cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12050778
title: Additional file 13 of Whole genome resequencing reveals an association of ABCC4 variants with preaxial polydactyly in pigs

description: Additional file 13: Table S9. The allele frequency of the top ten highly associated SNPs between population in this study and unpublished data. Chr: Chromosome; Pos (Ssc10.2): Position in Sus scrofa 10.2; Ref: Reference allele; Ref_Freq_A: Reference allele frequency of population in this study; Ref_Freq_B: Reference allele frequency of population in unpublished data; Alt1: Alternative allele 1; Alt1_Freq_A: Alternative allele 1 frequency of population in this study; Alt1_Freq_B: Alternative allele 1 frequency of population in unpublished data; Alt2: Alternative allele 2; Alt2_Freq_A: Alternative allele 2 frequency of population in this study; Alt2_Freq_B: Alternative allele 2 frequency of population in unpublished data.
DOI: 10.6084/m9.figshare.12050784.v1
title: Additional file 14 of Whole genome resequencing reveals an association of ABCC4 variants with preaxial polydactyly in pigs

description: Additional file 14: Table S10. The genotype of the top ten highly associated SNPs between population in this study and the 559 unpublished data set. Pos: Physical position; Ssc: Sus scrofa; Ref: Reference allele; Alt: Altered allele; GT_A: Genotypes of affected cases; GT_U: Genotypes of unaffected controls; GT_C: Genotypes of validation data set; The number “0” represent reference allele and “1” represent altered allele; The number behind the genotype in brackets represent the number of this genotype’s individuals; IGR: Intergenic region. The bold italic highlighted rows (*) represent the SNPs which identified by genome scanning (Additional file 5: Table S5).
DOI: 10.6084/m9.figshare.12050778.v1
title: Additional file 13 of Whole genome resequencing reveals an association of ABCC4 variants with preaxial polydactyly in pigs

description: Additional file 13: Table S9. The allele frequency of the top ten highly associated SNPs between population in this study and unpublished data. Chr: Chromosome; Pos (Ssc10.2): Position in Sus scrofa 10.2; Ref: Reference allele; Ref_Freq_A: Reference allele frequency of population in this study; Ref_Freq_B: Reference allele frequency of population in unpublished data; Alt1: Alternative allele 1; Alt1_Freq_A: Alternative allele 1 frequency of population in this study; Alt1_Freq_B: Alternative allele 1 frequency of population in unpublished data; Alt2: Alternative allele 2; Alt2_Freq_A: Alternative allele 2 frequency of population in this study; Alt2_Freq_B: Alternative allele 2 frequency of population in unpublished data.
DOI: 10.6084/m9.figshare.12050769
title: Additional file 12 of Whole genome resequencing reveals an association of ABCC4 variants with preaxial polydactyly in pigs

description: Additional file 12: Table S8. The genotyping of the highly differentiated INDELs between PPD affected and normal pigs. Pos: Physical position; Ref: Reference allele; Alt: Altered allele; GT_A: Genotypes of cases; GT_U: Genotypes of controls; The number “0” represent reference allele and “1” represent altered allele; The number behind the genotype in brackets represent the number of this genotype’s individuals; DAF_A: Derived allele frequency in cases; DAF_U: Derived allele frequency in controls; IGR: intergenic region.
DOI: 10.6084/m9.figshare.12050763
title: Additional file 11 of Whole genome resequencing reveals an association of ABCC4 variants with preaxial polydactyly in pigs

description: Additional file 11: Table S7. Phased genotyping results of the top ten highly associated SNPs. The bold italic highlighted columns represent the affected individuals. The bold italic highlighted rows (*) represent the missense mutation SNP which located in the third exon of ABCC4.
DOI: 10.6084/m9.figshare.12050763.v1
title: Additional file 11 of Whole genome resequencing reveals an association of ABCC4 variants with preaxial polydactyly in pigs

description: Additional file 11: Table S7. Phased genotyping results of the top ten highly associated SNPs. The bold italic highlighted columns represent the affected individuals. The bold italic highlighted rows (*) represent the missense mutation SNP which located in the third exon of ABCC4.
DOI: 10.6084/m9.figshare.12050769.v1
title: Additional file 12 of Whole genome resequencing reveals an association of ABCC4 variants with preaxial polydactyly in pigs

