cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19386573.v1
title: Additional file 2 of Unveiling how vitrification affects the porcine blastocyst: clues from a transcriptomic study

description: Additional file 2: Table S2. All identified transcripts in IVC vs. CO embryos.
DOI: 10.6084/m9.figshare.19386576
title: Additional file 3 of Unveiling how vitrification affects the porcine blastocyst: clues from a transcriptomic study

description: Additional file 3: Table S3. All identified transcripts in VIT vs. IVC embryos.
DOI: 10.6084/m9.figshare.19386573
title: Additional file 2 of Unveiling how vitrification affects the porcine blastocyst: clues from a transcriptomic study

description: Additional file 2: Table S2. All identified transcripts in IVC vs. CO embryos.
DOI: 10.6084/m9.figshare.19386576.v1
title: Additional file 3 of Unveiling how vitrification affects the porcine blastocyst: clues from a transcriptomic study

description: Additional file 3: Table S3. All identified transcripts in VIT vs. IVC embryos.
DOI: 10.6084/m9.figshare.19386579
title: Additional file 4 of Unveiling how vitrification affects the porcine blastocyst: clues from a transcriptomic study

description: Additional file 4: Table S4. Differentially expressed genes (DEGs) in embryos for the VIT vs. CO comparison (FDR
DOI: 10.6084/m9.figshare.19386579.v1
title: Additional file 4 of Unveiling how vitrification affects the porcine blastocyst: clues from a transcriptomic study

description: Additional file 4: Table S4. Differentially expressed genes (DEGs) in embryos for the VIT vs. CO comparison (FDR
DOI: 10.6084/m9.figshare.19386582
title: Additional file 5 of Unveiling how vitrification affects the porcine blastocyst: clues from a transcriptomic study

description: Additional file 5: Table S7. Differentially expressed genes (DEGs) in embryos for the VIT vs. CO comparison (FDR 2). Table S8. Differentially expressed genes (DEGs) in embryos for the IVC vs. CO comparison (FDR 2). Table S9. Differentially expressed genes (DEGs) in embryos for the VIT vs. IVC comparison (FDR 2).
DOI: 10.6084/m9.figshare.19386582.v1
title: Additional file 5 of Unveiling how vitrification affects the porcine blastocyst: clues from a transcriptomic study

description: Additional file 5: Table S7. Differentially expressed genes (DEGs) in embryos for the VIT vs. CO comparison (FDR 2). Table S8. Differentially expressed genes (DEGs) in embryos for the IVC vs. CO comparison (FDR 2). Table S9. Differentially expressed genes (DEGs) in embryos for the VIT vs. IVC comparison (FDR 2).
DOI: 10.6084/m9.figshare.19386585
title: Additional file 6 of Unveiling how vitrification affects the porcine blastocyst: clues from a transcriptomic study

description: Additional file 6: Table S10. Venn Diagram. The overlap of DEG among all based only on FDR 2. Table S11. List of gene comparisons among studies. Table S12. Proportions of genes up and down-regulated in the different embryo groups based on DEG and log 2 FC. Table S13. Ortholog annotation from Jan 2019 used in the study.
DOI: 10.6084/m9.figshare.19386585.v1
title: Additional file 6 of Unveiling how vitrification affects the porcine blastocyst: clues from a transcriptomic study

description: Additional file 6: Table S10. Venn Diagram. The overlap of DEG among all based only on FDR 2. Table S11. List of gene comparisons among studies. Table S12. Proportions of genes up and down-regulated in the different embryo groups based on DEG and log 2 FC. Table S13. Ortholog annotation from Jan 2019 used in the study.
DOI: 10.6084/m9.figshare.19386588
title: Additional file 7 of Unveiling how vitrification affects the porcine blastocyst: clues from a transcriptomic study

