cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12134688
title: Additional file 2 of Functional and genomic characterization of three novel cell lines derived from a metastatic gallbladder cancer tumor

description: Additional file 2. Gene expression of normalized transcripts per million in Chilean GBC cell lines.
DOI: 10.6084/m9.figshare.12134691.v1
title: Additional file 2 of microRNA profiling in the Weddell seal suggests novel regulatory mechanisms contributing to diving adaptation

description: Additional file 2: Table S1. small RNA reads aligned against the final set of 559 high confidence miRNA loci. For each locus, the full hairpin sequence is shown, followed by the set of reads (one per line) perfectly matching the locus (with the corresponding abundance) and the predictive secondary structure of the miRNA hairpin.
DOI: 10.6084/m9.figshare.12134697.v1
title: Additional file 3 of Functional and genomic characterization of three novel cell lines derived from a metastatic gallbladder cancer tumor

description: Additional file 3. Exonic mutations in Chilean GBC cell lines.
DOI: 10.6084/m9.figshare.12134688.v1
title: Additional file 2 of Functional and genomic characterization of three novel cell lines derived from a metastatic gallbladder cancer tumor

description: Additional file 2. Gene expression of normalized transcripts per million in Chilean GBC cell lines.
DOI: 10.6084/m9.figshare.12134664
title: Additional file 2 of Identification and validation of mutation points associated with waxy phenotype in cassava

description: Table S1. List of cassava clones used in screening with single nucleotide amplified polymorphism [SNAP] markers.
DOI: 10.6084/m9.figshare.12134664.v1
title: Additional file 2 of Identification and validation of mutation points associated with waxy phenotype in cassava

description: Table S1. List of cassava clones used in screening with single nucleotide amplified polymorphism [SNAP] markers.
DOI: 10.6084/m9.figshare.12134646
title: Additional file 1 of Relationship of patient safety culture with factors influencing working environment such as working hours, the number of night shifts, and the number of days off among healthcare workers in Japan: a cross-sectional study

description: Additional file 1. Table A1. Patient Safety Culture Scores and SD in all Respondents.
DOI: 10.6084/m9.figshare.12134640
title: Additional file 8 of Transcriptomic diversity in seedling roots of European flint maize in response to cold

description: Additional file 8: Table S7: Gene ontology (GO) terms enriched (p
DOI: 10.6084/m9.figshare.12134643
title: Additional file 9 of Transcriptomic diversity in seedling roots of European flint maize in response to cold

description: Additional file 9: Table S8: Characteristics of the 563 genes associated to growth rate at cold conditions (cf. Fig. 4).
DOI: 10.6084/m9.figshare.12134646.v1
title: Additional file 1 of Relationship of patient safety culture with factors influencing working environment such as working hours, the number of night shifts, and the number of days off among healthcare workers in Japan: a cross-sectional study

description: Additional file 1. Table A1. Patient Safety Culture Scores and SD in all Respondents.
DOI: 10.6084/m9.figshare.12134634
title: Additional file 7 of Transcriptomic diversity in seedling roots of European flint maize in response to cold

description: Additional file 7: Table S6: Characteristics of genes exclusively expressed in the three most cold tolerant genotypes (see Fig. 5d).
DOI: 10.6084/m9.figshare.12134640.v1
title: Additional file 8 of Transcriptomic diversity in seedling roots of European flint maize in response to cold

description: Additional file 8: Table S7: Gene ontology (GO) terms enriched (p
DOI: 10.6084/m9.figshare.12134643.v1
title: Additional file 9 of Transcriptomic diversity in seedling roots of European flint maize in response to cold

description: Additional file 9: Table S8: Characteristics of the 563 genes associated to growth rate at cold conditions (cf. Fig. 4).
DOI: 10.6084/m9.figshare.12134628
title: Additional file 6 of Transcriptomic diversity in seedling roots of European flint maize in response to cold

description: Additional file 6: Table S5: Characteristics of the 3254 cold tolerant genes (see Fig. 3).
DOI: 10.6084/m9.figshare.12134628.v1
title: Additional file 6 of Transcriptomic diversity in seedling roots of European flint maize in response to cold

description: Additional file 6: Table S5: Characteristics of the 3254 cold tolerant genes (see Fig. 3).
DOI: 10.6084/m9.figshare.12134634.v1
title: Additional file 7 of Transcriptomic diversity in seedling roots of European flint maize in response to cold

description: Additional file 7: Table S6: Characteristics of genes exclusively expressed in the three most cold tolerant genotypes (see Fig. 5d).
DOI: 10.6084/m9.figshare.12134622
title: Additional file 5 of Transcriptomic diversity in seedling roots of European flint maize in response to cold

