cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3704602_d1
title: Additional file 1: Table S1. of Differential Regulation of Starch-synthetic Gene Expression in Endosperm Between Indica and Japonica Rice Cultivars

description: List of primers used for expression analysis. (XLSX 31 kb)
DOI: 10.6084/m9.figshare.c.3704656_d1.v1
title: MOESM1 of De novo transcriptome assembly, functional annotation and differential gene expression analysis of juvenile and adult E. fetida, a model oligochaete used in ecotoxicological studies

description: Additional file 1: Table S1. Functional annotation of the Trinity generated transcriptome file.
DOI: 10.6084/m9.figshare.c.3704653_d1.v1
title: Additional file 6: Table S5. of Leaf transcriptome analysis of a subtropical evergreen broadleaf plant, wild oil-tea camellia (Camellia oleifera), revealing candidate genes for cold acclimation

description: Differentially expressed genes at T5 versus T10/T14/T18, showing gene sequences, gene expression levels in different temperature groups and details of functional annotations. (XLSX 46 kb)
DOI: 10.6084/m9.figshare.c.3704656_d1
title: MOESM1 of De novo transcriptome assembly, functional annotation and differential gene expression analysis of juvenile and adult E. fetida, a model oligochaete used in ecotoxicological studies

description: Additional file 1: Table S1. Functional annotation of the Trinity generated transcriptome file.
DOI: 10.6084/m9.figshare.c.3704635_d6.v1
title: Additional file 3: of Drug voyager: a computational platform for exploring unintended drug action

description: Predicted side effects of drugs. The list of 11,152 novel side effects of drugs spanning 39 drugs and 1,598 side effects. (XLSX 179 kb)
DOI: 10.6084/m9.figshare.c.3704653_d1
title: Additional file 6: Table S5. of Leaf transcriptome analysis of a subtropical evergreen broadleaf plant, wild oil-tea camellia (Camellia oleifera), revealing candidate genes for cold acclimation

description: Differentially expressed genes at T5 versus T10/T14/T18, showing gene sequences, gene expression levels in different temperature groups and details of functional annotations. (XLSX 46 kb)
DOI: 10.6084/m9.figshare.c.3704635_d6
title: Additional file 3: of Drug voyager: a computational platform for exploring unintended drug action

description: Predicted side effects of drugs. The list of 11,152 novel side effects of drugs spanning 39 drugs and 1,598 side effects. (XLSX 179 kb)
DOI: 10.6084/m9.figshare.c.3704653_d2.v1
title: Additional file 1: Table S1. of Leaf transcriptome analysis of a subtropical evergreen broadleaf plant, wild oil-tea camellia (Camellia oleifera), revealing candidate genes for cold acclimation

description: Primers designed for detecting simple sequence repeats (SSRs) in genes of Camellia oleifera. (XLSX 3329 kb)
DOI: 10.6084/m9.figshare.c.3704653_d2
title: Additional file 1: Table S1. of Leaf transcriptome analysis of a subtropical evergreen broadleaf plant, wild oil-tea camellia (Camellia oleifera), revealing candidate genes for cold acclimation

description: Primers designed for detecting simple sequence repeats (SSRs) in genes of Camellia oleifera. (XLSX 3329 kb)
DOI: 10.6084/m9.figshare.c.3704653_d5.v1
title: Additional file 4: Table S4. of Leaf transcriptome analysis of a subtropical evergreen broadleaf plant, wild oil-tea camellia (Camellia oleifera), revealing candidate genes for cold acclimation

description: Genes containing insertion/deletions (InDels) in Camellia oleifera. (XLSX 3536 kb)
DOI: 10.6084/m9.figshare.c.3704653_d4.v1
title: Additional file 2: Table S2. of Leaf transcriptome analysis of a subtropical evergreen broadleaf plant, wild oil-tea camellia (Camellia oleifera), revealing candidate genes for cold acclimation

description: Single nucleotide polymorphism (SNP) positions in genes of Camellia oleifera. Genotypes of samples from Jinggang (JG01-04) and Lu (LS01-04) mountains are shown. (XLSX 8324 kb)
DOI: 10.6084/m9.figshare.c.3705616_d2.v1
title: Additional file 2 of Conserved expression of transposon-derived non-coding transcripts in primate stem cells

description: Table of values for figures 1 and 2 and table 1. (TXT 1220 kb)
DOI: 10.6084/m9.figshare.c.3705616_d3.v1
title: Additional file 3 of Conserved expression of transposon-derived non-coding transcripts in primate stem cells

