cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3642479_d1.v1
title: Additional file 3: Table S2. of Transcriptome analysis of the painted lady butterfly, Vanessa cardui during wing color pattern development

description: Differentially expressed (DE) transcripts (≥500 bp) for each comparison between wing development stages (LL vs. EP, EP vs. PO, PO vs. LM). Information provided on fold change, FDR p-value, RPKM and gene name for each contig. Up-regulated genes are highlighted in pink and down-regulated genes are highlighted in green. This table also includes the complete list of all 9, 376 differentially expressed transcripts. (XLSX 645 kb)
DOI: 10.6084/m9.figshare.c.3642479_d2.v1
title: Additional file 6: Table S5. of Transcriptome analysis of the painted lady butterfly, Vanessa cardui during wing color pattern development

description: Differentially expressed genes (FDR p
DOI: 10.6084/m9.figshare.c.3642479_d3.v1
title: Additional file 5: Table S4. of Transcriptome analysis of the painted lady butterfly, Vanessa cardui during wing color pattern development

description: Differentially expressed genes (FDR p
DOI: 10.6084/m9.figshare.c.3642479_d6.v1
title: Additional file 7: Table S6. of Transcriptome analysis of the painted lady butterfly, Vanessa cardui during wing color pattern development

description: Comparison of butterfly transcriptomes reveals 28 contigs common to Vanessa cardui, Junonia coenia, Danaus plexippus and Heliconius melpomene which received no significant hits to NCBI (1E-3). Contigs highlighted in grey are differentially expressed in V. cardui across the developmental stages, shown in red (up-regulated) or green (down-regulated). Blast results for all comparisons to V. cardui including Bicyclus anynana brain transcriptome and Bombyx mori are also presented. (XLSX 4847Â kb)
DOI: 10.6084/m9.figshare.c.3642479_d7.v1
title: Additional file 4: Table S3. of Transcriptome analysis of the painted lady butterfly, Vanessa cardui during wing color pattern development

description: BLAST2GO PRO gene ontology classification for differentially expressed genes (FDR p
DOI: 10.6084/m9.figshare.c.3642485_d3.v1
title: Additional file 2: of Student self-reported communication skills, knowledge and confidence across standardised patient, virtual and traditional clinical learning environments

description: Quantitative data. Includes all data used for statistical analysis. Demographic and prior experience variables have been removed from the data file to ensure the confidentiality of participants and clinical educators. (XLS 79Â kb)
DOI: 10.6084/m9.figshare.c.3642488_d1.v1
title: Additional file 1: of Spotting the enemy within: Targeted silencing of foreign DNA in mammalian genomes by the KrĂźppel-associated box zinc finger protein family

description: KRAB domain sequences of human and mouse KRAB-ZFPs in Multi-FASTA format. See Fig. 3 for details. (FA 34 kb)
DOI: 10.6084/m9.figshare.c.3642497_d1.v1
title: MOESM3 of Pharmacogenetics driving personalized medicine: analysis of genetic polymorphisms related to breast cancer medications in Italian isolated populations

description: Additional file 3: Table S3. Consequence annotation for analyzed variants from ANNOVAR.
DOI: 10.15468/dl.b98u35
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-76.29575 6.75698,-75.99232 5.09822,-72.71526 2.56963,-71.74428 5.5028,-76.29575 6.75698))",
 "TaxonKey is Scaura Schwarz, 1938"
 ]
}

 The dataset includes 8 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038071-241126133413365/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.3642656_d1.v1
title: Additional file 2: Table S1. of Promoter hypermethylation of SHOX2 and SEPT9 is a potential biomarker for minimally invasive diagnosis in adenocarcinomas of the biliary tract

description: Clinicopathological data of the 20 biliary tract cancer cases and 100 gender- and age-matched controls included in plasma study. (XLSX 116 kb)
DOI: 10.6084/m9.figshare.c.3642659_d5.v1
title: Additional file 3: Table S1. of Low-power photodynamic therapy induces survival signaling in perihilar cholangiocarcinoma cells

description: Overview of transcriptional targets of the five survival pathways. Official gene names are listed that were derived from the Hugo Gene Nomenclature Committee (HGNC) along with their Genbank accession numbers (Gene ID). (XLSX 16Â kb)
DOI: 10.6084/m9.figshare.c.3642659_d2.v1
title: Additional file 5: Table S2. of Low-power photodynamic therapy induces survival signaling in perihilar cholangiocarcinoma cells

