cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11806179.v3
title: Database of Neoproterozoic U-Pb geochronology and Hf isotopic data for the Adelaide Superbasin

description: This excel file contains all the relevant raw and processed zircon age data with an explanation of the formulas used, references and sample location data. <br><br>The paper interpreting this data is submitted to Precambrian Research.<br><br>Version 2 contains corrections to samples PR5 and PR6 that should have been Wilmington Formation and Bonney Sandstone respectively<br><br>Version 3 contains revisions to the formulas and the addition of some data (including Hf) from Keeman et al. 2020.<br>The information sheet has been further updated. The data in V3 was used to generate all figures in Lloyd et al. 2020 (Precambrian Research, revisions submitted). RefID: 9 is new data published with this database and accompanying paper.<br>
DOI: 10.6084/m9.figshare.11806134
title: Patient 15 for Nick

description: Patient 15 AND the list of CPMG data for all patients
DOI: 10.6084/m9.figshare.11806134.v2
title: Patient 15 for Nick

description: Patient 15 AND the list of CPMG data for all patients
DOI: 10.6084/m9.figshare.11806134.v1
title: Patient 15 for Nick

description: Patient 15 AND the list of CPMG data for all patients
DOI: 10.6084/m9.figshare.11805732
title: Additional file 3 of A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preference

description: Additional file 3 : Figure S1. Quality scores and accuracy of Illumina Hiseq 100-bp paired end reads for H. caudiculatum and H. dentatum after quality filters. Bad quality reads that showed values 20 on the histogram were discarded. All reads above the value of 30 indicates 99.9% of accuracy, regarding to bases correctly read by the sequencer, Figure S2. Training progress of the average distances of genes of H. caudiculatum and H. dentatum using Self-Organizing Maps showing the effect of neighborhood shrinking to include the winning unit, i.e., when the vectors in the dataset reach the closest similarity. Figure S3. Codebbook vectors for H. caudiculatum and H. dentatum showing the clusters of differentially expresed genes with maximum neighbouring after training process. The codebook vectors represent the expression profile of genes associated to a given state after the constructionof the map
DOI: 10.6084/m9.figshare.11805738
title: Additional file 4 of A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preference

description: Additional file 4: Dataset S6. Compiled GO enrichment data for H. caudiculatum, Dataset S7. Compiled GO enrichment data for H. dentatum.
DOI: 10.6084/m9.figshare.11805738.v1
title: Additional file 4 of A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preference

description: Additional file 4: Dataset S6. Compiled GO enrichment data for H. caudiculatum, Dataset S7. Compiled GO enrichment data for H. dentatum.
DOI: 10.6084/m9.figshare.11805726
title: Additional file 1 of A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preference

description: Additional file 1: Table S1. Statistics for RNA-seq libraries sequencing of H. caudiculatum (Hca) and H. dentatum (Hdent) for each of their hydrated states. Statistics shows total number of reads (No. of reads), high quality reads that passed quality control (No. of HQ reads), reads that were mapped to transcriptomes (No. of mapped reads) and their percentage of mapping (Mapping rate) Table S2. Assembly statistics for H. caudiculatum and H. dentatum transcriptomes before (raw) and after refinement (filtered). The total number of transcripts (No. transcripts), number of trinity components (Trinity components), putative transcriptome in mega base pairs (Transcriptome Size), basic statistics on transcript lengths (Average, median, minimum and maximum) and assembly quality as N50 (N50) Table S3. Blast results for H. caudiculatum and H. dentatum against SwissProt database. Table shows the counts distribution per sequence size (Size range) of blast hit (Blast Hit) and missing hits (Unknow) and the cumulative percentages (Cums %)
DOI: 10.6084/m9.figshare.11805729
title: Additional file 2 of A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preference