description: Additional file 5: Table S4: Gene ontology (GO) terms enriched (p
DOI: 10.6084/m9.figshare.12134613
title: Additional file 4 of Transcriptomic diversity in seedling roots of European flint maize in response to cold

description: Additional file 4: Table S3: Up- (1) or down regulated (− 1) genes differentially expressed between cold and control conditions in the 21 genotypes. No differential expression is depicted as 0. Sum indicates the sum of differential expression scores (1, 0, − 1) across genotypes, sum tolerant lines and sum susceptible lines are the sums of all genotypes in the respective class.
DOI: 10.6084/m9.figshare.12134613.v1
title: Additional file 4 of Transcriptomic diversity in seedling roots of European flint maize in response to cold

description: Additional file 4: Table S3: Up- (1) or down regulated (− 1) genes differentially expressed between cold and control conditions in the 21 genotypes. No differential expression is depicted as 0. Sum indicates the sum of differential expression scores (1, 0, − 1) across genotypes, sum tolerant lines and sum susceptible lines are the sums of all genotypes in the respective class.
DOI: 10.6084/m9.figshare.12134622.v1
title: Additional file 5 of Transcriptomic diversity in seedling roots of European flint maize in response to cold

description: Additional file 5: Table S4: Gene ontology (GO) terms enriched (p
DOI: 10.6084/m9.figshare.12134607
title: Additional file 3 of Transcriptomic diversity in seedling roots of European flint maize in response to cold

description: Additional file 3: Table S2: Characteristics of the 148 genes differentially expressed between cold and control conditions (see Fig. 3).
DOI: 10.6084/m9.figshare.12134604
title: Additional file 1 of Construction of engineered yeast producing ammonia from glutamine and soybean residues (okara)

description: Additional file 1: Table S1. MRM conditions for the quantification of amino acids from soybean residues by LC–MS/MS. l-glutamine-13C5,15N2, and labeled amino acid standards [50 μg/mL algae hydrolysate amino acid mixture (U-13C, 97%–99%; U-15N, 97%–99%; Cambridge Isotope Laboratories CNLM-452-0.5)] as an IS were used for quantification of amino acids in pretreated soybean residues.
DOI: 10.6084/m9.figshare.12134598
title: Additional file 2 of Transcriptomic diversity in seedling roots of European flint maize in response to cold

description: Additional file 2: Table S1: Overview of the sample distribution within genotype, treatment, biological replication, RNA-Seq output, and mapping results.
DOI: 10.6084/m9.figshare.12134604.v1
title: Additional file 1 of Construction of engineered yeast producing ammonia from glutamine and soybean residues (okara)

description: Additional file 1: Table S1. MRM conditions for the quantification of amino acids from soybean residues by LC–MS/MS. l-glutamine-13C5,15N2, and labeled amino acid standards [50 μg/mL algae hydrolysate amino acid mixture (U-13C, 97%–99%; U-15N, 97%–99%; Cambridge Isotope Laboratories CNLM-452-0.5)] as an IS were used for quantification of amino acids in pretreated soybean residues.
DOI: 10.6084/m9.figshare.12134607.v1
title: Additional file 3 of Transcriptomic diversity in seedling roots of European flint maize in response to cold

description: Additional file 3: Table S2: Characteristics of the 148 genes differentially expressed between cold and control conditions (see Fig. 3).
DOI: 10.6084/m9.figshare.12134598.v1
title: Additional file 2 of Transcriptomic diversity in seedling roots of European flint maize in response to cold

description: Additional file 2: Table S1: Overview of the sample distribution within genotype, treatment, biological replication, RNA-Seq output, and mapping results.
DOI: 10.6084/m9.figshare.12134619
title: Atmospheric dynamics patterns in southern central Asia since 800 ka revealed by loess-paleosol sequences in Tajikistan

description: This dataset includes the depth and age sequences of loess grain size &gt;25 mm fraction (GT25), Lightness and frequency-dependent magnetic susceptibility (χ<sub>fd</sub>) in Darri Kalon (DK) section of Tajikistan.
DOI: 10.6084/m9.figshare.12134577
title: Additional file 10 of Transcriptomic diversity in seedling roots of European flint maize in response to cold

description: Additional file 10: Table S9: Gene ontology (GO) terms enriched (p
DOI: 10.6084/m9.figshare.12134577.v1
title: Additional file 10 of Transcriptomic diversity in seedling roots of European flint maize in response to cold

