cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25982/101788.79/1828290
title: A KBase Case Study on Genome-wide Transcriptomics and Plant Primary Metabolism in Sorghum

description: A better understanding of the genetic and metabolic mechanisms that confer stress resistance and tolerance in plants is key to engineering new crops through advanced breeding technologies. This requires a systems biology approach that builds on a genome-wide understanding of the regulation of gene expression, plant metabolism, physiology and growth. In this study, we examine the response to drought stress in Sorghum, as we leverage the tools for transcriptomics and plant metabolic modeling we have implemented at the U.S. Department of Energy Systems Biology Knowledgebase (KBase). KBase enables researchers worldwide to collaborate and advance research by allowing them to upload private or public data into the KBase Narrative Interface, empowering them to analyze this data using a rich, extensible array of computational and data-analytics tools, and allows them to securely share scientific workflows and conclusions. We demonstrate how to use the current RNA-seq tools in KBase, applicable to both plants and microbes, to assemble and quantify long transcripts and identify differentially expressed genes effectively. More specifically, we demonstrate the utility of the platform by identifying key genes that are differentially expressed during drought-stress in Sorghum bicolor, which is an important sustainable production crop plant. We then show how to use KBase tools to predict the membership of genes in metabolic pathways and examine expression data in the context of metabolic subsystems. We demonstrate the power of the platform by making the data analysis and interpretation available to the biologists in the reproducible, re-usable, point-and-click format of a KBase Narrative thus promoting FAIR (Findable, Accessible, Interoperable and Reusable) guiding principles for scientific data management and stewardship.
DOI: 10.6084/m9.figshare.16926901
title: Supporting-Information

description: New paleomagnetic and chronological constraints on the Late Triassic position of the Eastern Qiangtang Terrane: Implications for the closure of the Paleo-Jinsha Ocean
DOI: 10.6084/m9.figshare.16926901.v3
title: Supporting-Information

description: New paleomagnetic and chronological constraints on the Late Triassic position of the Eastern Qiangtang Terrane: Implications for the closure of the Paleo-Jinsha Ocean
DOI: 10.5281/zenodo.5774370
title: Neural dynamics model testing dataset

description: These datasets are used to reproduce the results of the neural dynamics model from the paper https://doi.org/10.1101/725382.
DOI: 10.5281/zenodo.5774369
title: Neural dynamics model testing dataset

description: These datasets are used to reproduce the results of the neural dynamics model from the paper https://doi.org/10.1101/725382.
DOI: 10.18112/openneuro.ds002898.v1.2.0
title: Monash rsPET-MR
DOI: 10.6084/m9.figshare.17210233
title: Additional file 3 of JNK signaling provides a novel therapeutic target for Rett syndrome

description: Additional file 3. Data relative to Figure 5
DOI: 10.6084/m9.figshare.17210233.v1
title: Additional file 3 of JNK signaling provides a novel therapeutic target for Rett syndrome

description: Additional file 3. Data relative to Figure 5
DOI: 10.6084/m9.figshare.17210238
title: Additional file 1 of Capacity of community advisory boards for effective engagement in clinical research: a mixed methods study

description: Additional file 1. Dataset.
DOI: 10.6084/m9.figshare.17210238.v1
title: Additional file 1 of Capacity of community advisory boards for effective engagement in clinical research: a mixed methods study

description: Additional file 1. Dataset.
DOI: 10.6084/m9.figshare.17210253
title: Additional file 1 of Transcriptomics of single dose and repeated carbon black and ozone inhalation co-exposure highlight progressive pulmonary mitochondrial dysfunction

description: Additional file 1. Raw data values used for generation of heat maps for real time PCR, ELISA, and primer sequences.
DOI: 10.6084/m9.figshare.17210253.v1
title: Additional file 1 of Transcriptomics of single dose and repeated carbon black and ozone inhalation co-exposure highlight progressive pulmonary mitochondrial dysfunction

description: Additional file 1. Raw data values used for generation of heat maps for real time PCR, ELISA, and primer sequences.
DOI: 10.6084/m9.figshare.17210256
title: Additional file 2 of Transcriptomics of single dose and repeated carbon black and ozone inhalation co-exposure highlight progressive pulmonary mitochondrial dysfunction

description: Additional file 2. Differential expression analyses.
DOI: 10.6084/m9.figshare.17210256.v1
title: Additional file 2 of Transcriptomics of single dose and repeated carbon black and ozone inhalation co-exposure highlight progressive pulmonary mitochondrial dysfunction