description: Table of coordinates for table 1. (TXT 869 kb)
DOI: 10.6084/m9.figshare.c.3705616_d2
title: Additional file 2 of Conserved expression of transposon-derived non-coding transcripts in primate stem cells

description: Table of values for figures 1 and 2 and table 1. (TXT 1220 kb)
DOI: 10.6084/m9.figshare.c.3706705_d4
title: Additional file 4 of Combining phylogenetic footprinting with motif models incorporating intra-motif dependencies

description: Tables of difference logos. The file contains for each of the 35 TFs a 10Ă 10 table of difference logos for a pair-wise visual comparison of species-specific motifs. (ZIP 26112 kb)
DOI: 10.6084/m9.figshare.c.3706705_d4.v1
title: Additional file 4 of Combining phylogenetic footprinting with motif models incorporating intra-motif dependencies

description: Tables of difference logos. The file contains for each of the 35 TFs a 10Ă 10 table of difference logos for a pair-wise visual comparison of species-specific motifs. (ZIP 26112 kb)
DOI: 10.6084/m9.figshare.c.3706753_d1.v1
title: Additional file 1: of Systems biology combining human- and animal-data miRNA and mRNA data identifies new targets in ureteropelvic junction obstruction

description: Differentially expressed miRNAs in human UPJ. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.c.3706753_d1
title: Additional file 1: of Systems biology combining human- and animal-data miRNA and mRNA data identifies new targets in ureteropelvic junction obstruction

description: Differentially expressed miRNAs in human UPJ. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.c.3706777_d2.v1
title: Additional file 2 of ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data

description: Simulated data inputs. An excel file containing bulk allele counts and single cell genotypes generated from the Generalized Dollo model used as input to ddClone and existing methods in simulation studies. These data were used to assess the performance of all methods considered in this study and resulted in Fig. 3. (XLSX 84 kb)
DOI: 10.6084/m9.figshare.c.3706786_d2.v1
title: Additional file 2 of Positive-Unlabeled Learning for inferring drug interactions based on heterogeneous attributes

description: The 589 inferred negatives for binary classification. This is Supplementary Table 1. (XLSX 18.1 kb)
DOI: 10.6084/m9.figshare.c.3706777_d2
title: Additional file 2 of ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data

description: Simulated data inputs. An excel file containing bulk allele counts and single cell genotypes generated from the Generalized Dollo model used as input to ddClone and existing methods in simulation studies. These data were used to assess the performance of all methods considered in this study and resulted in Fig. 3. (XLSX 84 kb)
DOI: 10.6084/m9.figshare.c.3706777_d3.v1
title: Additional file 3 of ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data

description: Real data inputs. An excel file containing bulk data allele counts and single cell genotypes from both TNBC xenograft and ITH HGSOvCa datasets used as input to ddClone and existing methods. These data were used to assess the performance of all methods considered in this study and resulted in Figs. 9 and 10. (XLSX 67 kb)
DOI: 10.6084/m9.figshare.c.3706786_d2
title: Additional file 2 of Positive-Unlabeled Learning for inferring drug interactions based on heterogeneous attributes

description: The 589 inferred negatives for binary classification. This is Supplementary Table 1. (XLSX 18.1 kb)
DOI: 10.6084/m9.figshare.c.3706786_d3.v1
title: Additional file 3 of Positive-Unlabeled Learning for inferring drug interactions based on heterogeneous attributes

description: The inferred 5892 DDIs and their probabilities. This is Supplementary Table 2. (XLSX 134 kb)
DOI: 10.6084/m9.figshare.c.3706777_d4.v1
title: Additional file 4 of ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data

description: Real data benchmarks. An excel file containing the multi-sample PyClone results for both TNBC xenograft and ITH HGSOvCa datasets used as benchmark to assess the performance of ddClone and existing methods. The performance metrics reported in Figs. 9 and 10 are measured against these results. (XLSX 32 kb)
DOI: 10.6084/m9.figshare.c.3706777_d3
title: Additional file 3 of ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data

description: Real data inputs. An excel file containing bulk data allele counts and single cell genotypes from both TNBC xenograft and ITH HGSOvCa datasets used as input to ddClone and existing methods. These data were used to assess the performance of all methods considered in this study and resulted in Figs. 9 and 10. (XLSX 67 kb)
DOI: 10.6084/m9.figshare.c.3706777_d4
title: Additional file 4 of ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data