description: Additional file 12: Table S8. The genotyping of the highly differentiated INDELs between PPD affected and normal pigs. Pos: Physical position; Ref: Reference allele; Alt: Altered allele; GT_A: Genotypes of cases; GT_U: Genotypes of controls; The number “0” represent reference allele and “1” represent altered allele; The number behind the genotype in brackets represent the number of this genotype’s individuals; DAF_A: Derived allele frequency in cases; DAF_U: Derived allele frequency in controls; IGR: intergenic region.
DOI: 10.6084/m9.figshare.12050751
title: Additional file 3 of Identification and evolutionary analysis of the nucleolar proteome of Giardia lamblia

description: Additional file 3: Supplementary Table S3. The IDs and sequences of the nucleolar proteins of Homo sapiens, A. thaliana, and S. cerevisiae used in this work.
DOI: 10.6084/m9.figshare.12050754
title: Additional file 4 of Identification and evolutionary analysis of the nucleolar proteome of Giardia lamblia

description: Additional file 4: Supplementary Table S4. Results of prediction of localization of Giardia-specific nucleolar proteins by the ProLoc program, the SubNucPred program, and the LOCTREE3 program.
DOI: 10.6084/m9.figshare.12050751.v1
title: Additional file 3 of Identification and evolutionary analysis of the nucleolar proteome of Giardia lamblia

description: Additional file 3: Supplementary Table S3. The IDs and sequences of the nucleolar proteins of Homo sapiens, A. thaliana, and S. cerevisiae used in this work.
DOI: 10.6084/m9.figshare.12050754.v1
title: Additional file 4 of Identification and evolutionary analysis of the nucleolar proteome of Giardia lamblia

description: Additional file 4: Supplementary Table S4. Results of prediction of localization of Giardia-specific nucleolar proteins by the ProLoc program, the SubNucPred program, and the LOCTREE3 program.
DOI: 10.6084/m9.figshare.12050745
title: Additional file 1 of Identification and evolutionary analysis of the nucleolar proteome of Giardia lamblia

description: Additional file 1: Supplementary Table S1. The putative nucleolar proteome of G. lamblia (GiNuP) contains 255 individual nucleolar proteins.
DOI: 10.6084/m9.figshare.12050748
title: Additional file 2 of Identification and evolutionary analysis of the nucleolar proteome of Giardia lamblia

description: Additional file 2: Supplementary Table S2. 799 orthologous groups among human nucleolar proteome, the whole proteome of Arabidopsis, and budding yeast proteome.
DOI: 10.6084/m9.figshare.12050745.v1
title: Additional file 1 of Identification and evolutionary analysis of the nucleolar proteome of Giardia lamblia

description: Additional file 1: Supplementary Table S1. The putative nucleolar proteome of G. lamblia (GiNuP) contains 255 individual nucleolar proteins.
DOI: 10.6084/m9.figshare.12050748.v1
title: Additional file 2 of Identification and evolutionary analysis of the nucleolar proteome of Giardia lamblia

description: Additional file 2: Supplementary Table S2. 799 orthologous groups among human nucleolar proteome, the whole proteome of Arabidopsis, and budding yeast proteome.
DOI: 10.6084/m9.figshare.12050682
title: Additional file 5 of Comprehensive analysis of mRNAs and miRNAs in the ovarian follicles of uniparous and multiple goats at estrus phase

description: Additional file 5. The significant KEGG pathways of DEmRNAs in large and small follicles from uniparous and multiple goats.
DOI: 10.6084/m9.figshare.12050676
title: Additional file 3 of Comprehensive analysis of mRNAs and miRNAs in the ovarian follicles of uniparous and multiple goats at estrus phase

description: Additional file 3. RNA-seq data of DEmiRNA expression in large and small follicles from uniparous and multiple goats.
DOI: 10.6084/m9.figshare.12050679
title: Additional file 4 of Comprehensive analysis of mRNAs and miRNAs in the ovarian follicles of uniparous and multiple goats at estrus phase