description: Additional file 10: Table S9: Gene ontology (GO) terms enriched (p
DOI: 10.6084/m9.figshare.12134550
title: Additional file 7 of Being red, blue and green: the genetic basis of coloration differences in the strawberry poison frog (Oophaga pumilio)

description: Additional file 7 SM Table 7: List of the color-associated genes, compiled from the literature and used for functional interpretation.
DOI: 10.6084/m9.figshare.12134550.v1
title: Additional file 7 of Being red, blue and green: the genetic basis of coloration differences in the strawberry poison frog (Oophaga pumilio)

description: Additional file 7 SM Table 7: List of the color-associated genes, compiled from the literature and used for functional interpretation.
DOI: 10.6084/m9.figshare.12134544
title: Additional file 6 of Being red, blue and green: the genetic basis of coloration differences in the strawberry poison frog (Oophaga pumilio)

description: Additional file 6 SM Table 6: Differentially expressed genes in skin samples of different color phenotypes of Oophaga pumilio and Dendrobates auratus [33].
DOI: 10.6084/m9.figshare.12134544.v1
title: Additional file 6 of Being red, blue and green: the genetic basis of coloration differences in the strawberry poison frog (Oophaga pumilio)

description: Additional file 6 SM Table 6: Differentially expressed genes in skin samples of different color phenotypes of Oophaga pumilio and Dendrobates auratus [33].
DOI: 10.6084/m9.figshare.12134532
title: Additional file 4 of Being red, blue and green: the genetic basis of coloration differences in the strawberry poison frog (Oophaga pumilio)

description: Additional file 4 SMTable 4: Results of the over-representation analysis of the 1445 genes found to be differentially expressed between color phenotypes of O. pumilio frogs. Analysis was conducted using ConsensusPathDB. GO category names whose hypergeometric p-value
DOI: 10.6084/m9.figshare.12134538
title: Additional file 5 of Being red, blue and green: the genetic basis of coloration differences in the strawberry poison frog (Oophaga pumilio)

description: Additional file 5 SM Table 5: Annotated SNPs showing signatures of positive selection in BayeScan analyses. Putative paralogs are denoted in the symbol column by a “_” followed by a number. Functional impact of SNPs was evaluated on the transcripts of each gene using SNPdat. SNPs on genes that also showed significant expression differences are highlighted in bold (see main text for further details).
DOI: 10.6084/m9.figshare.12134532.v1
title: Additional file 4 of Being red, blue and green: the genetic basis of coloration differences in the strawberry poison frog (Oophaga pumilio)

description: Additional file 4 SMTable 4: Results of the over-representation analysis of the 1445 genes found to be differentially expressed between color phenotypes of O. pumilio frogs. Analysis was conducted using ConsensusPathDB. GO category names whose hypergeometric p-value
DOI: 10.6084/m9.figshare.12134538.v1
title: Additional file 5 of Being red, blue and green: the genetic basis of coloration differences in the strawberry poison frog (Oophaga pumilio)

description: Additional file 5 SM Table 5: Annotated SNPs showing signatures of positive selection in BayeScan analyses. Putative paralogs are denoted in the symbol column by a “_” followed by a number. Functional impact of SNPs was evaluated on the transcripts of each gene using SNPdat. SNPs on genes that also showed significant expression differences are highlighted in bold (see main text for further details).
DOI: 10.6084/m9.figshare.12134526
title: Additional file 3 of Being red, blue and green: the genetic basis of coloration differences in the strawberry poison frog (Oophaga pumilio)

description: Additional file 3 SMTable 3: Results of the functional classification of gene expression clusters at the pathway level. The results were obtained in PANTHER using the symbols of the differentially expressed genes mapped against the Xenopus tropicalis annotation.
DOI: 10.6084/m9.figshare.12134517
title: Additional file 2 of Being red, blue and green: the genetic basis of coloration differences in the strawberry poison frog (Oophaga pumilio)

description: Additional file 2 SMTable 2: Results of the differential expression analysis between blue, green and red color phenotypes of O. pumilio, obtained using Sleuth software. For each gene, the number of transcripts compared, q-value, expression pattern and color-associated function are presented. Putative paralogs are denoted in the symbol column by a “_” followed by a number.
DOI: 10.6084/m9.figshare.12134526.v1
title: Additional file 3 of Being red, blue and green: the genetic basis of coloration differences in the strawberry poison frog (Oophaga pumilio)

