cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20329363
title: Additional file 12 of Electronic cigarette liquids impair metabolic cooperation and alter proteomic profiles in V79 cells

description: Additional file 12: Table S5. The list of all PTMs, specific peptides and proteins affected by e-cigarette treatment.
DOI: 10.6084/m9.figshare.20329363.v1
title: Additional file 12 of Electronic cigarette liquids impair metabolic cooperation and alter proteomic profiles in V79 cells

description: Additional file 12: Table S5. The list of all PTMs, specific peptides and proteins affected by e-cigarette treatment.
DOI: 10.6084/m9.figshare.20329387
title: Additional file 7 of Electronic cigarette liquids impair metabolic cooperation and alter proteomic profiles in V79 cells

description: Additional file 7: Figure S7. Western blot of Cx43 and tubulin as endogenous control in V79 cells after 72h treatments. Control (1; 5; 9) ECL-N (2; 6; 10) ECL (3; 7; 11) NIC (4; 8; 12).
DOI: 10.6084/m9.figshare.20329387.v1
title: Additional file 7 of Electronic cigarette liquids impair metabolic cooperation and alter proteomic profiles in V79 cells

description: Additional file 7: Figure S7. Western blot of Cx43 and tubulin as endogenous control in V79 cells after 72h treatments. Control (1; 5; 9) ECL-N (2; 6; 10) ECL (3; 7; 11) NIC (4; 8; 12).
DOI: 10.6084/m9.figshare.20329390
title: Additional file 8 of Electronic cigarette liquids impair metabolic cooperation and alter proteomic profiles in V79 cells

description: Additional file 8: Table S1. The list of all proteins found in all V79 cell treatments.
DOI: 10.6084/m9.figshare.20329393
title: Additional file 9 of Electronic cigarette liquids impair metabolic cooperation and alter proteomic profiles in V79 cells

description: Additional file 9: Table S2. The list of significantly upregulated and downregulated proteins in V79 cell treatments by protein mass spectrometry relative label-free quantification.
DOI: 10.6084/m9.figshare.20329390.v1
title: Additional file 8 of Electronic cigarette liquids impair metabolic cooperation and alter proteomic profiles in V79 cells

description: Additional file 8: Table S1. The list of all proteins found in all V79 cell treatments.
DOI: 10.6084/m9.figshare.20329393.v1
title: Additional file 9 of Electronic cigarette liquids impair metabolic cooperation and alter proteomic profiles in V79 cells

description: Additional file 9: Table S2. The list of significantly upregulated and downregulated proteins in V79 cell treatments by protein mass spectrometry relative label-free quantification.
DOI: 10.6084/m9.figshare.20329434
title: Additional file 6 of Differentiated kidney tubular cell-derived extracellular vesicles enhance maturation of tubuloids

description: Additional file 6: Table S2. List of all proteins identified in EV-OAT1 and its expression levels in respect to EV-14.4.
DOI: 10.6084/m9.figshare.20329434.v1
title: Additional file 6 of Differentiated kidney tubular cell-derived extracellular vesicles enhance maturation of tubuloids

description: Additional file 6: Table S2. List of all proteins identified in EV-OAT1 and its expression levels in respect to EV-14.4.
DOI: 10.6084/m9.figshare.20329437
title: Additional file 7 of Differentiated kidney tubular cell-derived extracellular vesicles enhance maturation of tubuloids

description: Additional file 7: Table S3. List of all proteins identified in TUB CM-OAT1 and its expression levels in respect to TUB CTR.
DOI: 10.6084/m9.figshare.20329437.v1
title: Additional file 7 of Differentiated kidney tubular cell-derived extracellular vesicles enhance maturation of tubuloids

description: Additional file 7: Table S3. List of all proteins identified in TUB CM-OAT1 and its expression levels in respect to TUB CTR.
DOI: 10.6084/m9.figshare.20329440
title: Additional file 8 of Differentiated kidney tubular cell-derived extracellular vesicles enhance maturation of tubuloids