description: Additional file 4. The significant Go term of DEmRNAs in large and small follicles from uniparous and multiple goats.
DOI: 10.6084/m9.figshare.12050673
title: Additional file 2 of Comprehensive analysis of mRNAs and miRNAs in the ovarian follicles of uniparous and multiple goats at estrus phase

description: Additional file 2. RNA-seq data of DEmRNA expression in large and small follicles from uniparous and multiple goats.
DOI: 10.6084/m9.figshare.12050679.v1
title: Additional file 4 of Comprehensive analysis of mRNAs and miRNAs in the ovarian follicles of uniparous and multiple goats at estrus phase

description: Additional file 4. The significant Go term of DEmRNAs in large and small follicles from uniparous and multiple goats.
DOI: 10.6084/m9.figshare.12050676.v1
title: Additional file 3 of Comprehensive analysis of mRNAs and miRNAs in the ovarian follicles of uniparous and multiple goats at estrus phase

description: Additional file 3. RNA-seq data of DEmiRNA expression in large and small follicles from uniparous and multiple goats.
DOI: 10.6084/m9.figshare.12050682.v1
title: Additional file 5 of Comprehensive analysis of mRNAs and miRNAs in the ovarian follicles of uniparous and multiple goats at estrus phase

description: Additional file 5. The significant KEGG pathways of DEmRNAs in large and small follicles from uniparous and multiple goats.
DOI: 10.6084/m9.figshare.12050673.v1
title: Additional file 2 of Comprehensive analysis of mRNAs and miRNAs in the ovarian follicles of uniparous and multiple goats at estrus phase

description: Additional file 2. RNA-seq data of DEmRNA expression in large and small follicles from uniparous and multiple goats.
DOI: 10.6084/m9.figshare.12050619
title: Additional file 1 of Burden of tumor mutations, neoepitopes, and other variants are weak predictors of cancer immunotherapy response and overall survival

description: Table S1. (summary of patient samples used for analysis), Table S2. (summary of patient clinical and DNA variant data), Table S3. (per-patient summary of driver variants and neoepitopes), Table S4. (modified neoepitope burdens), Table S5. (tumor-specific splice junction burdens), Table S6. (tumor-specific retained intron and retained intron epitope burdens), Table S7. (processed neoepitope burdens).
DOI: 10.6084/m9.figshare.12050622
title: Additional file 12 of Persistent DNA damage triggers activation of the integrated stress response to promote cell survival under nutrient restriction

description: Additional file 12: Table S4: All raw data for this study.
DOI: 10.6084/m9.figshare.12050622.v1
title: Additional file 12 of Persistent DNA damage triggers activation of the integrated stress response to promote cell survival under nutrient restriction

description: Additional file 12: Table S4: All raw data for this study.
DOI: 10.6084/m9.figshare.12050619.v1
title: Additional file 1 of Burden of tumor mutations, neoepitopes, and other variants are weak predictors of cancer immunotherapy response and overall survival

description: Table S1. (summary of patient samples used for analysis), Table S2. (summary of patient clinical and DNA variant data), Table S3. (per-patient summary of driver variants and neoepitopes), Table S4. (modified neoepitope burdens), Table S5. (tumor-specific splice junction burdens), Table S6. (tumor-specific retained intron and retained intron epitope burdens), Table S7. (processed neoepitope burdens).
DOI: 10.5517/ccdc.csd.cc251yz5
title: CCDC 1997887: Experimental Crystal Structure Determination

description: Related Article: Li-Cheng Song, Wei Chen, Li Feng|2020|New J.Chem.|44|14015|doi:10.1039/D0NJ02586K
DOI: 10.5517/ccdc.csd.cc251z07
title: CCDC 1997888: Experimental Crystal Structure Determination

description: Related Article: Li-Cheng Song, Wei Chen, Li Feng|2020|New J.Chem.|44|14015|doi:10.1039/D0NJ02586K
DOI: 10.5517/ccdc.csd.cc2521nz
title: CCDC 1997970: Experimental Crystal Structure Determination

description: Related Article: Marco Farinone, Joanna Cybińska, Miłosz Pawlicki|2020|Org.Chem.Front.|7|2391|doi:10.1039/D0QO00481B
DOI: 10.5517/ccdc.csd.cc22z328
title: CCDC 1935549: Experimental Crystal Structure Determination