description: Real data benchmarks. An excel file containing the multi-sample PyClone results for both TNBC xenograft and ITH HGSOvCa datasets used as benchmark to assess the performance of ddClone and existing methods. The performance metrics reported in Figs. 9 and 10 are measured against these results. (XLSX 32 kb)
DOI: 10.6084/m9.figshare.c.3706786_d3
title: Additional file 3 of Positive-Unlabeled Learning for inferring drug interactions based on heterogeneous attributes

description: The inferred 5892 DDIs and their probabilities. This is Supplementary Table 2. (XLSX 134 kb)
DOI: 10.6084/m9.figshare.c.3706777_d5.v1
title: Additional file 5 of ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data

description: List of mutually exclusive mutations (MEMs). A zip archive of five txt files that list the MEMs (see the main text) found in TNBC xenograft and ITH HGSOvCa datasets as well as the MEMs merged by PyClone and multi-sample PyClone. (ZIP 7 kb)
DOI: 10.6084/m9.figshare.c.3706786_d4.v1
title: Additional file 4 of Positive-Unlabeled Learning for inferring drug interactions based on heterogeneous attributes

description: The inferred 5300 CYP-Dependent DDIs and associating CYPs. This is Supplementary Table 3. (XLSX 177 kb)
DOI: 10.6084/m9.figshare.c.3706786_d4
title: Additional file 4 of Positive-Unlabeled Learning for inferring drug interactions based on heterogeneous attributes

description: The inferred 5300 CYP-Dependent DDIs and associating CYPs. This is Supplementary Table 3. (XLSX 177 kb)
DOI: 10.6084/m9.figshare.c.3706786_d5.v1
title: Additional file 5 of Positive-Unlabeled Learning for inferring drug interactions based on heterogeneous attributes

description: The inferred 592 CYP-Independent DDIs. This is Supplementary Table 4. (XLSX 18.2 kb)
DOI: 10.6084/m9.figshare.c.3706777_d5
title: Additional file 5 of ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data

description: List of mutually exclusive mutations (MEMs). A zip archive of five txt files that list the MEMs (see the main text) found in TNBC xenograft and ITH HGSOvCa datasets as well as the MEMs merged by PyClone and multi-sample PyClone. (ZIP 7 kb)
DOI: 10.6084/m9.figshare.c.3706786_d5
title: Additional file 5 of Positive-Unlabeled Learning for inferring drug interactions based on heterogeneous attributes

description: The inferred 592 CYP-Independent DDIs. This is Supplementary Table 4. (XLSX 18.2 kb)
DOI: 10.6084/m9.figshare.c.3706792_d3.v1
title: Additional file 3: Table S1. of A genome-wide analysis of the lysophosphatidate acyltransferase (LPAAT) gene family in cotton: organization, expression, sequence variation, and association with seed oil content and fiber quality

description: Sequences of primers used for studies of GhLPAAT expression. Table S2. Sequences of primers of GhLPAATs to identify single nucleotide polymorphic markers (SNPs) based on single strand conformation polymporphism (SSCP). Table S3. Domain analysis and annotation. Table S4. Oil and protein quantitative trait loci (QTL). Table S5. Identification of putative sequence variation (SNPs) by SOAPsnp in NMGA-062 vs. NMGA-105 database. L indicates SNP only exists in long fiber length line NMGA-062 (fiber length, 32.58 mm) when compared with the sequenced genome sequence of TM-1. S indicates SNP only exists in short fiber length line NMGA-105 (fiber length, 27.06 mm) when compared with the sequenced genome sequence of TM-1. L/S indicates SNP exists in the two lines. Table S6. Identification of putative SNPs by SOAPsnp in Xuzhou 142 vs. Xuzhou 142 fl database. WT indicates SNP only exists in Xuzhou 142 when compared with the sequenced genome sequence of TM-1. fl indicates SNP only exists in Xuzhou 142 fl when compared with the sequenced genome sequence of TM-1. WT/fl indicates SNP exists in the two lines. The polymorphic SSCP marker is shown in red color. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.c.3708169_d1.v1
title: Additional file 10: of Normalization and microbial differential abundance strategies depend upon data characteristics

