cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7692944
title: Additional file 7: of Molecular characterization of carbendazim resistance of Fusarium species complex that causes sugarcane pokkah boeng disease

description: Table S5. GO functional enrichment of the DEGs in SJ51M and its corresponding wild type strain SJ51. SJ51_C and SJ51M_C represented without carbendazim treatment, while SJ51_E and SJ51M_E represented exposed to carbendazim treatment. (XLSX 47 kb)
DOI: 10.6084/m9.figshare.7692944.v1
title: Additional file 7: of Molecular characterization of carbendazim resistance of Fusarium species complex that causes sugarcane pokkah boeng disease

description: Table S5. GO functional enrichment of the DEGs in SJ51M and its corresponding wild type strain SJ51. SJ51_C and SJ51M_C represented without carbendazim treatment, while SJ51_E and SJ51M_E represented exposed to carbendazim treatment. (XLSX 47 kb)
DOI: 10.6084/m9.figshare.15032917
title: Additional file 2 of Genetic basis of maize kernel oil-related traits revealed by high-density SNP markers in a recombinant inbred line population

description: Additional file 2: Table S1. Single QTLs for 19 oil-related traits identified in this study.
DOI: 10.6084/m9.figshare.10314404
title: Table S2. Placental cell markers from single cell RNA sequencing.

description: Cluster-specific markers emerged from pairwise comparison among the clusters are ranked by normalized expression UMI counts from the most abundant to the least (log<sub>2</sub>FC&gt;1, FDR&lt;0.01).
DOI: 10.6084/m9.figshare.10314407
title: Table S3. Placental cell type-specific sexually dimorphic genes.

description: Fold changes of top sexually dimorphic genes (ILog<sub>2</sub>FCI&gt;1, FDR&lt;0.01, shown in bold) in each cluster are presented in Table S3A (upregulated in cells from male conceptions) and Table S3B (upregulated from female conceptions). The significantly sexually dimorphic expression patterns (FDR&lt;0.01) of these genes, although may not meet the criteria of ILog<sub>2</sub>FCI&gt;1 in some clusters, are shown for all clusters. Asterisk (*) indicates the genes that are expressed in less than 5% of cells (excluded in Figure 2B).
DOI: 10.6084/m9.figshare.7692974
title: Additional file 2: of CeModule: an integrative framework for discovering regulatory patterns from genomic data in cancer

description: Table S1. The list of all the identified modules that involving lncRNAs, miRNAs and mRNAs. (XLSX 248 kb)
DOI: 10.6084/m9.figshare.7692974.v1
title: Additional file 2: of CeModule: an integrative framework for discovering regulatory patterns from genomic data in cancer

description: Table S1. The list of all the identified modules that involving lncRNAs, miRNAs and mRNAs. (XLSX 248 kb)
DOI: 10.6084/m9.figshare.7692977
title: Additional file 3: of CeModule: an integrative framework for discovering regulatory patterns from genomic data in cancer

description: Table S3. Results of the enriched GO biological processes for the identified modules. (XLSX 620 kb)
DOI: 10.6084/m9.figshare.7692977.v1
title: Additional file 3: of CeModule: an integrative framework for discovering regulatory patterns from genomic data in cancer

description: Table S3. Results of the enriched GO biological processes for the identified modules. (XLSX 620 kb)
DOI: 10.6084/m9.figshare.10314419
title: Table S5. Trophoblast subcluster markers in human first trimester

description: Markers specifically expressed in sub-clusters of trophoblast cells (log<sub>2</sub>FC&gt;1,
FDR&lt;0.01), selected from pairwise comparison among the seven sub-clusters are
ranked by normalized UMI counts from the most abundant to the least. No markers
emerged for sub-cluster 1 and 7 from pairwise comparison, therefore markers of
sub-clusters 2, 3, 4, 5, 6 are included in the table. Human first trimester placenta single cell RNA-sequencing.
DOI: 10.6084/m9.figshare.10314425
title: Table S1. Patient demographics and pregnancy outcomes.