description: Additional file 8: Table S4. List of all proteins identified in TUB EV-OAT1 and its expression levels in respect to TUB CTR.
DOI: 10.6084/m9.figshare.20329440.v1
title: Additional file 8 of Differentiated kidney tubular cell-derived extracellular vesicles enhance maturation of tubuloids

description: Additional file 8: Table S4. List of all proteins identified in TUB EV-OAT1 and its expression levels in respect to TUB CTR.
DOI: 10.6084/m9.figshare.20329443
title: Additional file 9 of Differentiated kidney tubular cell-derived extracellular vesicles enhance maturation of tubuloids

description: Additional file 9: Table S5. List of all proteins identified in TUB EV-OAT1 and its expression levels in respect to TUB CM-OAT1.
DOI: 10.6084/m9.figshare.20329443.v1
title: Additional file 9 of Differentiated kidney tubular cell-derived extracellular vesicles enhance maturation of tubuloids

description: Additional file 9: Table S5. List of all proteins identified in TUB EV-OAT1 and its expression levels in respect to TUB CM-OAT1.
DOI: 10.6084/m9.figshare.20110694
title: Additional file 1 of Preventive potential of nano silver fluoride versus sodium fluoride varnish on enamel caries like lesions in primary teeth: in vitro study

description: Additional file 1. Study data.
DOI: 10.6084/m9.figshare.20110694.v1
title: Additional file 1 of Preventive potential of nano silver fluoride versus sodium fluoride varnish on enamel caries like lesions in primary teeth: in vitro study

description: Additional file 1. Study data.
DOI: 10.6084/m9.figshare.20329215.v1
title: Supplementary Table S7

description: Differential peaks annotation of keratinocytes.
DOI: 10.6084/m9.figshare.20329545
title: Additional file 2 of Geospatial distribution of relative cesarean section rates within the USA

description: Additional file 2: Table S1. Summary demographics of all counties in each C-section group identified by geospatial analysis along with the p-values of the ANOVA test and the t-test comparing high-high to low-low.
DOI: 10.6084/m9.figshare.20329545.v1
title: Additional file 2 of Geospatial distribution of relative cesarean section rates within the USA

description: Additional file 2: Table S1. Summary demographics of all counties in each C-section group identified by geospatial analysis along with the p-values of the ANOVA test and the t-test comparing high-high to low-low.
DOI: 10.6084/m9.figshare.6321242.v3
title: Cannabinoid receptors in NSCLC

description: The raws represent NSCLC patients. The survival data and Ct(Cp) values measured by QPCR and immunochemistry are placed and ordered in the columns.
DOI: 10.5281/zenodo.6832198
title: Shihua cave stalagmite CS01C d18O, d13C, lamina thickness, and stalagmite SHD1311 d18O during early Holocene 11.3 - 10 ka BP