description: Additional file 2: Dataset S1. Matrix of the DE genes among pairwise comparissons between frond's hydration states of H. caudiculatum. Columns indicates de sequnce ID (id), fold change (log FC), counts per million (log CPM), the significance (PValue), the false discovery rate value (FDR), and the normalized counts for each hydration state (HcaFH.matrix, HcaD.matrix, and HcaRH.matrix), Dataset S2. Matrix of the DE genes among pairwise comparissons between frond's hydration states of H. dentatum. Columns indicates de sequnce ID (id), fold change (log FC), counts per million (log CPM), the significance (PValue), the false discovery rate value (FDR), and the normalized counts for each hydration state (HdFH, HdD, and HdRH), Dataset S3. Matrix showing those highly abundant genes without significant changes between frond's hydration states of H. caudiculatum and H. dentatum. Columns shows the gene id, transcript id, the counts abundance for each hydration state, the UniProt ID, the percentage of similitud of the Blast query, and the Protein Name, Dataset S4. Matrix of the Self-Organizing Maps output for the Nodes 2, 3 and 6 for H. caudiculatum, Dataset S5. Matrix of the Self-Organizing Maps output for the Nodes 1, 2 and 4 to 6 for H. dentatum.
DOI: 10.6084/m9.figshare.11805729.v1
title: Additional file 2 of A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preference

description: Additional file 2: Dataset S1. Matrix of the DE genes among pairwise comparissons between frond's hydration states of H. caudiculatum. Columns indicates de sequnce ID (id), fold change (log FC), counts per million (log CPM), the significance (PValue), the false discovery rate value (FDR), and the normalized counts for each hydration state (HcaFH.matrix, HcaD.matrix, and HcaRH.matrix), Dataset S2. Matrix of the DE genes among pairwise comparissons between frond's hydration states of H. dentatum. Columns indicates de sequnce ID (id), fold change (log FC), counts per million (log CPM), the significance (PValue), the false discovery rate value (FDR), and the normalized counts for each hydration state (HdFH, HdD, and HdRH), Dataset S3. Matrix showing those highly abundant genes without significant changes between frond's hydration states of H. caudiculatum and H. dentatum. Columns shows the gene id, transcript id, the counts abundance for each hydration state, the UniProt ID, the percentage of similitud of the Blast query, and the Protein Name, Dataset S4. Matrix of the Self-Organizing Maps output for the Nodes 2, 3 and 6 for H. caudiculatum, Dataset S5. Matrix of the Self-Organizing Maps output for the Nodes 1, 2 and 4 to 6 for H. dentatum.
DOI: 10.6084/m9.figshare.11805732.v1
title: Additional file 3 of A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preference

description: Additional file 3 : Figure S1. Quality scores and accuracy of Illumina Hiseq 100-bp paired end reads for H. caudiculatum and H. dentatum after quality filters. Bad quality reads that showed values 20 on the histogram were discarded. All reads above the value of 30 indicates 99.9% of accuracy, regarding to bases correctly read by the sequencer, Figure S2. Training progress of the average distances of genes of H. caudiculatum and H. dentatum using Self-Organizing Maps showing the effect of neighborhood shrinking to include the winning unit, i.e., when the vectors in the dataset reach the closest similarity. Figure S3. Codebbook vectors for H. caudiculatum and H. dentatum showing the clusters of differentially expresed genes with maximum neighbouring after training process. The codebook vectors represent the expression profile of genes associated to a given state after the constructionof the map
DOI: 10.6084/m9.figshare.11805726.v1
title: Additional file 1 of A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preference