description: Additional file 7. Functional analysis of transcripts altered in vitrified, in vitro culture and control embryos. Contains: Table S1. Annotation of DEG in the three embryo comparisons: VIT vs. CO, IVC vs. CO and VIT vs. IVC. Table S2. Enrichment analysis of DEG in in the three embryo comparisons: VIT vs. CO, IVC vs. CO and VIT vs. IVC. Table S3. Membership data for embryo term by Metascape analysis. Table S4. Membership data for oxidative damage term by Metascape analysis. Table S5. Membership data for cell arrest term by Metascape analysis. Table S6. Membership data for stress response term by Metascape analysis. Table S7. List of genes derived from SOTA clustering analysis VIT vs. IVC comparison. Table S8. Functional analysis from cluster genes 1-4 derived from Metascape. Table S9. Enrichment annotation analysis from cluster genes 1-4 derived from Metascape. Table S10. Gene expression profile across samples for selected genes validated by qPCR.
DOI: 10.6084/m9.figshare.19386588.v1
title: Additional file 7 of Unveiling how vitrification affects the porcine blastocyst: clues from a transcriptomic study

description: Additional file 7. Functional analysis of transcripts altered in vitrified, in vitro culture and control embryos. Contains: Table S1. Annotation of DEG in the three embryo comparisons: VIT vs. CO, IVC vs. CO and VIT vs. IVC. Table S2. Enrichment analysis of DEG in in the three embryo comparisons: VIT vs. CO, IVC vs. CO and VIT vs. IVC. Table S3. Membership data for embryo term by Metascape analysis. Table S4. Membership data for oxidative damage term by Metascape analysis. Table S5. Membership data for cell arrest term by Metascape analysis. Table S6. Membership data for stress response term by Metascape analysis. Table S7. List of genes derived from SOTA clustering analysis VIT vs. IVC comparison. Table S8. Functional analysis from cluster genes 1-4 derived from Metascape. Table S9. Enrichment annotation analysis from cluster genes 1-4 derived from Metascape. Table S10. Gene expression profile across samples for selected genes validated by qPCR.
DOI: 10.6084/m9.figshare.19386597
title: Additional file 10 of Comparative analysis of Streptococcus suis genomes identifies novel candidate virulence-associated genes in North American isolates

description: Additional file 10: Prokka annotations of MGE drafts. List of prokka annotations of the plasmid, ICE, IME, composite transposon, and 89 K PAI draft sequences identified in this study.
DOI: 10.6084/m9.figshare.19386597.v1
title: Additional file 10 of Comparative analysis of Streptococcus suis genomes identifies novel candidate virulence-associated genes in North American isolates

description: Additional file 10: Prokka annotations of MGE drafts. List of prokka annotations of the plasmid, ICE, IME, composite transposon, and 89 K PAI draft sequences identified in this study.
DOI: 10.6084/m9.figshare.19386600
title: Additional file 1 of Comparative analysis of Streptococcus suis genomes identifies novel candidate virulence-associated genes in North American isolates

description: Additional file 1: Genome assembly and annotation statistics of S. suis isolates (n = 208). Genome assembly and annotation statistics, such as predicted genome length, number of contigs, GC %, average genome coverage, and number of protein coding sequences, for each of the 208 S. suis isolates in the training set.
DOI: 10.6084/m9.figshare.19386600.v1
title: Additional file 1 of Comparative analysis of Streptococcus suis genomes identifies novel candidate virulence-associated genes in North American isolates

description: Additional file 1: Genome assembly and annotation statistics of S. suis isolates (n = 208). Genome assembly and annotation statistics, such as predicted genome length, number of contigs, GC %, average genome coverage, and number of protein coding sequences, for each of the 208 S. suis isolates in the training set.
DOI: 10.6084/m9.figshare.19386603
title: Additional file 2 of Comparative analysis of Streptococcus suis genomes identifies novel candidate virulence-associated genes in North American isolates

description: Additional file 2: Gene clusters (n = 8231) identified in Roary analysis of S. suis genomes (n = 208). Binary matrix representing the presence (1) and absence (0) of all 8231 gene clusters identified by the Roary analysis performed on all 208 S. suis genomes.
DOI: 10.6084/m9.figshare.19386606
title: Additional file 3 of Comparative analysis of Streptococcus suis genomes identifies novel candidate virulence-associated genes in North American isolates

description: Additional file 3: COG functional classifications for the 995 pan-gene clusters that met the criteria. Results of the BLAST searches against the Predicted Cluster of Orthologous Groups (COG) database. Classification as core or accessory and present (yes) or absent (no) in each pathotype was provided for each pan-gene cluster.
DOI: 10.6084/m9.figshare.19386603.v1
title: Additional file 2 of Comparative analysis of Streptococcus suis genomes identifies novel candidate virulence-associated genes in North American isolates