description: Additional file 3 SMTable 3: Results of the functional classification of gene expression clusters at the pathway level. The results were obtained in PANTHER using the symbols of the differentially expressed genes mapped against the Xenopus tropicalis annotation.
DOI: 10.6084/m9.figshare.12134517.v1
title: Additional file 2 of Being red, blue and green: the genetic basis of coloration differences in the strawberry poison frog (Oophaga pumilio)

description: Additional file 2 SMTable 2: Results of the differential expression analysis between blue, green and red color phenotypes of O. pumilio, obtained using Sleuth software. For each gene, the number of transcripts compared, q-value, expression pattern and color-associated function are presented. Putative paralogs are denoted in the symbol column by a “_” followed by a number.
DOI: 10.6084/m9.figshare.12134490
title: Additional file 2 of Who should decide for local health services? A mixed methods study of preferences for decision-making in the decentralized Philippine health system

description: Additional file 2. Anonymized dataset of responses to the online survey
DOI: 10.6084/m9.figshare.12134490.v1
title: Additional file 2 of Who should decide for local health services? A mixed methods study of preferences for decision-making in the decentralized Philippine health system

description: Additional file 2. Anonymized dataset of responses to the online survey
DOI: 10.6084/m9.figshare.12134382
title: Additional file 11 of PGRMC1 effects on metabolism, genomic mutation and CpG methylation imply crucial roles in animal biology and disease

description: Additional file 11 File S1. A zip archive containing excel files with the most significant pathways enrichment results from methylomics analysis including those of Fig. S7B, Table S2 and Table S3. The archive unpacks as five separate folders, each containing the following pathways analysis results. A) All GO enrichments for each cell comparison significant below the adjP =0.001 level. B) All GO enrichments that were uique to a particular cell comparison. C) KEGG enriched pathways for each cell comparison, with analyses performed separately on hypermethyalted (files labelled up) and hyperemethylated (files labelled down) probes. These correspond to the pathways of of Fig. S7B. D) All KEGG enriched pathways from C which were unique to a particular cell comparison. E) All All Reactome enriched pathways for each cell comparison significant below the adjP =0.05 level.
DOI: 10.6084/m9.figshare.12134382.v1
title: Additional file 11 of PGRMC1 effects on metabolism, genomic mutation and CpG methylation imply crucial roles in animal biology and disease

description: Additional file 11 File S1. A zip archive containing excel files with the most significant pathways enrichment results from methylomics analysis including those of Fig. S7B, Table S2 and Table S3. The archive unpacks as five separate folders, each containing the following pathways analysis results. A) All GO enrichments for each cell comparison significant below the adjP =0.001 level. B) All GO enrichments that were uique to a particular cell comparison. C) KEGG enriched pathways for each cell comparison, with analyses performed separately on hypermethyalted (files labelled up) and hyperemethylated (files labelled down) probes. These correspond to the pathways of of Fig. S7B. D) All KEGG enriched pathways from C which were unique to a particular cell comparison. E) All All Reactome enriched pathways for each cell comparison significant below the adjP =0.05 level.
DOI: 10.6084/m9.figshare.12134307
title: Additional file 7 of Reduced serum levels of pro-inflammatory chemokines in fragile X syndrome

description: Additional file 7: Table S6. Correlations and associated adjusted p-values for each biomarker pair among the 16 features identified by K-sparse clustering in healthy controls and FXS patients. For each biomarker pair, correlations r coefficients and the corresponding adjusted p-values are presented in upper triangle and lower triangle, respectively. Adjusted p-values
DOI: 10.6084/m9.figshare.12134304
title: Additional file 6 of Reduced serum levels of pro-inflammatory chemokines in fragile X syndrome

description: Additional file 6: Table S5.W matrix highlighting the respective discriminative weight of each feature in the 4 dimensions of the K-sparse model
DOI: 10.6084/m9.figshare.12134295
title: Additional file 3 of Reduced serum levels of pro-inflammatory chemokines in fragile X syndrome

description: Additional file 3: Table S2. Comparison analysis of serum biomarkers levels in FXS patients and controls in the whole dataset (N = 54) and in a reduced dataset consisting of male individuals (N = 44). Minimum (Min), first quantile (Q1), median, third quantile (Q3), maximum (Max), mean, standard deviation (SD) are indicated for each group. The r effect size statistic, raw p-values (p-value) and adjusted p-values for the Mann–Whitney U-test, are indicated both for the full dataset (N = 54, n = 25 FXS patients, n = 29 controls) and for the dataset reduced to male individuals (N = 44, n = 20 FXS patients, n = 24 controls).
DOI: 10.6084/m9.figshare.12134298
title: Additional file 4 of Reduced serum levels of pro-inflammatory chemokines in fragile X syndrome