description: Related Article: Maria Mazur, Michał Mrozowicz, Włodzimierz Buchowicz, Mariola Koszytkowska-Stawińska, Radosław Kamiński, Zbigniew Ochal, Patrycja Wińska, Maria Bretner|2020|Dalton Trans.|49|11504|doi:10.1039/D0DT01975E
DOI: 10.5517/ccdc.csd.cc22z339
title: CCDC 1935550: Experimental Crystal Structure Determination

description: Related Article: Maria Mazur, Michał Mrozowicz, Włodzimierz Buchowicz, Mariola Koszytkowska-Stawińska, Radosław Kamiński, Zbigniew Ochal, Patrycja Wińska, Maria Bretner|2020|Dalton Trans.|49|11504|doi:10.1039/D0DT01975E
DOI: 10.6084/m9.figshare.12050403
title: Additional file 1 of Mixture toxicity in the Erft River: assessment of ecological risks and toxicity drivers

description: Additional file 1. Additional tables.
DOI: 10.5517/ccdc.csd.cc25474q
title: CCDC 2000062: Experimental Crystal Structure Determination

description: Related Article: Varun Kumar, Mohamed El-Massaoudi, Smaail Radi, Kristof Van Hecke, Aurelian Rotaru, Yann Garcia|2020|New J.Chem.|44|13902|doi:10.1039/D0NJ02823A
DOI: 10.6084/m9.figshare.12050403.v1
title: Additional file 1 of Mixture toxicity in the Erft River: assessment of ecological risks and toxicity drivers

description: Additional file 1. Additional tables.
DOI: 10.5517/ccdc.csd.cc255glf
title: CCDC 2001254: Experimental Crystal Structure Determination

description: Related Article: Joan Soldevila-Sanmartín, Xavier Montaner, Teresa Calvet, Mercè Font-Bardia, Josefina Pons|2020|Polyhedron|188|114686|doi:10.1016/j.poly.2020.114686
DOI: 10.5517/ccdc.csd.cc255gnh
title: CCDC 2001256: Experimental Crystal Structure Determination

description: Related Article: Joan Soldevila-Sanmartín, Xavier Montaner, Teresa Calvet, Mercè Font-Bardia, Josefina Pons|2020|Polyhedron|188|114686|doi:10.1016/j.poly.2020.114686
DOI: 10.5517/ccdc.csd.cc255gpj
title: CCDC 2001257: Experimental Crystal Structure Determination

description: Related Article: Joan Soldevila-Sanmartín, Xavier Montaner, Teresa Calvet, Mercè Font-Bardia, Josefina Pons|2020|Polyhedron|188|114686|doi:10.1016/j.poly.2020.114686
DOI: 10.5517/ccdc.csd.cc256ncf
title: CCDC 2002394: Experimental Crystal Structure Determination

description: Related Article: M. P. Chrysouli, C. N. Banti, N. Kourkoumelis, E. E. Moushi, A. J. Tasiopoulos, A. Douvalis, C. Papachristodoulou, A. G. Hatzidimitriou, T. Bakas, S. K. Hadjikakou|2020|Dalton Trans.|49|11522|doi:10.1039/D0DT01665A
DOI: 10.6084/m9.figshare.12050340
title: Additional file 2 of Transcriptomic analysis of marine endophytic fungi extract identifies highly enriched anti-fungal fractions targeting cancer pathways in HepG2 cell lines