description: Here we present results of <sup>230</sup>Th dating, stable isotope and lamina thickness data from two stalagmites (CS01C and SHD1311) from Shihua Cave (latitude 39´47°N, longitude 115´56°E; altitude 251 m a.s.l. at the entrance), northern China, during 11.32 to 10 ka BP. CS01C developed with clear annual lamina. The age model of CS01C is based on lamina counting. The age model of SHD1311 is established using the COPRA algorithm. The variability of stalagmite δ<sup>18</sup>O records is interpreted as a proxy of regional summer monsoon precipitation and/or EASM intensity. Stalagmite δ<sup>18</sup>O records show two weak summer monsoon events at 10.9 and 10.3 ka. The 10.9-ka event occurred from 10.93–10.79 ka BP for ~140 yr and features a “W”-shaped structure. The 10.3-ka event, also known as the ice-rafted debris event 7 in the North Atlantic, lasted ~260 yr with an asymmetric double-plunging structure.
description: Dataset1: 230Th dating results for stalagmites CS01C and SHD1311; Dataset2: CS01C δ18O and δ13C record and lamina counting age model (Correction: in this dataset, the correct depth unit is "µm", and the depth unit "mm" in the data file is wrong ); Dataset3: CS01C lamina thickness; Dataset4: SHD1311 δ18O record and COPRA age model; Dataset5: age ensemble of CS01C δ18O calculated by BAM algorithm(Correction: in this dataset, the correct depth unit is "µm", and the depth unit "mm" in the data file is wrong ); Dataset6: age ensemble of CS01C lamina thickness calculated by BAM algorithm; Dataset7: age ensemble of SHD1311 δ18O calculated by COPRA algorithm.
description: {"references": ["Miaofa, Li., Fang, Wang., Binggui, Cai., Qi, Cao., Hai, Cheng., Chuan-Chou, Shen., Ming, Tan., R. Lawrence, Edwards. Timing and structure of 10.9 and 10.3 ka BP events revealed by annually laminated stalagmite records from Shihua Cave, northern China. Paleoceanography and Paleoclimatology. (under review)"]}
DOI: 10.6084/m9.figshare.19519105
title: Pangenome analysis of 882 V. cholerae genomes and detection of clade-specific genes

description: the synteny-aware pangenome pipeline Panaroo (v1.2.3) was run on the 882 assembled <i>V. cholerae</i> genome set with the option “--clean-mode strict” and default parameters otherwise.<br>To identify clade-specific accessory gene presence/absence patterns, we used custom R scripts (https://github.com/flass/yemenpaper) to compare the the gene presence/absence table output of Panaroo, to the mapped genome tree. Based on lists of genomes assigned to various clades and clusters, we identify accessory genes that are specific of a focus clade in contrast to a background group or a sister clade, considering the contrast significant when the Bonferonni-corrected p-value is below 0.05 and when the frequency of an allele is above 0.8 in the focus clade and below 0.2 in the background clade, or conversely.
DOI: 10.6084/m9.figshare.18304961
title: ML tree of 33 mapped V. cholerae Clade D genomes

description: Maximum-likelihood phylogeny of the 33 mapped V. cholerae Clade D (including ST555) genomes.<br>For variant calling, Illumina short reads were mapped against the novel reference strain CNRVC190247 genome. We mapped all 21 short read sets from 2018-2019 Yemeni <i>V. cholerae </i>isolates, provided read mapping were mapped at a sufficient depth (see below); we also mapped read sets from 12 contextual <i>V. cholerae</i> isolates linked to ST555. Reads were trimmed with Trimmomatic, mapped to both CNRVC190247 reference chromosomes with BWA-MEM. All mapped genomes had an average read depth above 5x over the two chromosomes and were deemed of sufficient read depth for analysis. We used the software suite samtools/bcftools v1.9 to call variants with a minimum coverage of 10x read depth, excluding indels. Resulting consensus sequences were combined and processed with snp-sites (Page et al., 2016) to produce a single nucleotide polymorphism (SNP) alignment featuring 91,312 positions.
DOI: 10.6084/m9.figshare.18304961.v1
title: ML tree of 33 mapped V. cholerae Clade D genomes

description: Maximum-likelihood phylogeny of the 33 mapped V. cholerae Clade D (including ST555) genomes.<br>For variant calling, Illumina short reads were mapped against the novel reference strain CNRVC190247 genome. We mapped all 21 short read sets from 2018-2019 Yemeni <i>V. cholerae </i>isolates, provided read mapping were mapped at a sufficient depth (see below); we also mapped read sets from 12 contextual <i>V. cholerae</i> isolates linked to ST555. Reads were trimmed with Trimmomatic, mapped to both CNRVC190247 reference chromosomes with BWA-MEM. All mapped genomes had an average read depth above 5x over the two chromosomes and were deemed of sufficient read depth for analysis. We used the software suite samtools/bcftools v1.9 to call variants with a minimum coverage of 10x read depth, excluding indels. Resulting consensus sequences were combined and processed with snp-sites (Page et al., 2016) to produce a single nucleotide polymorphism (SNP) alignment featuring 91,312 positions.
DOI: 10.6084/m9.figshare.16611823
title: core-genome tree of 882 assembled genomes

