additional file 1 of Combined metabolic activators improve cognitive functions in Alzheimer’s disease patients: a randomised, double-blinded, placebo-controlled phase-II trial

description: Additional file 1: Dataset S1. Collection of samples of CMA and placebo groups and the measured values of clinical indicators before and after treatment.
DOI: 10.6084/m9.figshare.26985685.v1
title: Additional file 1 of Combined metabolic activators improve cognitive functions in Alzheimer’s disease patients: a randomised, double-blinded, placebo-controlled phase-II trial

description: Additional file 1: Dataset S1. Collection of samples of CMA and placebo groups and the measured values of clinical indicators before and after treatment.
DOI: 10.6084/m9.figshare.26985694
title: Additional file 4 of Combined metabolic activators improve cognitive functions in Alzheimer’s disease patients: a randomised, double-blinded, placebo-controlled phase-II trial

description: Additional file 4: Dataset S2. Statistical analysis of clinical indicators between different visits or groups.
DOI: 10.6084/m9.figshare.26985694.v1
title: Additional file 4 of Combined metabolic activators improve cognitive functions in Alzheimer’s disease patients: a randomised, double-blinded, placebo-controlled phase-II trial

description: Additional file 4: Dataset S2. Statistical analysis of clinical indicators between different visits or groups.
DOI: 10.6084/m9.figshare.26985700
title: Additional file 6 of Combined metabolic activators improve cognitive functions in Alzheimer’s disease patients: a randomised, double-blinded, placebo-controlled phase-II trial

description: Additional file 6: Dataset S3. Plasma metabolomics data for each patient before and after treatment and statistical analysis of plasma metabolites between different visits or groups.
DOI: 10.6084/m9.figshare.26985700.v1
title: Additional file 6 of Combined metabolic activators improve cognitive functions in Alzheimer’s disease patients: a randomised, double-blinded, placebo-controlled phase-II trial

description: Additional file 6: Dataset S3. Plasma metabolomics data for each patient before and after treatment and statistical analysis of plasma metabolites between different visits or groups.
DOI: 10.6084/m9.figshare.26985703
title: Additional file 7 of Combined metabolic activators improve cognitive functions in Alzheimer’s disease patients: a randomised, double-blinded, placebo-controlled phase-II trial

description: Additional file 7: Dataset S4. The association between the plasma level of the four supplements serine, carnitine, cysteine and nicotinamide riboside with the plasma levels of other metabolites.
DOI: 10.6084/m9.figshare.26985703.v1
title: Additional file 7 of Combined metabolic activators improve cognitive functions in Alzheimer’s disease patients: a randomised, double-blinded, placebo-controlled phase-II trial

description: Additional file 7: Dataset S4. The association between the plasma level of the four supplements serine, carnitine, cysteine and nicotinamide riboside with the plasma levels of other metabolites.
DOI: 10.6084/m9.figshare.26985706
title: Additional file 8 of Combined metabolic activators improve cognitive functions in Alzheimer’s disease patients: a randomised, double-blinded, placebo-controlled phase-II trial

description: Additional file 8: Dataset S5. Plasma proteomics data were generated with the Olink cardiometabolic, inflammation, neurology and oncology panels for each patient before and after treatment and statistical analysis of plasma proteins between different visits or groups.
DOI: 10.6084/m9.figshare.26985706.v1
title: Additional file 8 of Combined metabolic activators improve cognitive functions in Alzheimer’s disease patients: a randomised, double-blinded, placebo-controlled phase-II trial

description: Additional file 8: Dataset S5. Plasma proteomics data were generated with the Olink cardiometabolic, inflammation, neurology and oncology panels for each patient before and after treatment and statistical analysis of plasma proteins between different visits or groups.
DOI: 10.6084/m9.figshare.26985709
title: Additional file 9 of Combined metabolic activators improve cognitive functions in Alzheimer’s disease patients: a randomised, double-blinded, placebo-controlled phase-II trial

description: Additional file 9: Dataset S6. Multi-Omics Network Data, including edges and nodes information. The network is presented in the iNetModels ( http://inetmodels.com ).
DOI: 10.6084/m9.figshare.26985709.v1
title: Additional file 9 of Combined metabolic activators improve cognitive functions in Alzheimer’s disease patients: a randomised, double-blinded, placebo-controlled phase-II trial

description: Additional file 9: Dataset S6. Multi-Omics Network Data, including edges and nodes information. The network is presented in the iNetModels ( http://inetmodels.com ).
DOI: 10.6084/m9.figshare.26985712
title: Additional file 10 of Combined metabolic activators improve cognitive functions in Alzheimer’s disease patients: a randomised, double-blinded, placebo-controlled phase-II trial

description: Additional file 10: Dataset S7. Structural magnetic resonance imaging analysis results
DOI: 10.6084/m9.figshare.26985712.v1
title: Additional file 10 of Combined metabolic activators improve cognitive functions in Alzheimer’s disease patients: a randomised, double-blinded, placebo-controlled phase-II trial

description: Additional file 10: Dataset S7. Structural magnetic resonance imaging analysis results
DOI: 10.15468/dl.brw9jg
title: Occurrence Download

description: A dataset containing 1711 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil)"
 ]
 }
 },
 "TaxonKey is Ficus asperifolia Miq.",
 "Continent is Africa"
 ]
}