description: Additional file 2: Table S1. Venn diagram HepG2 V1 vs. HepG2 control sets, (following tables provided as sheets in the excel file) Table S2. Venn diagram HepG2 V3 vs. HepG2 control sets Table S3:. Venn diagram HepG2 V5 vs. HepG2 control sets Table S4. Venn diagram HepG2 V1, HepG2 V3, HepG2 V5 and HepG2 control sets Table S5. Overrepresented KEGG pathways in the down-regulated genes between HepG2 V1 vs. HepG2 control sets Table S6. Overrepresented KEGG pathways in the up-regulated genes between HepG2 V1 vs. HepG2 control set Table S7. Overrepresented KEGG pathways in the down-regulated genes between HepG2 V3 vs. HepG2 control sets Table S8. Overrepresented KEGG pathways in the up-regulated genes between HepG2 V3 vs. HepG2 control sets Table S9. Overrepresented KEGG pathways in the down-regulated genes between HepG2 V5 vs. HepG2 control sets Table S10. Overrepresented KEGG pathways in the up-regulated genes between HepG2 V5 vs. HepG2 control sets Table S11. Overrepresented gene ontologies in the subset of 26 genes expressed in HepG2 V1, V3 and V5 but not in HepG2 control from the venn diagram in Fig. 7d Table S12. Detailed listing and functional annotation via the DAVID functional annotation of the subset of 26 genes expressed in HepG2 V1, V3 and V5 but not in HepG2 control from the venn diagram in Fig. 7d Table S13. Results of CentriMo (MEME suite) motif enrichment analysis of the 300 bp upstream of the transcription start site for the genes down-regulated in HEPG2 treated with V1 vs. untreated HEPG2. Table S14. Results of CentriMo (MEME suite) motif enrichment analysis of the 300 bp upstream of the transcription start site for the genes down-regulated in HEPG2 treated with V3 vs. untreated HEPG2. Table S15. Results of CentriMo (MEME suite) motif enrichment analysis of the 300 bp upstream of the transcription start site for the genes down-regulated in HEPG2 treated with V5 vs. untreated HEPG2. Table S16. Results of CentriMo (MEME suite) motif enrichment analysis of the 300 bp upstream of the transcription start site for the genes up-regulated in HEPG2 treated with V1 vs. untreated HEPG2. Table S17. Results of CentriMo (MEME suite) motif enrichment analysis of the 300 bp upstream of the transcription start site for the genes up-regulated in HEPG2 treated with V3 vs. untreated HEPG2. Table S18. Results of CentriMo (MEME suite) motif enrichment analysis of the 300 bp upstream of the transcription start site for the genes up-regulated in HEPG2 treated with V5 vs. untreated HEPG2. Table S19. Summary of the 20 most significant results of all CentriMo (MEME suite) motif enrichment analyses.
DOI: 10.6084/m9.figshare.12050340.v1
title: Additional file 2 of Transcriptomic analysis of marine endophytic fungi extract identifies highly enriched anti-fungal fractions targeting cancer pathways in HepG2 cell lines

description: Additional file 2: Table S1. Venn diagram HepG2 V1 vs. HepG2 control sets, (following tables provided as sheets in the excel file) Table S2. Venn diagram HepG2 V3 vs. HepG2 control sets Table S3:. Venn diagram HepG2 V5 vs. HepG2 control sets Table S4. Venn diagram HepG2 V1, HepG2 V3, HepG2 V5 and HepG2 control sets Table S5. Overrepresented KEGG pathways in the down-regulated genes between HepG2 V1 vs. HepG2 control sets Table S6. Overrepresented KEGG pathways in the up-regulated genes between HepG2 V1 vs. HepG2 control set Table S7. Overrepresented KEGG pathways in the down-regulated genes between HepG2 V3 vs. HepG2 control sets Table S8. Overrepresented KEGG pathways in the up-regulated genes between HepG2 V3 vs. HepG2 control sets Table S9. Overrepresented KEGG pathways in the down-regulated genes between HepG2 V5 vs. HepG2 control sets Table S10. Overrepresented KEGG pathways in the up-regulated genes between HepG2 V5 vs. HepG2 control sets Table S11. Overrepresented gene ontologies in the subset of 26 genes expressed in HepG2 V1, V3 and V5 but not in HepG2 control from the venn diagram in Fig. 7d Table S12. Detailed listing and functional annotation via the DAVID functional annotation of the subset of 26 genes expressed in HepG2 V1, V3 and V5 but not in HepG2 control from the venn diagram in Fig. 7d Table S13. Results of CentriMo (MEME suite) motif enrichment analysis of the 300 bp upstream of the transcription start site for the genes down-regulated in HEPG2 treated with V1 vs. untreated HEPG2. Table S14. Results of CentriMo (MEME suite) motif enrichment analysis of the 300 bp upstream of the transcription start site for the genes down-regulated in HEPG2 treated with V3 vs. untreated HEPG2. Table S15. Results of CentriMo (MEME suite) motif enrichment analysis of the 300 bp upstream of the transcription start site for the genes down-regulated in HEPG2 treated with V5 vs. untreated HEPG2. Table S16. Results of CentriMo (MEME suite) motif enrichment analysis of the 300 bp upstream of the transcription start site for the genes up-regulated in HEPG2 treated with V1 vs. untreated HEPG2. Table S17. Results of CentriMo (MEME suite) motif enrichment analysis of the 300 bp upstream of the transcription start site for the genes up-regulated in HEPG2 treated with V3 vs. untreated HEPG2. Table S18. Results of CentriMo (MEME suite) motif enrichment analysis of the 300 bp upstream of the transcription start site for the genes up-regulated in HEPG2 treated with V5 vs. untreated HEPG2. Table S19. Summary of the 20 most significant results of all CentriMo (MEME suite) motif enrichment analyses.
DOI: 10.6084/m9.figshare.12050253
title: Additional file 2 of De novo assembly of the olive fruit fly (Bactrocera oleae) genome with linked-reads and long-read technologies minimizes gaps and provides exceptional Y chromosome assembly