description: Demographic and pregnancy outcome information is shown for 4 patients in RNA-Seq analysis, 6 patients in single cell RNA-Seq analysis as well as demographic information for 7 patients in immunostaining who underwent termination.
DOI: 10.6084/m9.figshare.7692986
title: Additional file 4: of CeModule: an integrative framework for discovering regulatory patterns from genomic data in cancer

description: Table S4. Results of the enriched KEGG pathways for the identified modules. (XLSX 105 kb)
DOI: 10.6084/m9.figshare.7692986.v1
title: Additional file 4: of CeModule: an integrative framework for discovering regulatory patterns from genomic data in cancer

description: Table S4. Results of the enriched KEGG pathways for the identified modules. (XLSX 105 kb)
DOI: 10.6084/m9.figshare.11887293
title: Additional file 2 of Heterosis analysis and underlying molecular regulatory mechanism in a wide-compatible neo-tetraploid rice line with long panicles

description: Additional file 2: Table S1. Origin and genotypes of autotetraploid and neo-tetraploid rice lines at pollen sterility loci, Sa, Sb, and Sc, and embryo sac fertility locus (S5), and their agronomic traits. Table S2. Means of mid-parent and high-parent heterosis in F1 during two seasons of 2017 and 2018. Table S3. Means of agronomic traits of F1 in two seasons of 2017 and 2018. Table S4a. Codes and names of the parents, hybrids, tissues and development stages. Table S4b. Summary of clean reads of transcriptome data from the two F1 hybrids (H1 × H8 and T485 × H8) and their parents. Table S5 Differentially expressed genes associated with the F1 hybrids compared to parents in flag leaf, leaf sheath, spikelet and main panicle axis. Table S6 Differentially expressed genes associated with parents in flag leaf, leaf sheath, spikelet and main panicle axis. Table S7 Gene IDs of differentially expressed genes that uniquely associated with F1 compared to parents and specific (DEGFu-sp) to flag leaf, leaf sheath, spikelet and main panicle axis. Table S8a Prominent functional categorization of genes in the eight tissues before and 5 days after flowering in the F1 hybrid (H1 × H8) by Gene ontology (GO) enrichment analysis. Table S8b Prominent functional categorization of genes in the eight tissues before and 5 days after flowering in the F1 hybrid (T485 × H8) by Gene ontology (GO) enrichment analysis. Table S8c List of the functional categorization of genes in the hybrids by Gene ontology (GO) enrichment analysis. Table S8d Common prominent functional categorization of genes by Gene ontology (GO) enrichment analysis. Table S8e KEGG Pathway analysis of DEGFu-sp to the two hybrids.
DOI: 10.6084/m9.figshare.11887293.v1
title: Additional file 2 of Heterosis analysis and underlying molecular regulatory mechanism in a wide-compatible neo-tetraploid rice line with long panicles

description: Additional file 2: Table S1. Origin and genotypes of autotetraploid and neo-tetraploid rice lines at pollen sterility loci, Sa, Sb, and Sc, and embryo sac fertility locus (S5), and their agronomic traits. Table S2. Means of mid-parent and high-parent heterosis in F1 during two seasons of 2017 and 2018. Table S3. Means of agronomic traits of F1 in two seasons of 2017 and 2018. Table S4a. Codes and names of the parents, hybrids, tissues and development stages. Table S4b. Summary of clean reads of transcriptome data from the two F1 hybrids (H1 × H8 and T485 × H8) and their parents. Table S5 Differentially expressed genes associated with the F1 hybrids compared to parents in flag leaf, leaf sheath, spikelet and main panicle axis. Table S6 Differentially expressed genes associated with parents in flag leaf, leaf sheath, spikelet and main panicle axis. Table S7 Gene IDs of differentially expressed genes that uniquely associated with F1 compared to parents and specific (DEGFu-sp) to flag leaf, leaf sheath, spikelet and main panicle axis. Table S8a Prominent functional categorization of genes in the eight tissues before and 5 days after flowering in the F1 hybrid (H1 × H8) by Gene ontology (GO) enrichment analysis. Table S8b Prominent functional categorization of genes in the eight tissues before and 5 days after flowering in the F1 hybrid (T485 × H8) by Gene ontology (GO) enrichment analysis. Table S8c List of the functional categorization of genes in the hybrids by Gene ontology (GO) enrichment analysis. Table S8d Common prominent functional categorization of genes by Gene ontology (GO) enrichment analysis. Table S8e KEGG Pathway analysis of DEGFu-sp to the two hybrids.
DOI: 10.6084/m9.figshare.7692992
title: Additional file 5: of CeModule: an integrative framework for discovering regulatory patterns from genomic data in cancer

