cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6274748
title: Additional file 7: of Comparative whole genome re-sequencing analysis in upland New Rice for Africa: insights into the breeding history and respective genome compositions

description: Table S6. Common introgression segments from CG 14. (XLSX 104Â kb)
DOI: 10.6084/m9.figshare.6274748.v1
title: Additional file 7: of Comparative whole genome re-sequencing analysis in upland New Rice for Africa: insights into the breeding history and respective genome compositions

description: Table S6. Common introgression segments from CG 14. (XLSX 104Â kb)
DOI: 10.6084/m9.figshare.6274751
title: Additional file 8: of Comparative whole genome re-sequencing analysis in upland New Rice for Africa: insights into the breeding history and respective genome compositions

description: Table S7. Location of xyloglucan fucosyltransferase genes on common long introgression segments from CG 14. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.6274751.v1
title: Additional file 8: of Comparative whole genome re-sequencing analysis in upland New Rice for Africa: insights into the breeding history and respective genome compositions

description: Table S7. Location of xyloglucan fucosyltransferase genes on common long introgression segments from CG 14. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.6275276
title: Original data collection. Co-occurrence patterns of ice-rafted dropstones and brachiopods in the Middle Permian Wandrawandian Siltstone of the southern Sydney Basin (southeastern Australia) and palaeoecological implications

description: Supplementary Material 1: Original data collection
DOI: 10.6084/m9.figshare.6275276.v1
title: Original data collection. Co-occurrence patterns of ice-rafted dropstones and brachiopods in the Middle Permian Wandrawandian Siltstone of the southern Sydney Basin (southeastern Australia) and palaeoecological implications

description: Supplementary Material 1: Original data collection
DOI: 10.6084/m9.figshare.6279758
title: Additional file 3: of Whole genome sequencing data of 1110 Mycobacterium tuberculosis isolates identifies insertions and deletions associated with drug resistance

description: The accession numbers of the validation data set. (XLSX 79Â kb)
DOI: 10.6084/m9.figshare.6279758.v1
title: Additional file 3: of Whole genome sequencing data of 1110 Mycobacterium tuberculosis isolates identifies insertions and deletions associated with drug resistance

description: The accession numbers of the validation data set. (XLSX 79Â kb)
DOI: 10.6084/m9.figshare.6279872
title: Additional file 1: of Correlation between the sagittal spinopelvic alignment and degenerative lumbar spondylolisthesis: a retrospective study

description: The dataset supporting the conclusions of this article. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.6279872.v1
title: Additional file 1: of Correlation between the sagittal spinopelvic alignment and degenerative lumbar spondylolisthesis: a retrospective study

description: The dataset supporting the conclusions of this article. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.6287312
title: Bioinformatic analyses of microRNA-targeted genes and microarray-identified genes correlated with Barrett's esophagus

description: Barrett's esophagus (BE) is defined as a metaplasia condition in the distal esophagus, in which the native squamous epithelium lining is replaced by a columnar epithelium with or without intestinal metaplasia. It is commonly accepted that BE is a precancerous lesion for esophageal adenocarcinoma. The aim of this study was to investigate the aberrant microRNAs (miRNAs) and differentially expressed genes (DEGs) associated with BE based on online microarray datasets. One miRNA and five gene expression profiling datasets were retrieved from the Gene Expression Omnibus Database. Aberrant microRNAs and DEGs were obtained using R/Bioconductor statistical analysis language and software. 23 dysregulated miRNAs and 632 DEGs demonstrating consistent expression tendencies in the five gene microarrays were identified in BE. Moreover, 1962 target genes of aberrant miRNAs were predicted using three bioinformatic tools, namely TargetScan, RNA22-HSA and miRDB. Ultimately, 93 target DEGs were obtained, after which functional annotation was performed on DAVID Bioinformatics Resources. Among Gene Ontology (GO) biological processes, digestive tract development and epithelial cell differentiation have demonstrated significant associations with BE pathogenesis. In addition, analysis of the KEGG pathways has revealed associations with cancer. To enable further study, one miRNA-target DEGs regulatory network was constructed using Cytoscape. 6 target DEGs demonstrated higher-degree distributions in the network, and ROC analysis indicated that FNDC3B may be the best potential biomarker for BE diagnosis. The data presented herein may provide new perspectives for exploring BE pathogenesis and may offer hits with regard to potential biomarkers in BE diagnosis, prediction and therapeutic evaluation.
DOI: 10.6084/m9.figshare.6287312.v1
title: Bioinformatic analyses of microRNA-targeted genes and microarray-identified genes correlated with Barrett's esophagus