description: Additional file 2. Differential expression analyses.
DOI: 10.6084/m9.figshare.17210295
title: Additional file 1 of qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE)

description: Additional file 1: Table S1. Metadata for RNA-seq datasets integrated in EucGenIE. In total 355 transcriptome datasets were integrated: 42 exAtlas datasets, 30 biotic interactions datasets and 283 transcriptomes from different F2 backcross individuals. Table S2. The 44 laccase genes detected in Eucalyptus with their corresponding BLASTP, HMMER and SignalP results. Genes encoding proteins with the three truncated domains of a canonical LAC and predicted to have a signal peptide were considered for analysis in this study. Table S3. Expression values in transcripts per million (TPM) of the 59 LAC/PRX genes, in the E. grandis exAtlas [35] and across biotic stress conditions [36–38]. Table S4. Secondary cell wall-related genes that were used for co-expression analysis. Table S5. Nine trait QTLs that co-locate with the eight LAC/PRX candidate genes from subnetwork 2 (Fig. 2, Table S3) or their eQTL positions. Table S6. Genes sharing eQTLs at the eleven eQTL positions associated with the eight LAC/PRX candidate genes from subnetwork 2 (Fig. 2, Additional file 1: Table S3). Table S7. Fisher's Exact Test results for enrichment of cell wall-related genes with eQTLs located at each of eleven eQTL positions, respectively, associated with the eight LAC/PRX candidate genes from subnetwork 2 (Fig. 2, Additional file 1: Table S3). Table S8. Transcription factors underlying the eleven eQTL peak positions associated with the eight LAC/PRX candidate genes from subnetwork 2 (Fig. 2, Additional file 1: Table S3). Table S9. Final score for ranking the eight LAC/PRX candidate genes from subnetwork 2 (Fig. 2, Additional file 1: Table S3) using multiple lines of evidence.
DOI: 10.6084/m9.figshare.17210295.v1
title: Additional file 1 of qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE)

description: Additional file 1: Table S1. Metadata for RNA-seq datasets integrated in EucGenIE. In total 355 transcriptome datasets were integrated: 42 exAtlas datasets, 30 biotic interactions datasets and 283 transcriptomes from different F2 backcross individuals. Table S2. The 44 laccase genes detected in Eucalyptus with their corresponding BLASTP, HMMER and SignalP results. Genes encoding proteins with the three truncated domains of a canonical LAC and predicted to have a signal peptide were considered for analysis in this study. Table S3. Expression values in transcripts per million (TPM) of the 59 LAC/PRX genes, in the E. grandis exAtlas [35] and across biotic stress conditions [36–38]. Table S4. Secondary cell wall-related genes that were used for co-expression analysis. Table S5. Nine trait QTLs that co-locate with the eight LAC/PRX candidate genes from subnetwork 2 (Fig. 2, Table S3) or their eQTL positions. Table S6. Genes sharing eQTLs at the eleven eQTL positions associated with the eight LAC/PRX candidate genes from subnetwork 2 (Fig. 2, Additional file 1: Table S3). Table S7. Fisher's Exact Test results for enrichment of cell wall-related genes with eQTLs located at each of eleven eQTL positions, respectively, associated with the eight LAC/PRX candidate genes from subnetwork 2 (Fig. 2, Additional file 1: Table S3). Table S8. Transcription factors underlying the eleven eQTL peak positions associated with the eight LAC/PRX candidate genes from subnetwork 2 (Fig. 2, Additional file 1: Table S3). Table S9. Final score for ranking the eight LAC/PRX candidate genes from subnetwork 2 (Fig. 2, Additional file 1: Table S3) using multiple lines of evidence.
DOI: 10.6084/m9.figshare.17210356.v1
title: Additional file 1 of Long-term effects of alcohol consumption on cognitive function in seniors: a cohort study in China

description: Additional file 1. List of variables explanation.
DOI: 10.6084/m9.figshare.17210356
title: Additional file 1 of Long-term effects of alcohol consumption on cognitive function in seniors: a cohort study in China

description: Additional file 1. List of variables explanation.
DOI: 10.6084/m9.figshare.17210359
title: Additional file 2 of Long-term effects of alcohol consumption on cognitive function in seniors: a cohort study in China

description: Additional file 2. List of variables incorporated in the variable selection process.
DOI: 10.6084/m9.figshare.17210359.v1
title: Additional file 2 of Long-term effects of alcohol consumption on cognitive function in seniors: a cohort study in China