description: Overview of primer sequences and resulting amplicon sizes (in bp) that were used for the validation of microarray expression levels using qRT-PCR. The primers are listed in the 5â ˛ to 3â ˛ direction. Primers were derived from RTPrimerDB ( http://www.rtprimerdb.org/ ), NCBI primer Blast ( http://www.ncbi.nlm.nih.gov/tools/primer-blast/ ), and qPrimerDepot ( http://primerdepot.nci.nih.gov/ ). Sequencing of the qRT-PCR products, which were analyzed using NCBI Blast ( http://blast.ncbi.nlm.nih.gov/Blast.cgi ), confirmed the correct identity of each product. (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.c.3642758_d4.v1
title: MOESM3 of Identification of epitopes recognised by mucosal CD4+ T-cell populations from cattle experimentally colonised with Escherichia coli O157:H7

description: Additional file 3. Theileria parva peptide sequences. Amino acid sequences of T. parva peptides used as negative controls for CD4+ T-cell stimulation assays.
DOI: 10.6084/m9.figshare.c.3642803_d1.v1
title: Additional file 1: of Non-invasive assessment of adrenocortical activity as a measure of stress in giraffe (Giraffa camelopardalis)

description: Full dataset in Microsoft Excel workbook format. (XLSX 61Â kb)
DOI: 10.6084/m9.figshare.c.3642911_d1.v1
title: Additional file 1: of Declining functional connectivity and changing hub locations in Alzheimerâ  s disease: an EEG study

description: The influence of the number of epochs. The number of epochs used for analyses influences the PLI outcomes. This supplement, including 1 figureand 1 table show that the PLI values become stable after 4 epochs of 8.192 seconds (4096 samples). (ZIP 66Â kb)
DOI: 10.15468/dl.8e3q3c
title: Occurrence Download

description: A dataset containing 785 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-72.68402 12.31355,-76.47881 10.44491,-76.99628 4.58023,-71.50534 -1.1982,-68.60175 1.33166,-67.30807 6.13265,-73.00025 9.63995,-72.68402 12.31355))",
 "TaxonKey is Tetragona Lepeletier & Audinet-Serville, 1828"
 ]
}

 The dataset includes 785 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038073-241126133413365/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.3642932_d1.v1
title: MOESM1 of Clinical utility of serum biomarkers in Duchenne muscular dystrophy

description: Additional file 1: Table S1. List of serum protein biomarkers indentified by mass spectrometry based proteome profiling and SomaScan technique References [44, 45].
DOI: 10.6084/m9.figshare.c.3642938_d3.v1
title: Additional file 2: of Feasibility of controlling hookworm infection through preventive chemotherapy: a simulation study using the individual-based WORMSIM modelling framework

description: Zip archive containing the JAVA-based WORMSIM modelling framework (version 2.58Ap9), including example input files (XML) for hookworm transmission and detailed documentation of the XML schema for input files. The contents of this zip archive are licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-nd/4.0/ or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA. By opening Additional File X, you agree to the aforementioned license. You are free to use and share (copy and redistribute the material in any medium or format) the material contained within Additional File 4 under the following terms: Attribution — You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. NonCommercial — You may not use the material for commercial purposes. NoDerivatives — If you remix, transform, or build upon the material, you may not distribute the modified material. (ZIP 5.69 MB)
DOI: 10.6084/m9.figshare.28049879
title: Hosta sp. raw GC-MS files

description: Metabolite extraction from Hosta sp. leaf tissue
DOI: 10.6084/m9.figshare.28049879.v1
title: Hosta sp. raw GC-MS files

description: Metabolite extraction from Hosta sp. leaf tissue
DOI: 10.6084/m9.figshare.c.3643070_d1.v1
title: MOESM1 of What is normal? Next generation sequencing-driven analysis of the human circulating miRNAOme

description: Additional file 1: S1. Sheet 1: Comprehensive list of raw and normalised expression values for all plasma miRNAs detected. Raw Sequencing Dataâ  The raw sequencing data (in fastq format) supporting the results of this article is available in the Short Read Archive (SRA) repository, [SRP064104 http://www.ncbi.nlm.nih.gov/sra ]. Sheet 2: Experiment IDs, PubMed IDs and metadata relating to the publically accessible datasets accessed for result validation.
DOI: 10.6084/m9.figshare.c.3643076_d1.v1
title: Additional file 3: of Genome-wide analysis of the transcriptional response to porcine reproductive and respiratory syndrome virus infection at the maternal/fetal interface and in the fetus