description: Code adapted from McMurdie and Holmes [18] to include additional methods and compositional effects. This code is the basis for Figure 6.
DOI: 10.6084/m9.figshare.c.3708169_d1
title: Additional file 10: of Normalization and microbial differential abundance strategies depend upon data characteristics

description: Code adapted from McMurdie and Holmes [18] to include additional methods and compositional effects. This code is the basis for Figure 6.
DOI: 10.15468/dl.qjt74k
title: Occurrence Download

description: A dataset containing 353767 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((56.52908 26.43288,56.33957 25.62746,56.39879 24.76282,56.97324 24.02846,58.4108 23.5258,58.84451 23.30412,59.59628 22.30176,59.24931 21.47289,58.54573 20.87533,58.4108 20.43198,58.22768 20.71148,57.89035 20.43198,57.65903 19.91152,57.7265 19.03446,56.74342 18.88989,56.53138 18.40799,56.25188 18.07065,55.33626 17.84898,55.15314 17.54056,55.11458 17.24178,54.95074 17.04902,53.98693 17.0683,52.2328 16.3358,51.88583 15.83462,51.41357 15.372,49.59197 14.78407,48.72455 14.37928,48.44504 14.1576,46.73911 13.64678,45.1681 13.23235,44.98498 12.97212,44.24285 12.84682,43.77058 12.76008,43.38983 12.73815,43.41455 12.529,43.4285 12.41099,43.20151 12.57333,43.4053 12.02127,42.97644 11.7876,42.73079 11.75591,42.50891 11.51818,43.16662 11.51818,43.6884 10.96437,44.3584 10.40761,44.94819 10.35571,45.86522 10.69633,46.58086 10.57706,48.33021 11.07006,49.56271 11.24499,50.2545 11.41198,53.67655 14.06748,55.13864 15.40312,60.02015 17.37101,61.73449 17.70389,63.53205 22.78033,62.58334 24.87749,61.18524 25.14379,59.63734 25.39345,58.17266 25.50996,57.27388 25.89277,57.04702 26.76388,56.52908 26.43288))",
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 The dataset includes 353767 records from 357 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038600-241126133413365/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.c.3709237_d1.v1
title: Additional file 1: Table S1. of SAG-QC: quality control of single amplified genome information by subtracting non-target sequences based on sequence compositions

description: Sensitivity and specificity of our approach to discriminate non-target sequences. (XLSX 34 kb)ďťż
DOI: 10.6084/m9.figshare.c.3709237_d2.v1
title: Additional file 2: Table S2. of SAG-QC: quality control of single amplified genome information by subtracting non-target sequences based on sequence compositions

description: List of taxa confirmed from contigs of E. coli SAGs and no template control. (XLSX 60 kb)
DOI: 10.6084/m9.figshare.c.3709270_d5.v1
title: Additional file 1: of Comparative analyses of glycerotoxin expression unveil a novel structural organization of the bloodworm venom system

description: Position of short amino acid sequences alongside the GLTx full-length transcripts. Short amino acid sequences were recovered through protein sequencing of purified glycerotoxin extracted out of the venom gland cocktail in G. tridactyla. Short amino acid sequences varying in length between 7â  18 amino acids served as reference in BLAST-searches to identify the neurotoxin in transcriptome libraries of G. tridactyla. (TXT 30 kb)
DOI: 10.6084/m9.figshare.c.3709288_d1.v1
title: Additional file 1: Figure S1. of Conservation of estrogen receptor function in invertebrate reproduction

description: The alignment of the ER LBD amino acid sequences of rotifer and human shows significant similarity. Conserved amino acids are green. Similar amino acids are cyan. Amino acids that directly interact with the estradiol ligand are boxed (rotifer, red; human; blue). These amino acids are highly conserved as well. (XLS 258 kb)
DOI: 10.6084/m9.figshare.c.3709270_d5
title: Additional file 1: of Comparative analyses of glycerotoxin expression unveil a novel structural organization of the bloodworm venom system

description: Position of short amino acid sequences alongside the GLTx full-length transcripts. Short amino acid sequences were recovered through protein sequencing of purified glycerotoxin extracted out of the venom gland cocktail in G. tridactyla. Short amino acid sequences varying in length between 7â  18 amino acids served as reference in BLAST-searches to identify the neurotoxin in transcriptome libraries of G. tridactyla. (TXT 30 kb)
DOI: 10.6084/m9.figshare.c.3709288_d1
title: Additional file 1: Figure S1. of Conservation of estrogen receptor function in invertebrate reproduction