description: Additional file 2. List of variables incorporated in the variable selection process.
DOI: 10.6084/m9.figshare.17210362.v1
title: Additional file 3 of Long-term effects of alcohol consumption on cognitive function in seniors: a cohort study in China

description: Additional file 3. Basic information for participants.
DOI: 10.6084/m9.figshare.17210362
title: Additional file 3 of Long-term effects of alcohol consumption on cognitive function in seniors: a cohort study in China

description: Additional file 3. Basic information for participants.
DOI: 10.6084/m9.figshare.17210368
title: Additional file 1 of Effectiveness of web application as educational media in increasing the caries risk knowledge and decreasing the caries risk score among dental students in Indonesia

description: Additional file 1: The main Data of answer of questionnaire of all respondents about result of evaluation of dental caries risk and the knowledge of respondent after using application web media.
DOI: 10.6084/m9.figshare.17210368.v1
title: Additional file 1 of Effectiveness of web application as educational media in increasing the caries risk knowledge and decreasing the caries risk score among dental students in Indonesia

description: Additional file 1: The main Data of answer of questionnaire of all respondents about result of evaluation of dental caries risk and the knowledge of respondent after using application web media.
DOI: 10.5281/zenodo.5784896
title: Genomic resequencing data in the northern bottlenose whale, Hyperoodon ampullatus

description: This dataset contains resequencing data used in our northern bottlenose whale genomics research. In this project, we analyzed population structure, demographic history, and signatures of selection. Source code for genomic analyses is available at github.com/edegreef/NBW-resequencing. Data uploaded here contain: <strong>NBW_all_variantcalls.vcf.gz</strong> - All variant calls, including both indels and SNPs <strong>NBW_SNPS_unfiltered.vcf.gz </strong>- Unfiltered SNPs <strong>NBW_SNPS_filtered_population_analyses.vcf.gz</strong> - Filtered SNPs for population analyses. Filtered for quality (removed qual &lt; 20, mq &lt; 30, qd &lt; 2, missingness &gt; 0.4), non-biallelic sites, autosomes, structural variants, minor allele count 2, minimum scaffold length 50kb <strong>NBW_SNPS_filtered_pruned_population_analyses.vcf.gz</strong> - Additionally LD-pruned with r2 &gt; 0.5 <strong>NBW_SNPS_filtered_demography_analyses.vcf.gz</strong> - Filtered SNPs for demography analyses. Filtered for quality, non-biallelic sites, autosomes, structural variants, minimum scaffold length 100kb. <strong>NBW_SNPS_filtered_imputed_haplotype_analyses.vcf.gz</strong> - Filtered and imputed SNPs for haplotype analyses. Filtered for quality, non-biallelic sites, autosomes, structural variants, max-missingness 0.1, minor allele count 2, minimum scaffold length 50kb. <strong>NBW_SNPS_filtered_Xchr.vcf.gz</strong> & <strong>NBW_SNPS_filtered_Ychr_males.vcf.gz</strong> - Filtered SNPs on X & Y chr. Filtered for quality, non-biallelic sites, structural variants, minor allele count 2, minimum scaffold length 50kb.
DOI: 10.6084/m9.figshare.17210548.v1
title: Additional file 1 of Reprogramming of RNA silencing triggered by cucumber mosaic virus infection in Arabidopsis

description: Additional file 1: Supplementary tables. Table S1. Libraries used in this study. Table S2. miRNA accumulation (RPM) in mock and CMV-infected sRNA libraries. Table S3. 21-nt mRNA-derived sRNA accumulation (RPM) in mock and CMV-infected sRNA libraries. Table S4. 21-nt TE-derived sRNA accumulation (RPM) in mock and CMV-infected sRNA libraries. Table S5. vsiRNA-targeted genes identified by PARE sequencing. Table S6. Primers used in this study.
DOI: 10.6084/m9.figshare.17210548
title: Additional file 1 of Reprogramming of RNA silencing triggered by cucumber mosaic virus infection in Arabidopsis

description: Additional file 1: Supplementary tables. Table S1. Libraries used in this study. Table S2. miRNA accumulation (RPM) in mock and CMV-infected sRNA libraries. Table S3. 21-nt mRNA-derived sRNA accumulation (RPM) in mock and CMV-infected sRNA libraries. Table S4. 21-nt TE-derived sRNA accumulation (RPM) in mock and CMV-infected sRNA libraries. Table S5. vsiRNA-targeted genes identified by PARE sequencing. Table S6. Primers used in this study.
DOI: 10.6084/m9.figshare.17210580
title: Additional file 10 of Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data