description: Barrett's esophagus (BE) is defined as a metaplasia condition in the distal esophagus, in which the native squamous epithelium lining is replaced by a columnar epithelium with or without intestinal metaplasia. It is commonly accepted that BE is a precancerous lesion for esophageal adenocarcinoma. The aim of this study was to investigate the aberrant microRNAs (miRNAs) and differentially expressed genes (DEGs) associated with BE based on online microarray datasets. One miRNA and five gene expression profiling datasets were retrieved from the Gene Expression Omnibus Database. Aberrant microRNAs and DEGs were obtained using R/Bioconductor statistical analysis language and software. 23 dysregulated miRNAs and 632 DEGs demonstrating consistent expression tendencies in the five gene microarrays were identified in BE. Moreover, 1962 target genes of aberrant miRNAs were predicted using three bioinformatic tools, namely TargetScan, RNA22-HSA and miRDB. Ultimately, 93 target DEGs were obtained, after which functional annotation was performed on DAVID Bioinformatics Resources. Among Gene Ontology (GO) biological processes, digestive tract development and epithelial cell differentiation have demonstrated significant associations with BE pathogenesis. In addition, analysis of the KEGG pathways has revealed associations with cancer. To enable further study, one miRNA-target DEGs regulatory network was constructed using Cytoscape. 6 target DEGs demonstrated higher-degree distributions in the network, and ROC analysis indicated that FNDC3B may be the best potential biomarker for BE diagnosis. The data presented herein may provide new perspectives for exploring BE pathogenesis and may offer hits with regard to potential biomarkers in BE diagnosis, prediction and therapeutic evaluation.
DOI: 10.6084/m9.figshare.6289865.v1
title: Additional file 10: of Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle

description: The ped PLINK file of SNP genotyping data for the 50 Laiwu pigs and 52 Yorkshire pigs. (TXT 21549Â kb)
DOI: 10.6084/m9.figshare.6289865
title: Additional file 10: of Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle

description: The ped PLINK file of SNP genotyping data for the 50 Laiwu pigs and 52 Yorkshire pigs. (TXT 21549Â kb)
DOI: 10.6084/m9.figshare.6289907
title: Additional file 11: of Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle

description: The map PLINK file of SNP genotyping data for the 50 Laiwu pigs and 52 Yorkshire pigs. (TXT 1544Â kb)
DOI: 10.6084/m9.figshare.6289907.v1
title: Additional file 11: of Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle

description: The map PLINK file of SNP genotyping data for the 50 Laiwu pigs and 52 Yorkshire pigs. (TXT 1544Â kb)
DOI: 10.6084/m9.figshare.6289961
title: Additional file 2: of Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle

description: Table S1. Summary of selected regions under positive selection detected by FST. (XLSX 51 kb)
DOI: 10.6084/m9.figshare.6289961.v1
title: Additional file 2: of Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle

description: Table S1. Summary of selected regions under positive selection detected by FST. (XLSX 51 kb)
DOI: 10.6084/m9.figshare.6289976
title: Additional file 1: of Development of a normal tissue complication probability (NTCP) model for radiation-induced hypothyroidism in nasopharyngeal carcinoma patients

description: Table S1. Spearmanâ s rank self-correlation matrix of clinical and dosimetric variables. (XLS 26 kb)
DOI: 10.6084/m9.figshare.6289976.v1
title: Additional file 1: of Development of a normal tissue complication probability (NTCP) model for radiation-induced hypothyroidism in nasopharyngeal carcinoma patients

description: Table S1. Spearmanâ s rank self-correlation matrix of clinical and dosimetric variables. (XLS 26 kb)
DOI: 10.6084/m9.figshare.6289979
title: Additional file 3: of Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle

description: Table S2. Summary of selected regions under positive selection detected by iHS (XLSX 47Â kb)
DOI: 10.6084/m9.figshare.6289979.v1
title: Additional file 3: of Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle

description: Table S2. Summary of selected regions under positive selection detected by iHS (XLSX 47Â kb)
DOI: 10.6084/m9.figshare.6289991
title: Additional file 4: of Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle

description: Table S3. Summary of selected regions under positive selection detected by CLR. (XLSX 23Â kb)
DOI: 10.6084/m9.figshare.6289991.v1
title: Additional file 4: of Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle

description: Table S3. Summary of selected regions under positive selection detected by CLR. (XLSX 23Â kb)
DOI: 10.6084/m9.figshare.6290000
title: Additional file 5: of Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle

description: Table S4. Summary of overlapping candidate regions under positive selection detected by at least two of the three methods FST, iHS and CLR. (XLSX 16Â kb)
DOI: 10.6084/m9.figshare.6290000.v1
title: Additional file 5: of Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle

description: Table S4. Summary of overlapping candidate regions under positive selection detected by at least two of the three methods FST, iHS and CLR. (XLSX 16Â kb)
DOI: 10.6084/m9.figshare.6290027
title: Additional file 6: of Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle

description: Table S5. Gene contents in candidate regions under positive selection. (XLSX 38Â kb)
DOI: 10.6084/m9.figshare.6290027.v1
title: Additional file 6: of Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle

description: Table S5. Gene contents in candidate regions under positive selection. (XLSX 38Â kb)
DOI: 10.6084/m9.figshare.6290036
title: Additional file 7: of Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle

description: Table S6. Significantly enriched Gene Ontology terms of candidate genes. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.6290036.v1
title: Additional file 7: of Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle

description: Table S6. Significantly enriched Gene Ontology terms of candidate genes. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.6290048
title: Additional file 8: of Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle

description: Table S7. Significantly enriched pathway of candidate genes. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.6290048.v1
title: Additional file 8: of Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle

description: Table S7. Significantly enriched pathway of candidate genes. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.6290057
title: Additional file 9: of Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle

description: Table S8. Summary of QTL overlapped with candidate selected regions. (XLSX 150Â kb)
DOI: 10.6084/m9.figshare.6290057.v1
title: Additional file 9: of Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle

description: Table S8. Summary of QTL overlapped with candidate selected regions. (XLSX 150Â kb)
DOI: 10.6084/m9.figshare.25469458
title: crosslinks_miR181enr_miR181a/b-1-KO_plus.bw

description: Non-chimeric crosslinks of Ago2 with enrichment for miR181 in mouse thymocytes, from miR181-eCLIP experiment in Verheyden & Klostermann et al 2024. Knockout of miR181a/b-1, merge of all 3 replicates, crosslinks from plus strand.
DOI: 10.6084/m9.figshare.25469458.v1
title: crosslinks_miR181enr_miR181a/b-1-KO_plus.bw

description: Non-chimeric crosslinks of Ago2 with enrichment for miR181 in mouse thymocytes, from miR181-eCLIP experiment in Verheyden & Klostermann et al 2024. Knockout of miR181a/b-1, merge of all 3 replicates, crosslinks from plus strand.
DOI: 10.6084/m9.figshare.6290198
title: Additional file 2: of Comparative genomics of the miniature wasp and pest control agent Trichogramma pretiosum

description: Table S13. GO terms overrepresented in chalcid-missing and chalcid-unique gene families. (XLSX 87 kb)
DOI: 10.6084/m9.figshare.6290198.v1
title: Additional file 2: of Comparative genomics of the miniature wasp and pest control agent Trichogramma pretiosum

description: Table S13. GO terms overrepresented in chalcid-missing and chalcid-unique gene families. (XLSX 87 kb)
DOI: 10.6084/m9.figshare.6290204
title: Additional file 3: of Comparative genomics of the miniature wasp and pest control agent Trichogramma pretiosum

description: Table S14. Trichogramma singleton genes identified by OrthoMCL, and the GO terms overrepresented in that set. (XLSX 97 kb)
DOI: 10.6084/m9.figshare.6290204.v1
title: Additional file 3: of Comparative genomics of the miniature wasp and pest control agent Trichogramma pretiosum

