cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9277385
title: Additional file 10: of GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

description: Table S10. Distribution of significant marker associations for flowering time and photoperiod response, evaluated under controlled environment cabinets and field conditions (three sites) in a GWAS panel of canola (XLSX 936 kb)
DOI: 10.6084/m9.figshare.9277385.v1
title: Additional file 10: of GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

description: Table S10. Distribution of significant marker associations for flowering time and photoperiod response, evaluated under controlled environment cabinets and field conditions (three sites) in a GWAS panel of canola (XLSX 936 kb)
DOI: 10.6084/m9.figshare.9277394
title: Additional file 11: of GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

description: Table S11. Candidate gene associated with flowering time and photoperiodic response in the GWAS and DH population. (XLS 35 kb)
DOI: 10.6084/m9.figshare.9277394.v1
title: Additional file 11: of GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

description: Table S11. Candidate gene associated with flowering time and photoperiodic response in the GWAS and DH population. (XLS 35 kb)
DOI: 10.6084/m9.figshare.9277406
title: Additional file 13: of GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

description: Table S13. Genetic correlation between different traits measured in the doubled haploid population from Skipton/Ag-Spectrum//Skipton across environments. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.9277406.v1
title: Additional file 13: of GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

description: Table S13. Genetic correlation between different traits measured in the doubled haploid population from Skipton/Ag-Spectrum//Skipton across environments. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.9277412
title: Additional file 14: of GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

description: Table S14. Genome-wide association analysis (eQTL) showing statistical association between Illumina SNP markers and expression data of BnC6.FT gene in 300 accessions of B. napus. Linear marker regression analysis was performed in the SVS package (Golden Helix). (XLSX 11 kb)
DOI: 10.6084/m9.figshare.9277412.v1
title: Additional file 14: of GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

description: Table S14. Genome-wide association analysis (eQTL) showing statistical association between Illumina SNP markers and expression data of BnC6.FT gene in 300 accessions of B. napus. Linear marker regression analysis was performed in the SVS package (Golden Helix). (XLSX 11 kb)
DOI: 10.6084/m9.figshare.9277418
title: Additional file 15: of GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

description: Table S15. Gene structures of different FT paralogs identified in the resequence data from 21 accessions of B. napus (test samples). Exon/intron genomic coordinates of the B. napus reference cultivar are based on the current gene models (annotation version 5). Numbers in the table represent lengths in base-pairs. Exon/intron length variation in the 21 accessions (in bold) is only counted for InDels that are homozygous. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.9277418.v1
title: Additional file 15: of GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

description: Table S15. Gene structures of different FT paralogs identified in the resequence data from 21 accessions of B. napus (test samples). Exon/intron genomic coordinates of the B. napus reference cultivar are based on the current gene models (annotation version 5). Numbers in the table represent lengths in base-pairs. Exon/intron length variation in the 21 accessions (in bold) is only counted for InDels that are homozygous. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.9277424
title: Additional file 16: of GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

description: Table S16. Summary of structural and polymorphic variation identified among 21 B. napus accessions representing GWAS and validation population used in this study. Numbers in table represent counts of unique variants observed across the 21 accessions. Abbreviations: SNV: structural nucleotide variant, InDel: Insertion-deletion, S = Number of segregating sites, ps = S/n, Î = ps/a1, Ď = nucleotide diversity, and D is the Tajima test statistic (Tajima, 1989). (XLSX 12 kb)
DOI: 10.6084/m9.figshare.9277424.v1
title: Additional file 16: of GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

description: Table S16. Summary of structural and polymorphic variation identified among 21 B. napus accessions representing GWAS and validation population used in this study. Numbers in table represent counts of unique variants observed across the 21 accessions. Abbreviations: SNV: structural nucleotide variant, InDel: Insertion-deletion, S = Number of segregating sites, ps = S/n, Î = ps/a1, Ď = nucleotide diversity, and D is the Tajima test statistic (Tajima, 1989). (XLSX 12 kb)
DOI: 10.6084/m9.figshare.17140930.v1
title: Additional file 3 of Repression of the expression of proinflammatory genes by mitochondrial transcription factor A is linked to its alternative splicing regulation in human lung epithelial cells