description: Gene function enrichment analysis results on DEG lists. Excel (.xlsx) file of three function enrichment analyses from the IPA software: biological function (BF), canonical Pathway (CP), and upstream regulator (UR), for each of the six DEG lists (18 tabs in total). (XLSX 801 kb)
DOI: 10.6084/m9.figshare.c.3643076_d2.v1
title: Additional file 2: of Genome-wide analysis of the transcriptional response to porcine reproductive and respiratory syndrome virus infection at the maternal/fetal interface and in the fetus

description: Lists of differentially expressed genes. Excel (.xlsx) file of the differentially expressed genes (DEGs) identified by the edgeR software from the six contrasts of the transcriptomic analysis. Results for each contrast are on a separate tab (6 tabs in total). (XLSX 656 kb)
DOI: 10.6084/m9.figshare.c.3643076_d3.v1
title: Additional file 6: of Genome-wide analysis of the transcriptional response to porcine reproductive and respiratory syndrome virus infection at the maternal/fetal interface and in the fetus

description: Gene function enrichment analysis results on WGCNA data. Excel (.xlsx) file of three function enrichment analyses from the IPA software: biological function (BF), canonical Pathway (CP), and upstream regulator (UR), for each of the modules from the six contrasts mentioned in the Results section (36 tabs in total). (XLSX 7834 kb)
DOI: 10.6084/m9.figshare.c.3643076_d5.v1
title: Additional file 4: of Genome-wide analysis of the transcriptional response to porcine reproductive and respiratory syndrome virus infection at the maternal/fetal interface and in the fetus

description: WGCNA module trait correlations. Excel file (.xlsx) of the modules identified for each of the six contrasts by the WGCNA software, their correlation with the traits of interest, and the statistical significance of that correlation (6 tabs in total). (XLSX 70 kb)
DOI: 10.6084/m9.figshare.c.3643076_d4.v1
title: Additional file 7: of Genome-wide analysis of the transcriptional response to porcine reproductive and respiratory syndrome virus infection at the maternal/fetal interface and in the fetus

description: Comparison of RNA-seq and RT-qPCR expression data for individual genes. Excel (.xlsx) file of log2 transformed fold differences, for both RNA-seq and RT-qPCR, for genes used for RT-qPCR validation of RNA-seq data from endometrium and thymus (2 tabs in total). (XLSX 37 kb)
DOI: 10.6084/m9.figshare.c.3643076_d7.v1
title: Additional file 5: of Genome-wide analysis of the transcriptional response to porcine reproductive and respiratory syndrome virus infection at the maternal/fetal interface and in the fetus

description: Gene significance and module membership results. Excel file (.xlsx) of the gene significance and module membership results from the WGCNA analysis for each of the six contrasts (6 tabs in total). (XLSX 1631 kb)
DOI: 10.5281/zenodo.14427665
title: Data for: Thioesters support efficient protein biosynthesis by the ribosome

description: Thioesters are critical chemical intermediates in numerous extant biochemical reactions and are invoked as key reagents during prebiotic peptide synthesis on an evolving Earth. Here we asked if a thioester could replace the native oxo-ester in acyl-tRNA substrates during protein biosynthesis by the ribosome. We prepared 3′-thio-3′-deoxyadenosine triphosphate in 10 steps from xylose and demonstrated that it is an effective substrate for the E. coli CCA-adding enzyme, which appends 3′-thio-3′-deoxyadenosine to truncated tRNAs ending with 3′-CC. Using a variety of aminoacyl-tRNA synthetases, flexizymes, or a direct thioester exchange reaction, we prepared a suite of 3′-thio-tRNAs acylated with α- and non-α-amino acids. All were recognized and utilized by wild-type Escherichia coli ribosomes during in vitro translation reactions to generate oligopeptides in yields commensurate with native oxo-ester tRNAs. These results indicate that thioester intermediates widely used in Nature can be co-opted to support the incorporation of natural α-amino acids as well as non-canonical monomers by the extant translational machinery for sequence-defined polymer synthesis.
DOI: 10.5281/zenodo.14427666
title: Data for: Thioesters support efficient protein biosynthesis by the ribosome