description: Pantagruel (Lassalle <i>et al.,</i> 2019) was used to infer a maximum-likelihood (ML) “core genome tree” from the concatenated alignments of 291 core-genome genes extracted from the 889 assembled <i>V. cholerae</i> genomes using the “-S” option and otherwise default parameters. The ML tree was computed from the resulting 37,170 polymorphic positions using RAxML v8.2.11 (model ASC_GTRGAMMAX using Stamatakis’ ascertainment bias correction; one starting parsimony tree; 200 rapid bootstraps for estimating branch supports). Seven genomes were removed from the tree as they were identified as contaminated genome assemblies based on the Pantagruel pangenome analysis, for a final total of 882 genomes, presented in the trees with the 'nocontam' tag in the file name.Core-genome gene families were selected as those resent in at least 884/889 genomes i.e. absent in maximum ~0.5% of the genomes; locus_tags of representative genes in genome assembly 33224_2#41 are listed with their predicted protein function in file 'pseudo-core-884-unicopy_families.representative_product.tab'.<br>the full concatenated alignment is given in 'pseudo-core-884-unicopy_concat_cds_0-genomes_contextallyemen2019.aln.gz'<br>the same alignment reduced to its SNP positions is given in 'pseudo-core-884-unicopy_concat_cds_0-genomes_contextallyemen2019.snp.aln.gz'<br>
DOI: 10.6084/m9.figshare.20329569.v1
title: Additional file 1 of The G1/S repressor WHI5 is expressed at similar levels throughout the cell cycle

description: Additional file 1. Raw quantitative data underlying Figure panels 1B and 2A.
DOI: 10.6084/m9.figshare.20329569
title: Additional file 1 of The G1/S repressor WHI5 is expressed at similar levels throughout the cell cycle

description: Additional file 1. Raw quantitative data underlying Figure panels 1B and 2A.
DOI: 10.6084/m9.figshare.20329629
title: Additional file 1 of Whole-Genome Sequencing of Rice Mutant Library Members Induced by N-Methyl-N-Nitrosourea Mutagenesis of Fertilized Egg Cells

description: Additional file 1. Table S1. Primer sets used for validation by PCR and Sanger sequencing. Table S2. NGS sequencing results of the 266 M1 mutants. Table S3. SNVs used for validation by Sanger sequencing. Table S4. Number of SNVs on each chromosome. Table S5. InDel variants used for validation by Sanger sequencing. Table S6. Classification of SNV effects predicted using snpEff. Table S7. Summary of the inheritance analysis of variants. Table S8. Abnormal phenotypes found in the M2 lines.
DOI: 10.6084/m9.figshare.20329629.v1
title: Additional file 1 of Whole-Genome Sequencing of Rice Mutant Library Members Induced by N-Methyl-N-Nitrosourea Mutagenesis of Fertilized Egg Cells

description: Additional file 1. Table S1. Primer sets used for validation by PCR and Sanger sequencing. Table S2. NGS sequencing results of the 266 M1 mutants. Table S3. SNVs used for validation by Sanger sequencing. Table S4. Number of SNVs on each chromosome. Table S5. InDel variants used for validation by Sanger sequencing. Table S6. Classification of SNV effects predicted using snpEff. Table S7. Summary of the inheritance analysis of variants. Table S8. Abnormal phenotypes found in the M2 lines.
DOI: 10.6084/m9.figshare.20329690
title: Additional file 1 of Computational analysis of potential candidate genes involved in the cold stress response of ten Rosaceae members

description: Additional file 1: Supplementary Table S1. Details of plants from Rosaceae family considered in this study.
DOI: 10.6084/m9.figshare.20329690.v1
title: Additional file 1 of Computational analysis of potential candidate genes involved in the cold stress response of ten Rosaceae members