description: Table S5. The list of regulatory modules enriched in miRNA cluster and miRNA family. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.7692992.v1
title: Additional file 5: of CeModule: an integrative framework for discovering regulatory patterns from genomic data in cancer

description: Table S5. The list of regulatory modules enriched in miRNA cluster and miRNA family. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.11887302
title: Additional file 3 of Heterosis analysis and underlying molecular regulatory mechanism in a wide-compatible neo-tetraploid rice line with long panicles

description: Additional file 3: Table S9a The common genes associated with kinase in DEGFu-sp to both hybrids. Table S9b The common genes associated with synthase in DEGFu-sp to both hybrids. Table S9c The common genes associated with NBS-LRR disease resistance protein or LRR receptor-like protein kinase in DEGFu-sp to both hybrids. Table S9d The common genes associated with transcription factors in DEGFu-sp to both hybrids. Table S9e The known genes associated with important agronomic traits detected from the DEGFu-sp to both hybrids. Table S10a Names of all DEGFu-sp-related QTLS in the F1 hybrids (H1 × H8 and T485 × H8). Table S10b Names of the DEGFu-sp yield-related QTLS in the F1 hybrids (H1 × H8 and T485 × H8). Table S10c Names of the DEGFu-sp-related common QTLS in the F1 hybrids (H1 × H8 and T485 × H8). Table S10d Names of the DEGFu-sp-related common QTLS among the four F1 hybrids (H1 × H8, T485 × H8, T449 × H1 and T452 × H3). Table S10e Names and differential expressions of important DEGFu-sp genes in F1 hybrid (H1 × H8). Table S10f Names and differential expression of important DEGFu-sp genes in F1 hybrid (T485 × H8).
DOI: 10.6084/m9.figshare.11887302.v1
title: Additional file 3 of Heterosis analysis and underlying molecular regulatory mechanism in a wide-compatible neo-tetraploid rice line with long panicles

description: Additional file 3: Table S9a The common genes associated with kinase in DEGFu-sp to both hybrids. Table S9b The common genes associated with synthase in DEGFu-sp to both hybrids. Table S9c The common genes associated with NBS-LRR disease resistance protein or LRR receptor-like protein kinase in DEGFu-sp to both hybrids. Table S9d The common genes associated with transcription factors in DEGFu-sp to both hybrids. Table S9e The known genes associated with important agronomic traits detected from the DEGFu-sp to both hybrids. Table S10a Names of all DEGFu-sp-related QTLS in the F1 hybrids (H1 × H8 and T485 × H8). Table S10b Names of the DEGFu-sp yield-related QTLS in the F1 hybrids (H1 × H8 and T485 × H8). Table S10c Names of the DEGFu-sp-related common QTLS in the F1 hybrids (H1 × H8 and T485 × H8). Table S10d Names of the DEGFu-sp-related common QTLS among the four F1 hybrids (H1 × H8, T485 × H8, T449 × H1 and T452 × H3). Table S10e Names and differential expressions of important DEGFu-sp genes in F1 hybrid (H1 × H8). Table S10f Names and differential expression of important DEGFu-sp genes in F1 hybrid (T485 × H8).
DOI: 10.6084/m9.figshare.7692998
title: Additional file 6: of CeModule: an integrative framework for discovering regulatory patterns from genomic data in cancer

description: Table S6. Known OV/UCEC-related lncRNAs/miRNAs/mRNAs and cancer-related lncRNAs/miRNAs/mRNAs in modules. (XLSX 52 kb)
DOI: 10.6084/m9.figshare.7692998.v1
title: Additional file 6: of CeModule: an integrative framework for discovering regulatory patterns from genomic data in cancer

description: Table S6. Known OV/UCEC-related lncRNAs/miRNAs/mRNAs and cancer-related lncRNAs/miRNAs/mRNAs in modules. (XLSX 52 kb)
DOI: 10.6084/m9.figshare.9790154
title: Additional file 11: of Genetic dissection of yield-related traits and mid-parent heterosis for those traits in maize (Zea mays L.)