description: Thioesters are critical chemical intermediates in numerous extant biochemical reactions and are invoked as key reagents during prebiotic peptide synthesis on an evolving Earth. Here we asked if a thioester could replace the native oxo-ester in acyl-tRNA substrates during protein biosynthesis by the ribosome. We prepared 3′-thio-3′-deoxyadenosine triphosphate in 10 steps from xylose and demonstrated that it is an effective substrate for the E. coli CCA-adding enzyme, which appends 3′-thio-3′-deoxyadenosine to truncated tRNAs ending with 3′-CC. Using a variety of aminoacyl-tRNA synthetases, flexizymes, or a direct thioester exchange reaction, we prepared a suite of 3′-thio-tRNAs acylated with α- and non-α-amino acids. All were recognized and utilized by wild-type Escherichia coli ribosomes during in vitro translation reactions to generate oligopeptides in yields commensurate with native oxo-ester tRNAs. These results indicate that thioester intermediates widely used in Nature can be co-opted to support the incorporation of natural α-amino acids as well as non-canonical monomers by the extant translational machinery for sequence-defined polymer synthesis.
DOI: 10.6084/m9.figshare.c.3643217_d1.v1
title: Additional file 5: of 
                     Snail-induced epithelial-to-mesenchymal transition of MCF-7 breast cancer cells: systems analysis of molecular changes and their effect on radiation and drug sensitivity

description: List of 164 network objects from the MetaCore human protein interactome that are statistically significantly over-connected to the genes differentially expressed between MCF-7-Snail and MCF-7-Control cells. (XLS 71 kb)
DOI: 10.6084/m9.figshare.c.3643277_d16.v1
title: Additional file 1: Table S1. of 
                     De novo transcriptomic assembly and profiling of Rigidoporus microporus during saprotrophic growth on rubber wood

description: Percentage of mapping of each sample. (XLSX 10Â kb)
DOI: 10.15468/dl.djw7j3
title: Occurrence Download

description: A dataset containing 1113 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-72.75018 12.31301,-76.46485 10.36617,-77.47183 3.76481,-76.3082 0.67672,-72.81732 0.58721,-71.58655 9.02352,-72.75018 12.31301))",
 "TaxonKey is Tetragonisca Moure, 1946"
 ]
}

 The dataset includes 1113 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038074-241126133413365/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.3643280_d2.v1
title: Additional file 1 of Do count-based differential expression methods perform poorly when genes are expressed in only one condition?

description: Table of statistics for zero-count genes. Table of zero-counts, differential statistics and S/N for the ENCODE dataset. (CSV 112 kb)
DOI: 10.6084/m9.figshare.c.3643295_d1.v1
title: Additional file 1: Table S1. of Genome-wide characterization of long intergenic non-coding RNAs (lincRNAs) provides new insight into viral diseases in honey bees Apis cerana and Apis mellifera

description: (A) Primers used for RT-PCR validation and (B) FPKM values of seven tissues of A. cerana used in this study. (XLS 328 kb)
DOI: 10.6084/m9.figshare.c.3643295_d3.v1
title: Additional file 6: Table S2. of Genome-wide characterization of long intergenic non-coding RNAs (lincRNAs) provides new insight into viral diseases in honey bees Apis cerana and Apis mellifera

description: Primers used in qRT-PCR analysis. (XLS 28 kb)
DOI: 10.6084/m9.figshare.c.3643295_d4.v1
title: Additional file 5: Dataset S3. of Genome-wide characterization of long intergenic non-coding RNAs (lincRNAs) provides new insight into viral diseases in honey bees Apis cerana and Apis mellifera

description: Sequenced PCR products of virus-specific lincRNAs. (TXT 1 kb)
DOI: 10.6084/m9.figshare.c.3643295_d2.v1
title: Additional file 2: Dataset S1. of Genome-wide characterization of long intergenic non-coding RNAs (lincRNAs) provides new insight into viral diseases in honey bees Apis cerana and Apis mellifera

description: Annotation of A. cerana lincRNAs. (GTF 1130 kb)
DOI: 10.6084/m9.figshare.c.3643295_d6.v1
title: Additional file 3: Dataset S2. of Genome-wide characterization of long intergenic non-coding RNAs (lincRNAs) provides new insight into viral diseases in honey bees Apis cerana and Apis mellifera