description: Additional file 1: Supplementary Table S1. Details of plants from Rosaceae family considered in this study.
DOI: 10.6084/m9.figshare.20329693
title: Additional file 2 of Computational analysis of potential candidate genes involved in the cold stress response of ten Rosaceae members

description: Additional file 2: Supplementary Table S2. Functions predicted for DEGs obtained from literature for F. vesca and M. domestica.
DOI: 10.6084/m9.figshare.20329693.v1
title: Additional file 2 of Computational analysis of potential candidate genes involved in the cold stress response of ten Rosaceae members

description: Additional file 2: Supplementary Table S2. Functions predicted for DEGs obtained from literature for F. vesca and M. domestica.
DOI: 10.6084/m9.figshare.20329696
title: Additional file 3 of Computational analysis of potential candidate genes involved in the cold stress response of ten Rosaceae members

description: Additional file 3: Supplementary Table S3. Chromosome information of syntelog genes identified from Rosaceae species.
DOI: 10.6084/m9.figshare.20329696.v1
title: Additional file 3 of Computational analysis of potential candidate genes involved in the cold stress response of ten Rosaceae members

description: Additional file 3: Supplementary Table S3. Chromosome information of syntelog genes identified from Rosaceae species.
DOI: 10.6084/m9.figshare.20329699
title: Additional file 4 of Computational analysis of potential candidate genes involved in the cold stress response of ten Rosaceae members

description: Additional file 4: Supplementary Table S4. Syntelog genes distribution in 32 gene family groups. Each groups include one or more genes from different Rosaceae species.
DOI: 10.6084/m9.figshare.20329699.v1
title: Additional file 4 of Computational analysis of potential candidate genes involved in the cold stress response of ten Rosaceae members

description: Additional file 4: Supplementary Table S4. Syntelog genes distribution in 32 gene family groups. Each groups include one or more genes from different Rosaceae species.
DOI: 10.6084/m9.figshare.20329702
title: Additional file 5 of Computational analysis of potential candidate genes involved in the cold stress response of ten Rosaceae members

description: Additional file 5: Supplementary Table S5. Popular transcription factor binding sites predicted for each syntelog genes using STIFAL. A z-score threshold of 1.5 was applied to filter out false positive hits. The position of binding sites in the 1000 bp promoter region has been included in the table.
DOI: 10.6084/m9.figshare.20329702.v1
title: Additional file 5 of Computational analysis of potential candidate genes involved in the cold stress response of ten Rosaceae members

description: Additional file 5: Supplementary Table S5. Popular transcription factor binding sites predicted for each syntelog genes using STIFAL. A z-score threshold of 1.5 was applied to filter out false positive hits. The position of binding sites in the 1000 bp promoter region has been included in the table.
DOI: 10.6084/m9.figshare.20329711
title: Additional file 8 of Computational analysis of potential candidate genes involved in the cold stress response of ten Rosaceae members

description: Additional file 8: Supplementary Table S6. The top 50 highly similar syntelog genes for F. vesca and M. domestica in other species were chosen based on their ADASS score.
DOI: 10.6084/m9.figshare.20329711.v1
title: Additional file 8 of Computational analysis of potential candidate genes involved in the cold stress response of ten Rosaceae members

description: Additional file 8: Supplementary Table S6. The top 50 highly similar syntelog genes for F. vesca and M. domestica in other species were chosen based on their ADASS score.
DOI: 10.6084/m9.figshare.20329734
title: Additional file 1 of Multivariate analysis of the effect of Chalazia on astigmatism in children

description: Additional file 1.
DOI: 10.6084/m9.figshare.20329734.v1
title: Additional file 1 of Multivariate analysis of the effect of Chalazia on astigmatism in children

description: Additional file 1.
DOI: 10.6084/m9.figshare.20329750
title: Additional file 1 of Genome-wide association and genotype by environment interactions for growth traits in U.S. Red Angus cattle