description: The alignment of the ER LBD amino acid sequences of rotifer and human shows significant similarity. Conserved amino acids are green. Similar amino acids are cyan. Amino acids that directly interact with the estradiol ligand are boxed (rotifer, red; human; blue). These amino acids are highly conserved as well. (XLS 258 kb)
DOI: 10.6084/m9.figshare.c.3709288_d2.v1
title: Additional file 2: Figure S2. of Conservation of estrogen receptor function in invertebrate reproduction

description: Six fluorescent synthetic ligands (AMIs) were tested for in vivo binding to ER in live rotifer neonates and with the yeast chemical complementation assay using a cloned rotifer ER LBD. These compounds were chosen because previous work verified their binding to the human ER LBD in yeast chemical complementation assays. These compounds fluoresce upon binding to their target [35]. Estradiol is the natural ligand for the human ER and does not fluoresce. (XLS 47 kb)
DOI: 10.6084/m9.figshare.c.3709270_d6.v1
title: Additional file 2: of Comparative analyses of glycerotoxin expression unveil a novel structural organization of the bloodworm venom system

description: Nucleotide alignment of GLTx full-length transcripts (SR23, contig 5772, contig 4317, and contig 4318) and three nearly full-length GLTx clones amplified from second strand cDNA (Cons_clone_5A, 6A, and 7) in G. tridactyla. (TXT 23 kb)
DOI: 10.6084/m9.figshare.c.3709270_d6
title: Additional file 2: of Comparative analyses of glycerotoxin expression unveil a novel structural organization of the bloodworm venom system

description: Nucleotide alignment of GLTx full-length transcripts (SR23, contig 5772, contig 4317, and contig 4318) and three nearly full-length GLTx clones amplified from second strand cDNA (Cons_clone_5A, 6A, and 7) in G. tridactyla. (TXT 23 kb)
DOI: 10.6084/m9.figshare.c.3709288_d2
title: Additional file 2: Figure S2. of Conservation of estrogen receptor function in invertebrate reproduction

description: Six fluorescent synthetic ligands (AMIs) were tested for in vivo binding to ER in live rotifer neonates and with the yeast chemical complementation assay using a cloned rotifer ER LBD. These compounds were chosen because previous work verified their binding to the human ER LBD in yeast chemical complementation assays. These compounds fluoresce upon binding to their target [35]. Estradiol is the natural ligand for the human ER and does not fluoresce. (XLS 47 kb)
DOI: 10.6084/m9.figshare.c.3709270_d7.v1
title: Additional file 3: of Comparative analyses of glycerotoxin expression unveil a novel structural organization of the bloodworm venom system

description: Protein-translated alignment of GLTx full-length transcripts (SR23, contig 5772, contig 4317, and contig 4318) and three nearly full-length GLTx clones amplified from second strand cDNA (Cons_clone_5A, 6A, and 7) in G. tridactyla. (TXT 7 kb)
DOI: 10.6084/m9.figshare.c.3709270_d7
title: Additional file 3: of Comparative analyses of glycerotoxin expression unveil a novel structural organization of the bloodworm venom system

description: Protein-translated alignment of GLTx full-length transcripts (SR23, contig 5772, contig 4317, and contig 4318) and three nearly full-length GLTx clones amplified from second strand cDNA (Cons_clone_5A, 6A, and 7) in G. tridactyla. (TXT 7 kb)
DOI: 10.6084/m9.figshare.c.3709306_d1.v1
title: Additional file 10: Simulated Dataset 2. of ProteoModlR for functional proteomic analysis

description: Normalization_dataset_no_error. The file contains a simulated datasets with identical intensity values for all peptides in all conditions. This dataset is provided as a reference to evaluate the accuracy of normalization strategies. (CSV 4 kb)
DOI: 10.15468/dl.zygpn6
title: Occurrence Download

description: A dataset containing 238045 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
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}

 The dataset includes 238045 records from 151 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038595-241126133413365/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.c.3710404_d1
title: Additional file 1: Table S1. of Recent range expansion of an intermediate host for animal schistosome parasites in the Indo-Australian Archipelago: phylogeography of the freshwater gastropod Indoplanorbis exustus in South and Southeast Asia

description: List of the samples included in this study. For each specimen, the GenBank accession number for the associated cox1 sequence, the authors who published the sequences and the collection date, locality and coordinates of the sample are provided. (XLSX 56Â kb)