description: Additional file 1: Table S1. Statistics for RNA-seq libraries sequencing of H. caudiculatum (Hca) and H. dentatum (Hdent) for each of their hydrated states. Statistics shows total number of reads (No. of reads), high quality reads that passed quality control (No. of HQ reads), reads that were mapped to transcriptomes (No. of mapped reads) and their percentage of mapping (Mapping rate) Table S2. Assembly statistics for H. caudiculatum and H. dentatum transcriptomes before (raw) and after refinement (filtered). The total number of transcripts (No. transcripts), number of trinity components (Trinity components), putative transcriptome in mega base pairs (Transcriptome Size), basic statistics on transcript lengths (Average, median, minimum and maximum) and assembly quality as N50 (N50) Table S3. Blast results for H. caudiculatum and H. dentatum against SwissProt database. Table shows the counts distribution per sequence size (Size range) of blast hit (Blast Hit) and missing hits (Unknow) and the cumulative percentages (Cums %)
DOI: 10.6084/m9.figshare.11805681
title: Additional file 8 of Targeted next-generation sequencing identifies novel variants in candidate genes for Parkinson’s disease in Black South African and Nigerian patients

description: Additional file 8: Table S5. Sequence variants found in the known PD genes.
DOI: 10.6084/m9.figshare.11805672
title: Additional file 5 of Genomic analysis of Spanish wheat landraces reveals their variability and potential for breeding

description: Additional file 5. File with the T. aestivum accession raw SNP genotyping results.
DOI: 10.6084/m9.figshare.11805672.v1
title: Additional file 5 of Genomic analysis of Spanish wheat landraces reveals their variability and potential for breeding

description: Additional file 5. File with the T. aestivum accession raw SNP genotyping results.
DOI: 10.6084/m9.figshare.11805681.v1
title: Additional file 8 of Targeted next-generation sequencing identifies novel variants in candidate genes for Parkinson’s disease in Black South African and Nigerian patients

description: Additional file 8: Table S5. Sequence variants found in the known PD genes.
DOI: 10.6084/m9.figshare.11805648
title: Additional file 3 of Targeted next-generation sequencing identifies novel variants in candidate genes for Parkinson’s disease in Black South African and Nigerian patients

description: Additional file 3: Table S3. Intron regions covered as part of the exon targets.
DOI: 10.6084/m9.figshare.11805651
title: Additional file 4 of Genomic analysis of Spanish wheat landraces reveals their variability and potential for breeding

description: Additional file 4. File with the T. aestivum accession raw DArT genotyping results.
DOI: 10.6084/m9.figshare.11805648.v1
title: Additional file 3 of Targeted next-generation sequencing identifies novel variants in candidate genes for Parkinson’s disease in Black South African and Nigerian patients

description: Additional file 3: Table S3. Intron regions covered as part of the exon targets.
DOI: 10.6084/m9.figshare.11805651.v1
title: Additional file 4 of Genomic analysis of Spanish wheat landraces reveals their variability and potential for breeding

description: Additional file 4. File with the T. aestivum accession raw DArT genotyping results.
DOI: 10.6084/m9.figshare.11805645
title: Additional file 2 of Targeted next-generation sequencing identifies novel variants in candidate genes for Parkinson’s disease in Black South African and Nigerian patients

description: Additional file 2: Table S2. Neurological Research panel information provided by Ion AmpliSeq™ (www.ampliseq.com).
DOI: 10.6084/m9.figshare.11805645.v1
title: Additional file 2 of Targeted next-generation sequencing identifies novel variants in candidate genes for Parkinson’s disease in Black South African and Nigerian patients

description: Additional file 2: Table S2. Neurological Research panel information provided by Ion AmpliSeq™ (www.ampliseq.com).
DOI: 10.6084/m9.figshare.11805633
title: Additional file 3 of Genomic analysis of Spanish wheat landraces reveals their variability and potential for breeding

description: Additional file 3. File with the T. durum accession raw SNP genotyping results.
DOI: 10.6084/m9.figshare.11805633.v1
title: Additional file 3 of Genomic analysis of Spanish wheat landraces reveals their variability and potential for breeding

description: Additional file 3. File with the T. durum accession raw SNP genotyping results.
DOI: 10.6084/m9.figshare.11805615
title: Additional file 1 of Genomic analysis of Spanish wheat landraces reveals their variability and potential for breeding