description: Additional file 3. Summary of sample names, description, the RNA-seq sequencing information and mapping results in each sample.
DOI: 10.6084/m9.figshare.17140933
title: Additional file 4 of Repression of the expression of proinflammatory genes by mitochondrial transcription factor A is linked to its alternative splicing regulation in human lung epithelial cells

description: Additional file 4. Gene expression level (FPKM).
DOI: 10.6084/m9.figshare.9277430
title: Additional file 17: of GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

description: Table S17. FT variant used for revealing diversity in BnaA07g33120D among 21 accessions resequenced. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.17140942.v1
title: Additional file 6 of Repression of the expression of proinflammatory genes by mitochondrial transcription factor A is linked to its alternative splicing regulation in human lung epithelial cells

description: Additional file 6. List of GO terms and KEGG pathways enriched by DEGs.
DOI: 10.6084/m9.figshare.9277430.v1
title: Additional file 17: of GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

description: Table S17. FT variant used for revealing diversity in BnaA07g33120D among 21 accessions resequenced. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.17140930
title: Additional file 3 of Repression of the expression of proinflammatory genes by mitochondrial transcription factor A is linked to its alternative splicing regulation in human lung epithelial cells

description: Additional file 3. Summary of sample names, description, the RNA-seq sequencing information and mapping results in each sample.
DOI: 10.6084/m9.figshare.17140942
title: Additional file 6 of Repression of the expression of proinflammatory genes by mitochondrial transcription factor A is linked to its alternative splicing regulation in human lung epithelial cells

description: Additional file 6. List of GO terms and KEGG pathways enriched by DEGs.
DOI: 10.6084/m9.figshare.17140954
title: Additional file 9 of Repression of the expression of proinflammatory genes by mitochondrial transcription factor A is linked to its alternative splicing regulation in human lung epithelial cells

description: Additional file 9. The GO enrichment analysis of the genes overlapped by DEG and AS.
DOI: 10.6084/m9.figshare.8228051
title: MOESM1 of Proteome analysis of xylose metabolism in Rhodotorula toruloides during lipid production

description: Additional file 1. Complete list of proteins detected during batch cultivation of R. toruloides in minimal medium containing either glucose or xylose and their relative expression values.
DOI: 10.6084/m9.figshare.9277436
title: Additional file 18: of GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

description: Table S18. FT variant used for revealing diversity in BnaC04g14850D among 21 accessions resequenced. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.9277436.v1
title: Additional file 18: of GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

description: Table S18. FT variant used for revealing diversity in BnaC04g14850D among 21 accessions resequenced. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.17140945
title: Additional file 7 of Repression of the expression of proinflammatory genes by mitochondrial transcription factor A is linked to its alternative splicing regulation in human lung epithelial cells

description: Additional file 7. Statistics and classification of known and novel alternative splcing events.
DOI: 10.6084/m9.figshare.8228066
title: MOESM3 of Proteome analysis of xylose metabolism in Rhodotorula toruloides during lipid production

description: Additional file 3. Relative levels of differentially expressed proteins in glucose-grown R. toruloides during either exponential cultivated phase or lipid production phase.
DOI: 10.6084/m9.figshare.19762452
title: CircRNA protein tyrosine phosphatase receptor type a suppresses proliferation and induces apoptosis of lung adenocarcinoma cells via regulation of microRNA-582-3p

description: Circular RNAs (circRNAs) are associated with cancer progression. The present study aimed to examine the function of circRNA protein tyrosine phosphatase receptor type A (circRNA_PTPRA) in lung cancer cells and elucidate the underlying molecular mechanisms. The levels of circRNA_PTPRA and microRNA (miRNA/miR)-582-3p were measured in lung cancer tissue and cells using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Cell proliferation and apoptosis were evaluated using an 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and flow cytometry, respectively. The expression of cyclin D1, caspase-3, and cleaved caspase-3 was assessed via western blotting. The sites of circRNA_PTPRA/miR-582-3p interaction were identified using StarBase, and validated using a dual-luciferase reporter assay. We observed that circRNA_PTPRA levels were remarkably decreased, and miR-582-3p expression was up-regulated in lung cancer tissues and cells. circRNA_PTPRA directly interacts with miR-582-3p and downregulates miR-582-3p expression in lung cancer cells. Moreover, an miR-582-3p inhibitor decreased lung cancer cell proliferation and promoted apoptosis. The overexpression of circRNA_PTPRA decreased cell proliferation and increased apoptotic cell numbers, whereas miR-582-3p overexpression reversed these effects. These findings demonstrate that the up-regulation of circRNA_PTPRA significantly reduces lung cancer cell proliferation and induces apoptosis by regulating miR-582-3p expression.
DOI: 10.6084/m9.figshare.8228087.v1
title: MOESM7 of Proteome analysis of xylose metabolism in Rhodotorula toruloides during lipid production