description: Annotation of A. mellifera lincRNAs. (GTF 403 kb)
DOI: 10.6084/m9.figshare.c.3643415_d2.v1
title: Additional file 13: Table S6. of Barley landraces are characterized by geographically heterogeneous genomic origins

description: Genome-wide ancestry as a function of distance from wild populations. Proportions of ancestry for individual landraces, and the great circle distance between each individual and the closest accession from each wild population.
DOI: 10.6084/m9.figshare.c.3643415_d1.v1
title: Additional file 9: Table S4 of Barley landraces are characterized by geographically heterogeneous genomic origins

description: Genome-wide proportion of ancestry among each landrace population. Genome-wide average proportions of genetic ancestry in barley landrace populations for all regions that have a probability of assignment &gt;95 %.
DOI: 10.6084/m9.figshare.c.3643415_d4.v1
title: Additional file 11: Table S5. of Barley landraces are characterized by geographically heterogeneous genomic origins

description: Predictive accuracy of SupportMix by cross-validation. Averaged across 50 runs of the genome-wide proportion of ancestry in subsets of wild barley analyzed as testing samples, using the remaining wild individuals as the validation dataset.
DOI: 10.6084/m9.figshare.c.3643415_d5.v1
title: Additional file 16: Table S8. of Barley landraces are characterized by geographically heterogeneous genomic origins

description: Summary of number of private alleles from wild barley populations present in the landraces. Average allele frequency of alleles private to wild populations in the landraces (in parenthesis). The number of private alleles in each wild population is shown in brackets.
DOI: 10.6084/m9.figshare.c.3643415_d9.v1
title: Additional file 1: Table S1. of Barley landraces are characterized by geographically heterogeneous genomic origins

description: 803 landrace accessions used in this study with latitude and longitude information.
DOI: 10.15468/dl.tbrpxh
title: Occurrence Download

description: A dataset containing 671 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-79.34614 2.65434,-73.34127 1.69667,-71.50357 12.61933,-75.25662 11.60989,-79.34614 2.65434))",
 "TaxonKey is Trigonisca Moure, 1950"
 ]
}

 The dataset includes 671 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038075-241126133413365/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.28049885
title: Hyacinthus orientalis raw GC-MS files

description: Metabolite extraction from Hyacinthus orientalis leaf tissue
DOI: 10.6084/m9.figshare.c.3643493_d4.v1
title: Additional file 10: Tables S5A and S5B. of Distinct gene expression program dynamics during erythropoiesis from human induced pluripotent stem cells compared with adult and cord blood progenitors

description: Both relate to Fig.Â 4 and contain annotations, linear expression values, statistical parameters and fold changes of differentially expressed genes between different populations during maturation of Adult and hiPSC Erythroblasts in SEM-i. Inclusion criteria for differentially expressed genes: B value of at least 2.945, p-value below 0.01, fold change of at least 2, and expression levels in all replicates at any population of at least 100. Erythroblasts were cultured for between 0 and 14 days (d0-d14). Upregulated and downregulated genes are listed separately in Table S5B. (XLSX 5326 kb)
DOI: 10.6084/m9.figshare.c.3643493_d10.v1
title: Additional file 20: Table S4. of Distinct gene expression program dynamics during erythropoiesis from human induced pluripotent stem cells compared with adult and cord blood progenitors

description: Relates to Fig.Â 3. Annotations, linear expression values, statistical parameters and fold changes of genes DE (B value at least 2.945, p-value below 0.01, fold change at least 2, and expression levels in all replicates at any population at least 100) between different populations during maturation of Adult Erythroblasts (AB-erythroblasts) in SEM-F or SEM-i, cultured for between 0 and 14 days (d0-d14). (XLSX 10526 kb)
DOI: 10.6084/m9.figshare.c.3643493_d14.v1
title: Additional file 2: of Distinct gene expression program dynamics during erythropoiesis from human induced pluripotent stem cells compared with adult and cord blood progenitors

description: Tables S1A and S1B. Both relate to Fig.Â 1. (XLSX 9540 kb)
DOI: 10.6084/m9.figshare.c.3643493_d17.v1
title: Additional file 4: Table S2. of Distinct gene expression program dynamics during erythropoiesis from human induced pluripotent stem cells compared with adult and cord blood progenitors

description: Linear expression values of all genes from all HSC sources studied that exceed a threshold linear expression level of 100 in all replicates of at least one population. (CSV 17480 kb)