description: Additional file 1. Excel file with the description of the accessions analyzed, passport data, population according to fastSTRUCTURE analysis, HMW-GS and VRN-A1 alleles. Sheet 1. Durum wheat. Sheet 2. Bread wheat. Sheet 3. Reference set.
DOI: 10.6084/m9.figshare.11805618
title: Additional file 2 of Genomic analysis of Spanish wheat landraces reveals their variability and potential for breeding

description: Additional file 2. File with the T. durum accession raw DArT genotyping results.
DOI: 10.6084/m9.figshare.11805615.v1
title: Additional file 1 of Genomic analysis of Spanish wheat landraces reveals their variability and potential for breeding

description: Additional file 1. Excel file with the description of the accessions analyzed, passport data, population according to fastSTRUCTURE analysis, HMW-GS and VRN-A1 alleles. Sheet 1. Durum wheat. Sheet 2. Bread wheat. Sheet 3. Reference set.
DOI: 10.6084/m9.figshare.11805618.v1
title: Additional file 2 of Genomic analysis of Spanish wheat landraces reveals their variability and potential for breeding

description: Additional file 2. File with the T. durum accession raw DArT genotyping results.
DOI: 10.6084/m9.figshare.11805552
title: Additional file 7 of Genetic diversity of Plasmodium vivax and Plasmodium falciparum lactate dehydrogenases in Myanmar isolates

description: Additional file 7: Table S5. Potential changes of in the stability of PfLDH caused by 19 mutations using three different predictors.
DOI: 10.6084/m9.figshare.11805552.v1
title: Additional file 7 of Genetic diversity of Plasmodium vivax and Plasmodium falciparum lactate dehydrogenases in Myanmar isolates

description: Additional file 7: Table S5. Potential changes of in the stability of PfLDH caused by 19 mutations using three different predictors.
DOI: 10.6084/m9.figshare.11805540
title: Additional file 6 of Genetic diversity of Plasmodium vivax and Plasmodium falciparum lactate dehydrogenases in Myanmar isolates

description: Additional file 6: Table S4. Potential changes of in the stability of PvLDH caused by 36 mutations using three different predictors.
DOI: 10.6084/m9.figshare.11805540.v1
title: Additional file 6 of Genetic diversity of Plasmodium vivax and Plasmodium falciparum lactate dehydrogenases in Myanmar isolates

description: Additional file 6: Table S4. Potential changes of in the stability of PvLDH caused by 36 mutations using three different predictors.
DOI: 10.6084/m9.figshare.11805507
title: Additional file 3 of Genetic diversity of Plasmodium vivax and Plasmodium falciparum lactate dehydrogenases in Myanmar isolates

description: Additional file 3: Table S3. The homology modeling templates (Top 40 hits).
DOI: 10.6084/m9.figshare.11805507.v1
title: Additional file 3 of Genetic diversity of Plasmodium vivax and Plasmodium falciparum lactate dehydrogenases in Myanmar isolates

description: Additional file 3: Table S3. The homology modeling templates (Top 40 hits).
DOI: 10.6084/m9.figshare.11805501
title: Additional file 2 of Genetic diversity of Plasmodium vivax and Plasmodium falciparum lactate dehydrogenases in Myanmar isolates

description: Additional file 2: Table S2. Accession numbers of global PvLDH sequences.
DOI: 10.6084/m9.figshare.11805495
title: Additional file 1 of Genetic diversity of Plasmodium vivax and Plasmodium falciparum lactate dehydrogenases in Myanmar isolates

description: Additional file 1: Table S1. Accession numbers of global PfLDH sequences.
DOI: 10.6084/m9.figshare.11805501.v1
title: Additional file 2 of Genetic diversity of Plasmodium vivax and Plasmodium falciparum lactate dehydrogenases in Myanmar isolates