description: Additional file 4: Table S3. Over-represented pathways based on the list of significantly downregulated chemokines in FXS patients
DOI: 10.6084/m9.figshare.12134301
title: Additional file 5 of Reduced serum levels of pro-inflammatory chemokines in fragile X syndrome

description: Additional file 5: Table S4. Silhouette values for each individual in the K-sparse clustering analysis with k = 2 and clustering accuracy based on samples class
DOI: 10.6084/m9.figshare.12134304.v1
title: Additional file 6 of Reduced serum levels of pro-inflammatory chemokines in fragile X syndrome

description: Additional file 6: Table S5.W matrix highlighting the respective discriminative weight of each feature in the 4 dimensions of the K-sparse model
DOI: 10.6084/m9.figshare.12134292
title: Additional file 2 of Reduced serum levels of pro-inflammatory chemokines in fragile X syndrome

description: Additional file 2: Table S1. Percentage of detection of biomarkers in FXS patients vs. healthy controls and inclusion of analytes
DOI: 10.6084/m9.figshare.12134298.v1
title: Additional file 4 of Reduced serum levels of pro-inflammatory chemokines in fragile X syndrome

description: Additional file 4: Table S3. Over-represented pathways based on the list of significantly downregulated chemokines in FXS patients
DOI: 10.6084/m9.figshare.12134301.v1
title: Additional file 5 of Reduced serum levels of pro-inflammatory chemokines in fragile X syndrome

description: Additional file 5: Table S4. Silhouette values for each individual in the K-sparse clustering analysis with k = 2 and clustering accuracy based on samples class
DOI: 10.6084/m9.figshare.12134307.v1
title: Additional file 7 of Reduced serum levels of pro-inflammatory chemokines in fragile X syndrome

description: Additional file 7: Table S6. Correlations and associated adjusted p-values for each biomarker pair among the 16 features identified by K-sparse clustering in healthy controls and FXS patients. For each biomarker pair, correlations r coefficients and the corresponding adjusted p-values are presented in upper triangle and lower triangle, respectively. Adjusted p-values
DOI: 10.6084/m9.figshare.12134292.v1
title: Additional file 2 of Reduced serum levels of pro-inflammatory chemokines in fragile X syndrome

description: Additional file 2: Table S1. Percentage of detection of biomarkers in FXS patients vs. healthy controls and inclusion of analytes
DOI: 10.6084/m9.figshare.12134295.v1
title: Additional file 3 of Reduced serum levels of pro-inflammatory chemokines in fragile X syndrome

description: Additional file 3: Table S2. Comparison analysis of serum biomarkers levels in FXS patients and controls in the whole dataset (N = 54) and in a reduced dataset consisting of male individuals (N = 44). Minimum (Min), first quantile (Q1), median, third quantile (Q3), maximum (Max), mean, standard deviation (SD) are indicated for each group. The r effect size statistic, raw p-values (p-value) and adjusted p-values for the Mann–Whitney U-test, are indicated both for the full dataset (N = 54, n = 25 FXS patients, n = 29 controls) and for the dataset reduced to male individuals (N = 44, n = 20 FXS patients, n = 24 controls).
DOI: 10.6084/m9.figshare.12134187
title: Additional file 3 of Computational models applied to metabolomics data hints at the relevance of glutamine metabolism in breast cancer

description: File S3: Cytoscape file of the network combining metabolomics and flux activities.
DOI: 10.6084/m9.figshare.12134184
title: Additional file 2 of Computational models applied to metabolomics data hints at the relevance of glutamine metabolism in breast cancer

description: File S2: Cytoscape file of the network combining gene expression and metabolomics data.
DOI: 10.6084/m9.figshare.12134187.v1
title: Additional file 3 of Computational models applied to metabolomics data hints at the relevance of glutamine metabolism in breast cancer

description: File S3: Cytoscape file of the network combining metabolomics and flux activities.
DOI: 10.6084/m9.figshare.12134178
title: Additional file 1 of Computational models applied to metabolomics data hints at the relevance of glutamine metabolism in breast cancer

description: File S1: Cytoscape file of metabolomics network.
DOI: 10.6084/m9.figshare.12134184.v1
title: Additional file 2 of Computational models applied to metabolomics data hints at the relevance of glutamine metabolism in breast cancer

description: File S2: Cytoscape file of the network combining gene expression and metabolomics data.
DOI: 10.6084/m9.figshare.12134178.v1
title: Additional file 1 of Computational models applied to metabolomics data hints at the relevance of glutamine metabolism in breast cancer

description: File S1: Cytoscape file of metabolomics network.