description: Additional file 10: Table S9. Correlation of drug sensitivity and Recurrent Heterogeneous Programs (RHP) Beyondcell scores.
DOI: 10.6084/m9.figshare.17210580.v1
title: Additional file 10 of Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data

description: Additional file 10: Table S9. Correlation of drug sensitivity and Recurrent Heterogeneous Programs (RHP) Beyondcell scores.
DOI: 10.6084/m9.figshare.17210583
title: Additional file 11 of Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data

description: Additional file 11: Table S10. Differential gene expression analysis of TC2 cells vs rest of TCs.
DOI: 10.6084/m9.figshare.17210583.v1
title: Additional file 11 of Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data

description: Additional file 11: Table S10. Differential gene expression analysis of TC2 cells vs rest of TCs.
DOI: 10.6084/m9.figshare.17210586
title: Additional file 12 of Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data

description: Additional file 12: Table S11. Differential EGFRi vulnerability analysis for undifferentiated cell lines in comparison to differentiated cells.
DOI: 10.6084/m9.figshare.17210586.v1
title: Additional file 12 of Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data

description: Additional file 12: Table S11. Differential EGFRi vulnerability analysis for undifferentiated cell lines in comparison to differentiated cells.
DOI: 10.6084/m9.figshare.17210589.v1
title: Additional file 13 of Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data

description: Additional file 13: Table S12. Differential sensitivity drugs for platinum-resistant patients for Stewart et al. dataset.
DOI: 10.6084/m9.figshare.17210589
title: Additional file 13 of Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data

description: Additional file 13: Table S12. Differential sensitivity drugs for platinum-resistant patients for Stewart et al. dataset.
DOI: 10.6084/m9.figshare.17210595
title: Additional file 2 of Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data

description: Additional file 2: Table S1. Beyondcell results for clusters and conditions with Ho et al. dataset.
DOI: 10.6084/m9.figshare.17210595.v1
title: Additional file 2 of Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data

description: Additional file 2: Table S1. Beyondcell results for clusters and conditions with Ho et al. dataset.
DOI: 10.6084/m9.figshare.17210598
title: Additional file 3 of Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data

description: Additional file 3: Table S2. Genes differentially expressed in cluster 5 for Ho et al. dataset.
DOI: 10.6084/m9.figshare.17210598.v1
title: Additional file 3 of Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data

description: Additional file 3: Table S2. Genes differentially expressed in cluster 5 for Ho et al. dataset.
DOI: 10.6084/m9.figshare.17210601
title: Additional file 4 of Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data

description: Additional file 4: Table S3. Cell distribution in clusters, cancer types and cell lines for Kinker et al. dataset.
DOI: 10.6084/m9.figshare.17210601.v1
title: Additional file 4 of Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data

description: Additional file 4: Table S3. Cell distribution in clusters, cancer types and cell lines for Kinker et al. dataset.
DOI: 10.6084/m9.figshare.17210607
title: Additional file 5 of Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data

description: Additional file 5: Table S4. Differential sensitivity drugs in cancer type and clusters for Kinker et al. dataset.
DOI: 10.6084/m9.figshare.17210607.v1
title: Additional file 5 of Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data

description: Additional file 5: Table S4. Differential sensitivity drugs in cancer type and clusters for Kinker et al. dataset.
DOI: 10.6084/m9.figshare.17210610
title: Additional file 6 of Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data

description: Additional file 6: Table S5. Beyondcell drug scores correlation modules for Kinker et al. dataset.
DOI: 10.6084/m9.figshare.17210610.v1
title: Additional file 6 of Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data

description: Additional file 6: Table S5. Beyondcell drug scores correlation modules for Kinker et al. dataset.
DOI: 10.6084/m9.figshare.17210613
title: Additional file 7 of Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data

description: Additional file 7: Table S6. Differential drug vulnerability analysis for TCs for Kinker et al. dataset using PRISM dataset.
DOI: 10.6084/m9.figshare.17210616.v1
title: Additional file 8 of Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data

description: Additional file 8: Table S7. Differential EGFRi vulnerability analysis for cell lines in TC1 in comparison to TC2 for Kinker et al. dataset using PRISM dataset.
DOI: 10.6084/m9.figshare.17210613.v1
title: Additional file 7 of Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data