description: Additional file 2: Table S2. Accession numbers of global PvLDH sequences.
DOI: 10.6084/m9.figshare.11805495.v1
title: Additional file 1 of Genetic diversity of Plasmodium vivax and Plasmodium falciparum lactate dehydrogenases in Myanmar isolates

description: Additional file 1: Table S1. Accession numbers of global PfLDH sequences.
DOI: 10.6084/m9.figshare.11805303
title: Additional file 9 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling

description: BIN code enrichment analysis on Venn gene lists. (XLSX 99 kb)
DOI: 10.6084/m9.figshare.11805300
title: Additional file 8 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling

description: Gene Ontology enrichment analysis of Biological Process category on Venn gene lists. (XLSX 307 kb)
DOI: 10.6084/m9.figshare.11805303.v1
title: Additional file 9 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling

description: BIN code enrichment analysis on Venn gene lists. (XLSX 99 kb)
DOI: 10.6084/m9.figshare.11805294
title: Additional file 7 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling

description: Functional categories representative of a response to WD. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.11805300.v1
title: Additional file 8 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling

description: Gene Ontology enrichment analysis of Biological Process category on Venn gene lists. (XLSX 307 kb)
DOI: 10.6084/m9.figshare.11805291
title: Additional file 6 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling

description: Differential expression analysis results per genotype, organ and week. (XLSX 27292 kb)
DOI: 10.6084/m9.figshare.11805291.v1
title: Additional file 6 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling

description: Differential expression analysis results per genotype, organ and week. (XLSX 27292 kb)
DOI: 10.6084/m9.figshare.11805294.v1
title: Additional file 7 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling

description: Functional categories representative of a response to WD. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.11805285
title: Additional file 8 of Identifying glycan motifs using a novel subtree mining approach

description: Additional file 8 Motifs from GLYMMR and glycan motif miner. Motifs extracted using GLYMMR and Glycan Miner Tool for a range of glycan microarray datasets.
DOI: 10.6084/m9.figshare.11805285.v1
title: Additional file 8 of Identifying glycan motifs using a novel subtree mining approach

description: Additional file 8 Motifs from GLYMMR and glycan motif miner. Motifs extracted using GLYMMR and Glycan Miner Tool for a range of glycan microarray datasets.
DOI: 10.6084/m9.figshare.11805273
title: Additional file 6 of Identifying glycan motifs using a novel subtree mining approach

description: Additional file 6 Training and test sets. CSV files for all training and test sets used for this manuscript.
DOI: 10.6084/m9.figshare.11805276
title: Additional file 3 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling

description: Statistics for the long-term WD experiment from day 12 to day 20. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.11805270
title: Additional file 2 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling

description: Statistics for the WD recovery experiment at day 6 and 8. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.11805273.v1
title: Additional file 6 of Identifying glycan motifs using a novel subtree mining approach

description: Additional file 6 Training and test sets. CSV files for all training and test sets used for this manuscript.
DOI: 10.6084/m9.figshare.11805267
title: Additional file 5 of Identifying glycan motifs using a novel subtree mining approach

description: Additional file 5 Details on lectins examined in this study. Glycan microarray data used in this study was obtained from the CFG. This file provides additional details to TableÂ 1 on the datasets used throughout this work.
DOI: 10.6084/m9.figshare.11805276.v1
title: Additional file 3 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling

description: Statistics for the long-term WD experiment from day 12 to day 20. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.11805267.v1
title: Additional file 5 of Identifying glycan motifs using a novel subtree mining approach

description: Additional file 5 Details on lectins examined in this study. Glycan microarray data used in this study was obtained from the CFG. This file provides additional details to TableÂ 1 on the datasets used throughout this work.
DOI: 10.6084/m9.figshare.11805270.v1
title: Additional file 2 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling

description: Statistics for the WD recovery experiment at day 6 and 8. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.11805258
title: Additional file 19 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling

description: Primer list. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.11805258.v1
title: Additional file 19 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling

description: Primer list. (XLSX 9 kb)