description: Additional file 7. Relative levels of differentially expressed proteins in R. toruloides grown on either glucose or xylose during lipid accumulation phase.
DOI: 10.6084/m9.figshare.9277445
title: Additional file 1: of GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

description: Table S1. Accessions used to assess natural variation in flowering time and photoperiodic response. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.19762452.v1
title: CircRNA protein tyrosine phosphatase receptor type a suppresses proliferation and induces apoptosis of lung adenocarcinoma cells via regulation of microRNA-582-3p

description: Circular RNAs (circRNAs) are associated with cancer progression. The present study aimed to examine the function of circRNA protein tyrosine phosphatase receptor type A (circRNA_PTPRA) in lung cancer cells and elucidate the underlying molecular mechanisms. The levels of circRNA_PTPRA and microRNA (miRNA/miR)-582-3p were measured in lung cancer tissue and cells using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Cell proliferation and apoptosis were evaluated using an 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and flow cytometry, respectively. The expression of cyclin D1, caspase-3, and cleaved caspase-3 was assessed via western blotting. The sites of circRNA_PTPRA/miR-582-3p interaction were identified using StarBase, and validated using a dual-luciferase reporter assay. We observed that circRNA_PTPRA levels were remarkably decreased, and miR-582-3p expression was up-regulated in lung cancer tissues and cells. circRNA_PTPRA directly interacts with miR-582-3p and downregulates miR-582-3p expression in lung cancer cells. Moreover, an miR-582-3p inhibitor decreased lung cancer cell proliferation and promoted apoptosis. The overexpression of circRNA_PTPRA decreased cell proliferation and increased apoptotic cell numbers, whereas miR-582-3p overexpression reversed these effects. These findings demonstrate that the up-regulation of circRNA_PTPRA significantly reduces lung cancer cell proliferation and induces apoptosis by regulating miR-582-3p expression.
DOI: 10.6084/m9.figshare.8228087
title: MOESM7 of Proteome analysis of xylose metabolism in Rhodotorula toruloides during lipid production

description: Additional file 7. Relative levels of differentially expressed proteins in R. toruloides grown on either glucose or xylose during lipid accumulation phase.
DOI: 10.6084/m9.figshare.9277445.v1
title: Additional file 1: of GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

description: Table S1. Accessions used to assess natural variation in flowering time and photoperiodic response. (XLSX 24 kb)
DOI: 10.5281/zenodo.3981105
title: Topological Network of the Dutch Fairway Information System

description: Topological fairway network derived from the Dutch Fairway Information System. The data is processed to be topological connected and usable for transport network analysis. Files <code>network_digital_twin_v0.1.yaml</code> This is the NetworkX file for the Rhine corridor extending from Rotterdam (NLD) to Basel (Switzerland). <code>network_digital_twin_v0.1.geojson</code> This is the geojson file for the Rhine corridor extending from Rotterdam (NLD) to Basel (Switzerland). Methodological information For details about the creation of the network see Build_FIS_network.ipynb. Source data for the network is available at https://www.vaarweginformatie.nl/. Sharing and Access information CC BY-SA 4.0 license applies: https://creativecommons.org/licenses/by-sa/4.0/.
DOI: 10.5281/zenodo.4578289
title: Topological Network of the Dutch Fairway Information System