description: Additional file 7: Table S6. Differential drug vulnerability analysis for TCs for Kinker et al. dataset using PRISM dataset.
DOI: 10.6084/m9.figshare.17210616
title: Additional file 8 of Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data

description: Additional file 8: Table S7. Differential EGFRi vulnerability analysis for cell lines in TC1 in comparison to TC2 for Kinker et al. dataset using PRISM dataset.
DOI: 10.6084/m9.figshare.17210619
title: Additional file 9 of Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data

description: Additional file 9: Table S8. Cell lines drug homogeneity for Kinker et al. dataset.
DOI: 10.6084/m9.figshare.17210619.v1
title: Additional file 9 of Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data

description: Additional file 9: Table S8. Cell lines drug homogeneity for Kinker et al. dataset.
DOI: 10.6084/m9.figshare.17210623
title: Additional file 3 of A unified evolutionary origin for the ubiquitous protein transporters SecY and YidC

description: Additional file 3. Structure-guided sequence alignment for the SecY halves.
DOI: 10.6084/m9.figshare.17210623.v1
title: Additional file 3 of A unified evolutionary origin for the ubiquitous protein transporters SecY and YidC

description: Additional file 3. Structure-guided sequence alignment for the SecY halves.
DOI: 10.6084/m9.figshare.17210626
title: Additional file 4 of A unified evolutionary origin for the ubiquitous protein transporters SecY and YidC

description: Additional file 4. Dali search results.
DOI: 10.6084/m9.figshare.17210626.v1
title: Additional file 4 of A unified evolutionary origin for the ubiquitous protein transporters SecY and YidC

description: Additional file 4. Dali search results.
DOI: 10.6084/m9.figshare.17210629
title: Additional file 5 of A unified evolutionary origin for the ubiquitous protein transporters SecY and YidC

description: Additional file 5. Predicted MJ0480/MJ0606 and TMCO1/C02orf24 structures.
DOI: 10.6084/m9.figshare.17210629.v1
title: Additional file 5 of A unified evolutionary origin for the ubiquitous protein transporters SecY and YidC

description: Additional file 5. Predicted MJ0480/MJ0606 and TMCO1/C02orf24 structures.
DOI: 10.6084/m9.figshare.17210641
title: Additional file 2 of Patterns of psychopathology and cognition in sex chromosome aneuploidy

description: Additional file 2: Supplementary Table 1. Demographic variables.
DOI: 10.6084/m9.figshare.17210641.v1
title: Additional file 2 of Patterns of psychopathology and cognition in sex chromosome aneuploidy

description: Additional file 2: Supplementary Table 1. Demographic variables.
DOI: 10.6084/m9.figshare.17210649
title: Additional file 2 of Mapping pre-harvest sprouting resistance loci in AAC Innova × AAC Tenacious spring wheat population

description: Additional file 2: Tables S1 to S9. Details of pre-harvest sprouting data, quantitative trait loci, associated markers, genetic/genomic positions, and previous studies.
DOI: 10.6084/m9.figshare.17210649.v1
title: Additional file 2 of Mapping pre-harvest sprouting resistance loci in AAC Innova × AAC Tenacious spring wheat population

description: Additional file 2: Tables S1 to S9. Details of pre-harvest sprouting data, quantitative trait loci, associated markers, genetic/genomic positions, and previous studies.
DOI: 10.6084/m9.figshare.17210685
title: Brazilian Tension Test from Triaxial testing on water permeability evolution of fractured shale

description: Data for Brazilian Tension Test
DOI: 10.6084/m9.figshare.17210682
title: Permeability Test from Triaxial testing on water permeability evolution of fractured shale

description: Data for Permeability Test
DOI: 10.6084/m9.figshare.17210682.v1
title: Permeability Test from Triaxial testing on water permeability evolution of fractured shale

description: Data for Permeability Test
DOI: 10.6084/m9.figshare.17210688
title: Uniaxial Compressive Test from Triaxial testing on water permeability evolution of fractured shale

description: Data for Uniaxial Compressive Test
DOI: 10.6084/m9.figshare.17210691.v1
title: NMR Test from Triaxial testing on water permeability evolution of fractured shale

description: Data for NMR Test
DOI: 10.6084/m9.figshare.17210688.v1
title: Uniaxial Compressive Test from Triaxial testing on water permeability evolution of fractured shale

description: Data for Uniaxial Compressive Test
DOI: 10.6084/m9.figshare.17210685.v1
title: Brazilian Tension Test from Triaxial testing on water permeability evolution of fractured shale

description: Data for Brazilian Tension Test