description: Genotypic and phenotypic data of the RIL and IF populations for the QTL analyses. (XLSX 1583 kb)
DOI: 10.6084/m9.figshare.9790154.v1
title: Additional file 11: of Genetic dissection of yield-related traits and mid-parent heterosis for those traits in maize (Zea mays L.)

description: Genotypic and phenotypic data of the RIL and IF populations for the QTL analyses. (XLSX 1583 kb)
DOI: 10.6084/m9.figshare.11887308
title: Additional file 4 of Heterosis analysis and underlying molecular regulatory mechanism in a wide-compatible neo-tetraploid rice line with long panicles

description: Additional file 4: Table S11a, b Gene IDs of DEGFu-sp-non-additive in the F1 hybrids. Table S11c,d Overlapped genes detected from DEGFu-sp-non-additive and cloned genes in F1 hybrids. Table S12a Overlapped genes detected from DEGFu-sp-cloned and mutant genes in H8 compared to H1. Table S12b Overlapped genes detected from DEGFu-sp-cloned and mutant genes in H8 compared to T485. Table S12c Overlapped genes detected from DEGFu-sp-cloned and all common mutant genes in H8 compared to H1 and T485. Table S13a Overlapped genes detected from DEGFu-sp and mutant genes in H8 compared to H1 and T485. Table S13b Overlapped genes detected from DEGFu-sp, mutant and cloned genes in H8 compared to H1 and T485. Table S14 Predicted protein-protein interaction analysis of the cloned genes in DEGFu-sp. Table S15 List of primers used for PCR and qRT-PCR. Table S16 Name of 7 yield-related QTLs.
DOI: 10.6084/m9.figshare.11887308.v1
title: Additional file 4 of Heterosis analysis and underlying molecular regulatory mechanism in a wide-compatible neo-tetraploid rice line with long panicles

description: Additional file 4: Table S11a, b Gene IDs of DEGFu-sp-non-additive in the F1 hybrids. Table S11c,d Overlapped genes detected from DEGFu-sp-non-additive and cloned genes in F1 hybrids. Table S12a Overlapped genes detected from DEGFu-sp-cloned and mutant genes in H8 compared to H1. Table S12b Overlapped genes detected from DEGFu-sp-cloned and mutant genes in H8 compared to T485. Table S12c Overlapped genes detected from DEGFu-sp-cloned and all common mutant genes in H8 compared to H1 and T485. Table S13a Overlapped genes detected from DEGFu-sp and mutant genes in H8 compared to H1 and T485. Table S13b Overlapped genes detected from DEGFu-sp, mutant and cloned genes in H8 compared to H1 and T485. Table S14 Predicted protein-protein interaction analysis of the cloned genes in DEGFu-sp. Table S15 List of primers used for PCR and qRT-PCR. Table S16 Name of 7 yield-related QTLs.
DOI: 10.6084/m9.figshare.7693001
title: Additional file 7: of CeModule: an integrative framework for discovering regulatory patterns from genomic data in cancer

description: Table S7. Differentially expressed miRNAs identified in modules. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7693001.v1
title: Additional file 7: of CeModule: an integrative framework for discovering regulatory patterns from genomic data in cancer

description: Table S7. Differentially expressed miRNAs identified in modules. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7693040
title: Additional file 13: of Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum

description: Table S5. Genome-wide correlation analyses of transposable elements with secondary metabolite clusters. (XLXS 18.9 kb)
DOI: 10.6084/m9.figshare.7693040.v1
title: Additional file 13: of Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum

description: Table S5. Genome-wide correlation analyses of transposable elements with secondary metabolite clusters. (XLXS 18.9 kb)
DOI: 10.6084/m9.figshare.11887353
title: Additional file 1 of Adjuvant chemotherapy could not bring survival benefit to HR-positive, HER2-negative, pT1b-c/N0–1/M0 invasive lobular carcinoma of the breast: a propensity score matching study based on SEER database

description: Supplementary Table 1. 14,844 initial samples - 14,844 initial record of HR-positive, HER2-negative, pT1b-c/N0–1/M0 ILC retrieved from SEER database.
DOI: 10.6084/m9.figshare.11887353.v2
title: Additional file 1 of Adjuvant chemotherapy could not bring survival benefit to HR-positive, HER2-negative, pT1b-c/N0–1/M0 invasive lobular carcinoma of the breast: a propensity score matching study based on SEER database

description: Supplementary Table 1. 14,844 initial samples - 14,844 initial record of HR-positive, HER2-negative, pT1b-c/N0–1/M0 ILC retrieved from SEER database.
DOI: 10.6084/m9.figshare.11887353.v1
title: Additional file 1 of Adjuvant chemotherapy could not bring survival benefit to HR-positive, HER2-negative, pT1b-c/N0–1/M0 invasive lobular carcinoma of the breast: a propensity score matching study based on SEER database

description: Supplementary Table 1. 14,844 initial samples - 14,844 initial record of HR-positive, HER2-negative, pT1b-c/N0–1/M0 ILC retrieved from SEER database.
DOI: 10.6084/m9.figshare.11887356.v1
title: Additional file 11 of lncRNA-PLACT1 sustains activation of NF-κB pathway through a positive feedback loop with IκBα/E2F1 axis in pancreatic cancer

description: Additional file 11: Clinical information on the patient cohort.
DOI: 10.5281/zenodo.10680419
title: Comparison of WAIC and posterior predictive approaches for N-mixture models
DOI: 10.5281/zenodo.10680420
title: Comparison of WAIC and posterior predictive approaches for N-mixture models
DOI: 10.6084/m9.figshare.11887356.v2
title: Additional file 11 of lncRNA-PLACT1 sustains activation of NF-κB pathway through a positive feedback loop with IκBα/E2F1 axis in pancreatic cancer

description: Additional file 11: Clinical information on the patient cohort.
DOI: 10.6084/m9.figshare.11887359
title: Additional file 2 of Adjuvant chemotherapy could not bring survival benefit to HR-positive, HER2-negative, pT1b-c/N0–1/M0 invasive lobular carcinoma of the breast: a propensity score matching study based on SEER database

description: Supplementary Table 2. 12,334 original samples - 12,334 record of HR-positive, HER2-negative, pT1b-c/N0–1/M0 ILC enrolled in the study.
DOI: 10.6084/m9.figshare.11887356
title: Additional file 11 of lncRNA-PLACT1 sustains activation of NF-κB pathway through a positive feedback loop with IκBα/E2F1 axis in pancreatic cancer

description: Additional file 11: Clinical information on the patient cohort.
DOI: 10.6084/m9.figshare.11887359.v2
title: Additional file 2 of Adjuvant chemotherapy could not bring survival benefit to HR-positive, HER2-negative, pT1b-c/N0–1/M0 invasive lobular carcinoma of the breast: a propensity score matching study based on SEER database

description: Supplementary Table 2. 12,334 original samples - 12,334 record of HR-positive, HER2-negative, pT1b-c/N0–1/M0 ILC enrolled in the study.
DOI: 10.6084/m9.figshare.11887359.v1
title: Additional file 2 of Adjuvant chemotherapy could not bring survival benefit to HR-positive, HER2-negative, pT1b-c/N0–1/M0 invasive lobular carcinoma of the breast: a propensity score matching study based on SEER database

description: Supplementary Table 2. 12,334 original samples - 12,334 record of HR-positive, HER2-negative, pT1b-c/N0–1/M0 ILC enrolled in the study.
DOI: 10.6084/m9.figshare.11887368
title: Additional file 3 of Adjuvant chemotherapy could not bring survival benefit to HR-positive, HER2-negative, pT1b-c/N0–1/M0 invasive lobular carcinoma of the breast: a propensity score matching study based on SEER database