description: Additional file 1: Description and acronym definitions for summary data. Summary data for all genome-wide association analyses (GWAA) and genotype-by-environment genome-wide association analyses (GxE GWAA) performed for bovine birth weight, weaning weight, and yearling weight in tabular format.
DOI: 10.6084/m9.figshare.20329750.v1
title: Additional file 1 of Genome-wide association and genotype by environment interactions for growth traits in U.S. Red Angus cattle

description: Additional file 1: Description and acronym definitions for summary data. Summary data for all genome-wide association analyses (GWAA) and genotype-by-environment genome-wide association analyses (GxE GWAA) performed for bovine birth weight, weaning weight, and yearling weight in tabular format.
DOI: 10.6084/m9.figshare.20329851
title: Additional file 2 of Psychostimulant-induced aberrant DNA methylation in an in vitro model of human peripheral blood mononuclear cells

description: Additional file 2: Table S1. Control vs Amphetamine hypermethylated genes (p &lt; 0.001). Table S2. Control vs Amphetamine hypomethylated genes (p &lt; 0.001). Table S3. Control vs Cocaine hypermethylated genes (p &lt; 0.001). Table S4. Control vs Cocaine hypomethylated genes (p &lt; 0.001).
DOI: 10.6084/m9.figshare.20329851.v1
title: Additional file 2 of Psychostimulant-induced aberrant DNA methylation in an in vitro model of human peripheral blood mononuclear cells

description: Additional file 2: Table S1. Control vs Amphetamine hypermethylated genes (p &lt; 0.001). Table S2. Control vs Amphetamine hypomethylated genes (p &lt; 0.001). Table S3. Control vs Cocaine hypermethylated genes (p &lt; 0.001). Table S4. Control vs Cocaine hypomethylated genes (p &lt; 0.001).
DOI: 10.6084/m9.figshare.20329905.v1
title: Additional file 1 of Characterization of polymorphic microsatellite markers for the Japanese endangered land snail Mandarina

description: Additional file 1. List of microsatellite markers tested in this study. The table includes locus name, repeat motif, amplicon size, forward and reverse primer sequences, and fluorescent label. A dagger (‡) indicates that loci were monomorphic. An asterisk (*) indicates that loci showed unclear or no amplification.
DOI: 10.6084/m9.figshare.20329905
title: Additional file 1 of Characterization of polymorphic microsatellite markers for the Japanese endangered land snail Mandarina

description: Additional file 1. List of microsatellite markers tested in this study. The table includes locus name, repeat motif, amplicon size, forward and reverse primer sequences, and fluorescent label. A dagger (‡) indicates that loci were monomorphic. An asterisk (*) indicates that loci showed unclear or no amplification.
DOI: 10.6084/m9.figshare.20329908
title: Additional file 2 of Characterization of polymorphic microsatellite markers for the Japanese endangered land snail Mandarina

description: Additional file 2. List of samples used in this study. The table includes sample name, species name, wild or captive, sampling year (or birth year in the case of captive samples), and sampling site (or founders’ sampling site in the case of captive samples).
DOI: 10.6084/m9.figshare.20329908.v1
title: Additional file 2 of Characterization of polymorphic microsatellite markers for the Japanese endangered land snail Mandarina

description: Additional file 2. List of samples used in this study. The table includes sample name, species name, wild or captive, sampling year (or birth year in the case of captive samples), and sampling site (or founders’ sampling site in the case of captive samples).
DOI: 10.6084/m9.figshare.20329911
title: Additional file 3 of Characterization of polymorphic microsatellite markers for the Japanese endangered land snail Mandarina

description: Additional file 3. List of combinations of markers in the multiplex PCR. The table includes combination name, loci in each combination, and fluorescent label. A dagger (‡) and an asterisk (*) indicate that loci were not available for M. chichijimana and M. suenoae, respectively.