description: Topological fairway network derived from the Dutch Fairway Information System. The data is processed to be topological connected and usable for transport network analysis. Files <code>network_digital_twin_v0.2.yaml</code> This is the human readable NetworkX file for the Rhine corridor extending from Rotterdam (NLD) to Basel (Switzerland). <code>network_digital_twin_v0.2.json</code> This is the json (for web) file for the Rhine corridor extending from Rotterdam (NLD) to Basel (Switzerland). <code>network_digital_twin_v0.2.pickle</code> This is the pickled (for performance) file for the Rhine corridor extending from Rotterdam (NLD) to Basel (Switzerland). <code>network_digital_twin_v0.2.zip</code> This is the shapefile (for gis) file for the Rhine corridor extending from Rotterdam (NLD) to Basel (Switzerland). Methodological information For details about the creation of the network see Build_FIS_network.ipynb. Updates in version 0.2.0: - added bathymetry info: mean, standard deviation , percentiles [0 (min), 5, 10, 50 (median), 90, 95, 100 (max)] - added new output formats: added shapely compatible geometry type Source data for the network is available at https://www.vaarweginformatie.nl/. Sharing and Access information CC BY-SA 4.0 license applies: https://creativecommons.org/licenses/by-sa/4.0/.
DOI: 10.6084/m9.figshare.17141032.v1
title: Additional file 5 of Rice Carbohydrate-Binding Malectin-Like Protein, OsCBM1, Contributes to Drought-Stress Tolerance by Participating in NADPH Oxidase-Mediated ROS Production

description: Additional file 5: Table S3. The original data of RNA-seq experiments.
DOI: 10.6084/m9.figshare.17140747
title: Additional file 1 of Angiogenesis-related lncRNAs predict the prognosis signature of stomach adenocarcinoma

description: Additional file 1 : Table S1. The angiogenesis-related genes extracted from the Molecular Signatures Database v4.0. Table S2. A total of 329 lncRNAs were defined as ARLnc. Table S3. The sequences of primers utilized in this study.
DOI: 10.6084/m9.figshare.8228078.v1
title: MOESM6 of Proteome analysis of xylose metabolism in Rhodotorula toruloides during lipid production

description: Additional file 6. Relative levels of differentially expressed proteins in R. toruloides cultivated on either glucose or xylose during late exponential growth phase.
DOI: 10.6084/m9.figshare.8228096.v1
title: MOESM8 of Proteome analysis of xylose metabolism in Rhodotorula toruloides during lipid production

description: Additional file 8. Relative levels of proteins involved in central carbon metabolism of R. toruloides.
DOI: 10.6084/m9.figshare.19762396
title: Circular_0086414 induces SPARC like 1 (<i>SPARCL1</i>) production to inhibit esophageal cancer cell proliferation, invasion and glycolysis and induce cell apoptosis by sponging miR-1290

description: Circular RNA (circRNA) plays an important role in cancer progression. Here, we investigated the function of circ_0086414 in the malignant progression of esophageal cancer (EC). RNA expression of circ_0086414, microRNA-1290 (miR-1290), and SPARC like 1 (<i>SPARCL1</i>) was detected by quantitative real-time polymerase chain reaction. The protein levels of N-cadherin, E-cadherin, and <i>SPARCL1</i> were checked by Western blotting analysis. Cell proliferation was investigated by 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), 5-Ethynyl-29-deoxyuridine (EdU), and cell colony formation assays. Cell invasion and apoptosis were analyzed by transwell invasion assay and flow cytometry analysis, respectively. Glycolysis was evaluated by analyzing glucose consumption and lactate production. In an xenograft mouse model, the effect of circ_0086414 on tumor tumorigenesis was investigated. The interactions among circ_0086414, miR-1290, and <i>SPARCL1</i> were identified by dual-luciferase reporter and RNA pull-down assays. Results showed that circ_0086414 and <i>SPARCL1</i> expression were significantly downregulated, while miR-1290 was upregulated in EC tissues and cells. EC patients with low circ_0086414 expression had a poor prognosis. Increasing circ_0086414 expression led to decreased EC cell proliferation, invasion and glycolysis and increased cell apoptosis, accompanied by a decrease of N-cadherin expression and an increase of E-cadherin expression. Also, the enforced expression of circ_0086414 delayed tumor tumorigenesis. Besides, circ_0086414 acted as a miR-1290 sponge and regulated EC cell processes by binding to the miRNA. MiR-1290 also participated in EC malignant progression through <i>SPARCL1</i>. Further, circ_0086414 stimulated <i>SPARCL1</i> production by negatively regulating miR-1290. Thus, circ_0086414 inhibited EC cell malignancy through the miR-1290/<i>SPARCL1</i> pathway, providing a reliable target for the therapy of EC.
DOI: 10.6084/m9.figshare.19762396.v1
title: Circular_0086414 induces SPARC like 1 (<i>SPARCL1</i>) production to inhibit esophageal cancer cell proliferation, invasion and glycolysis and induce cell apoptosis by sponging miR-1290