description: Additional file 2: Table S1. Sequencing libraries used, sequence results, and kmer optimization for the GCA_001188975.2 assembly. Table S2. Comparison of assembly quality of the 3 main assemblies. Table S3. Assembly statistics for 9 different assemblies generated. Table S4. Comparison of assembly quality of the 3 Y chromosome assemblies. Table S5. Sequences of the primers used for the validation of Y-chromosome specific scaffolds. Table S6. Mapping positions and primers used to generate 9 new B. oleae DNA markers in this study. Table S7. Scaffold/contig localization on B. oleae chromosomes. Table S8. Distribution of the B. oleae Transposable elements in the genome assembly. Table S9. Samples and tissues used for the transcriptome sequencing and assembly. Table S10. Summary of the Trinity transcriptome generated from sequencing all the tissues in Supplementary Table S7. Table S11. Assessment of the completeness of the Trinity de novo transcriptome assembly. Table S12. Orthologous genes among 6 closely related insects. Table S13. Genes that peak at different metamorphic stages. Table S14. Gene ontology enrichment analysis for genes that peak at different metamorphic stages. Table S15. Datasets submitted to NCBI and their corresponding accession numbers and description. Table S16. Sources of proteomes and genomes used in Supplementary figures.
DOI: 10.6084/m9.figshare.12050253.v1
title: Additional file 2 of De novo assembly of the olive fruit fly (Bactrocera oleae) genome with linked-reads and long-read technologies minimizes gaps and provides exceptional Y chromosome assembly

description: Additional file 2: Table S1. Sequencing libraries used, sequence results, and kmer optimization for the GCA_001188975.2 assembly. Table S2. Comparison of assembly quality of the 3 main assemblies. Table S3. Assembly statistics for 9 different assemblies generated. Table S4. Comparison of assembly quality of the 3 Y chromosome assemblies. Table S5. Sequences of the primers used for the validation of Y-chromosome specific scaffolds. Table S6. Mapping positions and primers used to generate 9 new B. oleae DNA markers in this study. Table S7. Scaffold/contig localization on B. oleae chromosomes. Table S8. Distribution of the B. oleae Transposable elements in the genome assembly. Table S9. Samples and tissues used for the transcriptome sequencing and assembly. Table S10. Summary of the Trinity transcriptome generated from sequencing all the tissues in Supplementary Table S7. Table S11. Assessment of the completeness of the Trinity de novo transcriptome assembly. Table S12. Orthologous genes among 6 closely related insects. Table S13. Genes that peak at different metamorphic stages. Table S14. Gene ontology enrichment analysis for genes that peak at different metamorphic stages. Table S15. Datasets submitted to NCBI and their corresponding accession numbers and description. Table S16. Sources of proteomes and genomes used in Supplementary figures.
DOI: 10.6084/m9.figshare.12050190
title: Additional file 3 of Comprehensive genome-wide identification of angiosperm upstream ORFs with peptide sequences conserved in various taxonomic ranges using a novel pipeline, ESUCA

description: Additional file 3 : Supplementary Table S3. Multiple CPuORF sequence alignments.