description: Supplementary Table 3. 3570 matched samples - 3570 record of HR-positive, HER2-negative, pT1b-c/N0–1/M0 ILC (including 1785 matched non-chemotherapy patients and 1785 chemotherapy patients).
DOI: 10.6084/m9.figshare.11887368.v2
title: Additional file 3 of Adjuvant chemotherapy could not bring survival benefit to HR-positive, HER2-negative, pT1b-c/N0–1/M0 invasive lobular carcinoma of the breast: a propensity score matching study based on SEER database

description: Supplementary Table 3. 3570 matched samples - 3570 record of HR-positive, HER2-negative, pT1b-c/N0–1/M0 ILC (including 1785 matched non-chemotherapy patients and 1785 chemotherapy patients).
DOI: 10.6084/m9.figshare.11887368.v1
title: Additional file 3 of Adjuvant chemotherapy could not bring survival benefit to HR-positive, HER2-negative, pT1b-c/N0–1/M0 invasive lobular carcinoma of the breast: a propensity score matching study based on SEER database

description: Supplementary Table 3. 3570 matched samples - 3570 record of HR-positive, HER2-negative, pT1b-c/N0–1/M0 ILC (including 1785 matched non-chemotherapy patients and 1785 chemotherapy patients).
DOI: 10.6084/m9.figshare.7693067
title: Additional file 17: of Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum

description: Table S6. Blast hits of the Cluster D genes to A. flavus genome and NCBI nr database (XLSX 15.3 kb)
DOI: 10.6084/m9.figshare.7693067.v1
title: Additional file 17: of Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum

description: Table S6. Blast hits of the Cluster D genes to A. flavus genome and NCBI nr database (XLSX 15.3 kb)
DOI: 10.6084/m9.figshare.11887380
title: Additional file 4 of Adjuvant chemotherapy could not bring survival benefit to HR-positive, HER2-negative, pT1b-c/N0–1/M0 invasive lobular carcinoma of the breast: a propensity score matching study based on SEER database

description: Additional file 4. Supplementary dofile: dofile for Stata
DOI: 10.6084/m9.figshare.11887380.v1
title: Additional file 4 of Adjuvant chemotherapy could not bring survival benefit to HR-positive, HER2-negative, pT1b-c/N0â€“1/M0 invasive lobular carcinoma of the breast: a propensity score matching study based on SEER database

description: Additional file 4. Supplementary dofile: dofile for Stata
DOI: 10.6084/m9.figshare.11887380.v2
title: Additional file 4 of Adjuvant chemotherapy could not bring survival benefit to HR-positive, HER2-negative, pT1b-c/N0–1/M0 invasive lobular carcinoma of the breast: a propensity score matching study based on SEER database

description: Additional file 4. Supplementary dofile: dofile for Stata
DOI: 10.6084/m9.figshare.11887386
title: Additional file 16 of lncRNA-PLACT1 sustains activation of NF-κB pathway through a positive feedback loop with IκBα/E2F1 axis in pancreatic cancer

description: Additional file 16: The original expression data of PLACT1 in TCGA dataset.
DOI: 10.6084/m9.figshare.11887386.v1
title: Additional file 16 of lncRNA-PLACT1 sustains activation of NF-κB pathway through a positive feedback loop with IκBα/E2F1 axis in pancreatic cancer

description: Additional file 16: The original expression data of PLACT1 in TCGA dataset.
DOI: 10.6084/m9.figshare.7693085
title: Additional file 19: of Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum

description: Table S7. Ortholog analysis of proteomes of all T. inflatum strains to cluster D genes. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.7693085.v1
title: Additional file 19: of Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum

description: Table S7. Ortholog analysis of proteomes of all T. inflatum strains to cluster D genes. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.11887386.v2
title: Additional file 16 of lncRNA-PLACT1 sustains activation of NF-κB pathway through a positive feedback loop with IκBα/E2F1 axis in pancreatic cancer

description: Additional file 16: The original expression data of PLACT1 in TCGA dataset.