description: Table S14. Trichogramma singleton genes identified by OrthoMCL, and the GO terms overrepresented in that set. (XLSX 97 kb)
DOI: 10.6084/m9.figshare.6290210
title: Additional file 4: of Comparative genomics of the miniature wasp and pest control agent Trichogramma pretiosum

description: Table S15. Trichogramma proteins identified to be rapidly evolving as compared to Nasonia, using Tajimaâ s relative rate test, along with overrepresented GO terms. (XLSX 119 kb)
DOI: 10.6084/m9.figshare.6290210.v1
title: Additional file 4: of Comparative genomics of the miniature wasp and pest control agent Trichogramma pretiosum

description: Table S15. Trichogramma proteins identified to be rapidly evolving as compared to Nasonia, using Tajimaâ s relative rate test, along with overrepresented GO terms. (XLSX 119 kb)
DOI: 10.6084/m9.figshare.6290216
title: Additional file 5: of Comparative genomics of the miniature wasp and pest control agent Trichogramma pretiosum

description: Table S16. Branch lengths of core hymenopteran proteins and overrepresented GO terms for sets of genes with the longest and shortest branches in different species. (XLSX 324 kb)
DOI: 10.6084/m9.figshare.6290216.v1
title: Additional file 5: of Comparative genomics of the miniature wasp and pest control agent Trichogramma pretiosum

description: Table S16. Branch lengths of core hymenopteran proteins and overrepresented GO terms for sets of genes with the longest and shortest branches in different species. (XLSX 324 kb)
DOI: 10.6084/m9.figshare.6290225
title: Additional file 6: of Comparative genomics of the miniature wasp and pest control agent Trichogramma pretiosum

description: Table S17. Proteins and overrepresented GO terms for within-genome rank comparisons. (XLSX 326 kb)
DOI: 10.6084/m9.figshare.6290225.v1
title: Additional file 6: of Comparative genomics of the miniature wasp and pest control agent Trichogramma pretiosum

description: Table S17. Proteins and overrepresented GO terms for within-genome rank comparisons. (XLSX 326 kb)
DOI: 10.6084/m9.figshare.6290231
title: Additional file 7: of Comparative genomics of the miniature wasp and pest control agent Trichogramma pretiosum

description: Table S18. Comparisons to a sexual genome. Proteins and overrepresented GO terms for proteins most diverged between sexual and asexual lines of Trichogramma, frameshifted, and dN/dS greater than 1. (XLSX 69 kb)
DOI: 10.6084/m9.figshare.6290231.v1
title: Additional file 7: of Comparative genomics of the miniature wasp and pest control agent Trichogramma pretiosum

description: Table S18. Comparisons to a sexual genome. Proteins and overrepresented GO terms for proteins most diverged between sexual and asexual lines of Trichogramma, frameshifted, and dN/dS greater than 1. (XLSX 69 kb)
DOI: 10.5281/zenodo.7906988
title: Respiratory Complex I Regulates Dendritic Cell Maturation in Explant Model of Human Tumor Immune Microenvironment

description: Source data for the paper, "Respiratory Complex I Regulates Dendritic Cell Maturation in Explant Model of Human Tumor Immune Microenvironment."This includes nanostring gene expression profiling of primary human tumor material  ("fresh" in the data, these samples are taken directly after enzymatic digestion) and the corresponding 3D Patient-Derived Explant Culture (PDEC). transfer_257851_files_0a119f4d.zip refers to the mouse spatial transcriptomics data.DE_results_Metformin/LPS files refer to differentially expressed genes of human monocyte-derived dendritic cells of 6 individual donors to control untreated dendritic cells after 24hr treatment.  Also includes the original Seurat.rds file for the scSEQ of primary tumor material (fresh) vs. PDEC
DOI: 10.5281/zenodo.7906989
title: Respiratory Complex I Regulates Dendritic Cell Maturation in Explant Model of Human Tumor Immune Microenvironment