description: Circular RNA (circRNA) plays an important role in cancer progression. Here, we investigated the function of circ_0086414 in the malignant progression of esophageal cancer (EC). RNA expression of circ_0086414, microRNA-1290 (miR-1290), and SPARC like 1 (<i>SPARCL1</i>) was detected by quantitative real-time polymerase chain reaction. The protein levels of N-cadherin, E-cadherin, and <i>SPARCL1</i> were checked by Western blotting analysis. Cell proliferation was investigated by 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), 5-Ethynyl-29-deoxyuridine (EdU), and cell colony formation assays. Cell invasion and apoptosis were analyzed by transwell invasion assay and flow cytometry analysis, respectively. Glycolysis was evaluated by analyzing glucose consumption and lactate production. In an xenograft mouse model, the effect of circ_0086414 on tumor tumorigenesis was investigated. The interactions among circ_0086414, miR-1290, and <i>SPARCL1</i> were identified by dual-luciferase reporter and RNA pull-down assays. Results showed that circ_0086414 and <i>SPARCL1</i> expression were significantly downregulated, while miR-1290 was upregulated in EC tissues and cells. EC patients with low circ_0086414 expression had a poor prognosis. Increasing circ_0086414 expression led to decreased EC cell proliferation, invasion and glycolysis and increased cell apoptosis, accompanied by a decrease of N-cadherin expression and an increase of E-cadherin expression. Also, the enforced expression of circ_0086414 delayed tumor tumorigenesis. Besides, circ_0086414 acted as a miR-1290 sponge and regulated EC cell processes by binding to the miRNA. MiR-1290 also participated in EC malignant progression through <i>SPARCL1</i>. Further, circ_0086414 stimulated <i>SPARCL1</i> production by negatively regulating miR-1290. Thus, circ_0086414 inhibited EC cell malignancy through the miR-1290/<i>SPARCL1</i> pathway, providing a reliable target for the therapy of EC.
DOI: 10.6084/m9.figshare.19762387
title: Bone mesenchymal stem cells (BMSCs)-derived exosomal microRNA-21-5p regulates Kruppel-like factor 3 (KLF3) to promote osteoblast proliferation <i>in vitro</i>

description: Bone mesenchymal stem cells (BMSCs)-derived exosomes (Exos) play important roles in osteoporosis, while the regulation of microRNA (miR)-21-5p remains unclear. The BMSCs-derived exosomes were isolated from femoral bone marrow of trauma patients, which were then used to stimulate human osteoblasts (hFOB1.19 cells). The miR-21-5p mimic or inhibitor was transfected into BMSCs to overexpress or knockdown miR-21-5p. The functions of miR-21-5p in osteoporosis were assessed by cell counting kit-8 (CCK-8) assay, alkaline phosphatase (ALP) staining and alizarin red staining assays. We found that BMSCs-derived exosomes could enhance proliferation, osteoblastic differentiation and ALP activity of hFOB1.19 cells. BMSCs-derived exosomes with upregulated miR-21-5p could further enhance these protective impacts compared with that in BMSCs-derived exosomes, while BMSCs-derived exosomes with downregulated miR-21-5p reduced these cell phenotypes. MiR-21-5p could directly bind to the 3’-untranslated region (UTR) of Kruppel-like factor 3 (KLF3), and knockdown of KLF3 obviously attenuated these inhibitory effects of BMSCs-derived exosomes with downregulated miR-21-5p on osteoblastic differentiation and ALP activity of hFOB1.19 cells. In summary, BMSCs-derived exosomal miR-21-5p improved osteoporosis through regulating KLF3, providing a potential therapeutic strategy for osteoporosis.