 The dataset includes 1711 records from 84 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011629-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.26985721
title: Additional file 1 of Folylpolyglutamate synthetase mRNA G-quadruplexes regulate its cell protrusion localization and enhance a cancer cell invasive phenotype upon folate repletion

description: Additional file 1: Table S1. G-quadruplex sequences found by QGRS Mapper in the 3'UTR of FPGS orthologs.
DOI: 10.6084/m9.figshare.26985721.v1
title: Additional file 1 of Folylpolyglutamate synthetase mRNA G-quadruplexes regulate its cell protrusion localization and enhance a cancer cell invasive phenotype upon folate repletion

description: Additional file 1: Table S1. G-quadruplex sequences found by QGRS Mapper in the 3'UTR of FPGS orthologs.
DOI: 10.6084/m9.figshare.26985769
title: Additional file 2 of Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication

description: Additional file 2. Sequence alignment and phylogenetic tree files for Fig. 1A, B, and Fig. 2F.
DOI: 10.6084/m9.figshare.26985772
title: Additional file 3 of Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication

description: Additional file 3 Synteny alignment for HPT1 and HPT2 across 7 Poales species.
DOI: 10.6084/m9.figshare.26985772.v1
title: Additional file 3 of Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication

description: Additional file 3 Synteny alignment for HPT1 and HPT2 across 7 Poales species.
DOI: 10.6084/m9.figshare.26985775
title: Additional file 4 of Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication

description: Additional file 4. SNP data for HPT2 in 300 barley pangenome lines and 109 Tibetan barley lines.
DOI: 10.6084/m9.figshare.26985769.v1
title: Additional file 2 of Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication

description: Additional file 2. Sequence alignment and phylogenetic tree files for Fig. 1A, B, and Fig. 2F.
DOI: 10.6084/m9.figshare.26985775.v1
title: Additional file 4 of Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication

description: Additional file 4. SNP data for HPT2 in 300 barley pangenome lines and 109 Tibetan barley lines.
DOI: 10.6084/m9.figshare.26985778
title: Additional file 5 of Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication

description: Additional file 5. PAML input and output files used for natural selection analysis in Table 1.
DOI: 10.6084/m9.figshare.26985778.v1
title: Additional file 5 of Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication

description: Additional file 5. PAML input and output files used for natural selection analysis in Table 1.
DOI: 10.6084/m9.figshare.26985781
title: Additional file 6 of Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication

description: Additional file 6. Phylogeny-based orthologous gene inference across barley, wild emmer, and bread wheat and calculated gene retention rate for each orthologous gene group (hierarchical orthologous gene group at node N1 in Fig. 4A).
DOI: 10.6084/m9.figshare.26985799
title: Additional file 12 of Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication

description: Additional file 12. Sequence alignment, phylogenetic trees, and natural selection analyses data for Fig. 5E-O.
DOI: 10.6084/m9.figshare.26985799.v1
title: Additional file 12 of Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication

description: Additional file 12. Sequence alignment, phylogenetic trees, and natural selection analyses data for Fig. 5E-O.
DOI: 10.6084/m9.figshare.26985802
title: Additional file 13 of Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication

description: Additional file 13. Gene annotation validation results of selected OGs genes in 15 wheat genome assemblies.
DOI: 10.6084/m9.figshare.26985802.v1
title: Additional file 13 of Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication

description: Additional file 13. Gene annotation validation results of selected OGs genes in 15 wheat genome assemblies.
DOI: 10.6084/m9.figshare.26985781.v1
title: Additional file 6 of Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication

description: Additional file 6. Phylogeny-based orthologous gene inference across barley, wild emmer, and bread wheat and calculated gene retention rate for each orthologous gene group (hierarchical orthologous gene group at node N1 in Fig. 4A).
DOI: 10.6084/m9.figshare.26985784
title: Additional file 7 of Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication

description: Additional file 7. Orthologous gene matrix (presence/absence) in barley, wild emmer, and bread wheat pangenome lines.
DOI: 10.6084/m9.figshare.26985805
title: Additional file 14 of Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication

description: Additional file 14. Original protoplast imaging files of barley.
DOI: 10.6084/m9.figshare.26985805.v1
title: Additional file 14 of Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication

description: Additional file 14. Original protoplast imaging files of barley.
DOI: 10.6084/m9.figshare.26985784.v1
title: Additional file 7 of Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication

description: Additional file 7. Orthologous gene matrix (presence/absence) in barley, wild emmer, and bread wheat pangenome lines.
DOI: 10.6084/m9.figshare.26985787
title: Additional file 8 of Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication

description: Additional file 8. List of the identified 326 HPT2-pattern-like genes (using barley as reference) and their corresponding gene retention rates in barley, wild emmer, and bread wheat.
DOI: 10.6084/m9.figshare.26985787.v1
title: Additional file 8 of Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication

description: Additional file 8. List of the identified 326 HPT2-pattern-like genes (using barley as reference) and their corresponding gene retention rates in barley, wild emmer, and bread wheat.
DOI: 10.6084/m9.figshare.26985790
title: Additional file 9 of Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication

description: Additional file 9. Gene duplication type data in Fig. 4C (326 HPT2-pattern-like genes) and Fig. 6B (three categories of genes).
DOI: 10.6084/m9.figshare.26985790.v1
title: Additional file 9 of Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication

description: Additional file 9. Gene duplication type data in Fig. 4C (326 HPT2-pattern-like genes) and Fig. 6B (three categories of genes).
DOI: 10.6084/m9.figshare.26985793
title: Additional file 10 of Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication

description: Additional file 10. Lists of identified genes and gene annotations used for functional enrichment analyses.
DOI: 10.6084/m9.figshare.26985793.v1
title: Additional file 10 of Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication

description: Additional file 10. Lists of identified genes and gene annotations used for functional enrichment analyses.