description: Source data for the paper, "Respiratory Complex I Regulates Dendritic Cell Maturation in Explant Model of Human Tumor Immune Microenvironment."This includes nanostring gene expression profiling of primary human tumor material  ("fresh" in the data, these samples are taken directly after enzymatic digestion) and the corresponding 3D Patient-Derived Explant Culture (PDEC). transfer_257851_files_0a119f4d.zip refers to the mouse spatial transcriptomics data.DE_results_Metformin/LPS files refer to differentially expressed genes of human monocyte-derived dendritic cells of 6 individual donors to control untreated dendritic cells after 24hr treatment.  Also includes the original Seurat.rds file for the scSEQ of primary tumor material (fresh) vs. PDEC
DOI: 10.6084/m9.figshare.6297671
title: Additional file 2: of Mutational analysis of epidermal and hyperproliferative type I keratins in mild and moderate psoriasis vulgaris patients: a possible role in the pathogenesis of psoriasis along with disease severity

description: Table S1. K14, K10, K16, and K17 missense mutated variants retrieved from ExAC database. The mutated sequences identical both in our study and ExAC database are indicated by boldfaced words. (XLSX 54Â kb)
DOI: 10.6084/m9.figshare.6297671.v1
title: Additional file 2: of Mutational analysis of epidermal and hyperproliferative type I keratins in mild and moderate psoriasis vulgaris patients: a possible role in the pathogenesis of psoriasis along with disease severity

description: Table S1. K14, K10, K16, and K17 missense mutated variants retrieved from ExAC database. The mutated sequences identical both in our study and ExAC database are indicated by boldfaced words. (XLSX 54Â kb)
DOI: 10.6084/m9.figshare.6297737
title: Additional file 1: of Differences between fast and slow muscles in scallops revealed through proteomics and transcriptomics

description: Table S1. The identification and annotation results of differentially expressed proteins (DEPs) between the striated and catch adductor muscles by the iTRAQ-based quantitative proteomics. There are a total of 474 DEPs identified between the two muscles, which include 198 upregulated and 276 downregulated DEPs. The functional annotation for these DEPs is associated with significantly enriched GO terms and KEGG pathways. (XLSX 135Â kb)
DOI: 10.6084/m9.figshare.6297737.v1
title: Additional file 1: of Differences between fast and slow muscles in scallops revealed through proteomics and transcriptomics

description: Table S1. The identification and annotation results of differentially expressed proteins (DEPs) between the striated and catch adductor muscles by the iTRAQ-based quantitative proteomics. There are a total of 474 DEPs identified between the two muscles, which include 198 upregulated and 276 downregulated DEPs. The functional annotation for these DEPs is associated with significantly enriched GO terms and KEGG pathways. (XLSX 135Â kb)
DOI: 10.6084/m9.figshare.6297887
title: MOESM1 of Biomarker microRNAs for prostate cancer metastasis: screened with a network vulnerability analysis model

description: Additional file 1. Literature-reported PCa microRNA biomarkers.
DOI: 10.6084/m9.figshare.6297887.v1
title: MOESM1 of Biomarker microRNAs for prostate cancer metastasis: screened with a network vulnerability analysis model

description: Additional file 1. Literature-reported PCa microRNA biomarkers.
DOI: 10.6084/m9.figshare.6297908
title: MOESM2 of Biomarker microRNAs for prostate cancer metastasis: screened with a network vulnerability analysis model

description: Additional file 2. The NSR, TFP and UTP values for microRNAs in the reconstructed human microRNA-mRNA network.
DOI: 10.6084/m9.figshare.6297908.v1
title: MOESM2 of Biomarker microRNAs for prostate cancer metastasis: screened with a network vulnerability analysis model

description: Additional file 2. The NSR, TFP and UTP values for microRNAs in the reconstructed human microRNA-mRNA network.
DOI: 10.6084/m9.figshare.6297929
title: MOESM3 of Biomarker microRNAs for prostate cancer metastasis: screened with a network vulnerability analysis model

description: Additional file 3. MPCa-specific microRNA-mRNA network.
DOI: 10.6084/m9.figshare.6297929.v1
title: MOESM3 of Biomarker microRNAs for prostate cancer metastasis: screened with a network vulnerability analysis model

description: Additional file 3. MPCa-specific microRNA-mRNA network.
DOI: 10.6084/m9.figshare.6297953
title: MOESM4 of Biomarker microRNAs for prostate cancer metastasis: screened with a network vulnerability analysis model

description: Additional file 4. MicroRNAs with significantly high NSR and TFP values in MPCa-specific microRNA-mRNA network. The p values were calculated using Wilcoxon signed-rank test.