description: Additional file 2: Gene clusters (n = 8231) identified in Roary analysis of S. suis genomes (n = 208). Binary matrix representing the presence (1) and absence (0) of all 8231 gene clusters identified by the Roary analysis performed on all 208 S. suis genomes.
DOI: 10.6084/m9.figshare.19386606.v1
title: Additional file 3 of Comparative analysis of Streptococcus suis genomes identifies novel candidate virulence-associated genes in North American isolates

description: Additional file 3: COG functional classifications for the 995 pan-gene clusters that met the criteria. Results of the BLAST searches against the Predicted Cluster of Orthologous Groups (COG) database. Classification as core or accessory and present (yes) or absent (no) in each pathotype was provided for each pan-gene cluster.
DOI: 10.6084/m9.figshare.19386609
title: Additional file 4 of Comparative analysis of Streptococcus suis genomes identifies novel candidate virulence-associated genes in North American isolates

description: Additional file 4: Gene clusters (n = 6407) identified in Roary analysis of S. suis genomes (n = 161). Binary matrix representing the presence (1) and absence (0) of all 6407 gene clusters identified by the Roary analysis performed on the 161 S. suis genomes representing only the pathogenic and commensal pathotypes.
DOI: 10.6084/m9.figshare.19386609.v1
title: Additional file 4 of Comparative analysis of Streptococcus suis genomes identifies novel candidate virulence-associated genes in North American isolates

description: Additional file 4: Gene clusters (n = 6407) identified in Roary analysis of S. suis genomes (n = 161). Binary matrix representing the presence (1) and absence (0) of all 6407 gene clusters identified by the Roary analysis performed on the 161 S. suis genomes representing only the pathogenic and commensal pathotypes.
DOI: 10.6084/m9.figshare.19386612.v1
title: Additional file 5 of Comparative analysis of Streptococcus suis genomes identifies novel candidate virulence-associated genes in North American isolates

description: Additional file 5: Novel candidate VAGs in S. suis serotypes and STs. Serotype-ST combinations of S. suis possessing the SSU_RS09525, SSU_RS09155, and SSU_RS03100 markers.
DOI: 10.6084/m9.figshare.19386612
title: Additional file 5 of Comparative analysis of Streptococcus suis genomes identifies novel candidate virulence-associated genes in North American isolates

description: Additional file 5: Novel candidate VAGs in S. suis serotypes and STs. Serotype-ST combinations of S. suis possessing the SSU_RS09525, SSU_RS09155, and SSU_RS03100 markers.
DOI: 10.6084/m9.figshare.19386615.v1
title: Additional file 6 of Comparative analysis of Streptococcus suis genomes identifies novel candidate virulence-associated genes in North American isolates

description: Additional file 6: Presence-absence of novel candidate VAGs in S. suis serotypes and STs. Binary matrix representing the presence (1) or absence (0) of the SSU_RS09525, SSU_RS09155, and SSU_RS03100 markers in the training set representing 20 serotypes and 58 STs.
DOI: 10.6084/m9.figshare.19386615
title: Additional file 6 of Comparative analysis of Streptococcus suis genomes identifies novel candidate virulence-associated genes in North American isolates

description: Additional file 6: Presence-absence of novel candidate VAGs in S. suis serotypes and STs. Binary matrix representing the presence (1) or absence (0) of the SSU_RS09525, SSU_RS09155, and SSU_RS03100 markers in the training set representing 20 serotypes and 58 STs.
DOI: 10.6084/m9.figshare.19386618
title: Additional file 7 of Comparative analysis of Streptococcus suis genomes identifies novel candidate virulence-associated genes in North American isolates

description: Additional file 7: ARGs, VAGs, and MGEs identified in S. suis genomes (n = 208). Binary matrix representing the presence (1/yes) and absence (0/no) of ARGs, MGEs, MGE-associated ARGs, and MGE-associated VAGs.
DOI: 10.6084/m9.figshare.19386618.v1
title: Additional file 7 of Comparative analysis of Streptococcus suis genomes identifies novel candidate virulence-associated genes in North American isolates

description: Additional file 7: ARGs, VAGs, and MGEs identified in S. suis genomes (n = 208). Binary matrix representing the presence (1/yes) and absence (0/no) of ARGs, MGEs, MGE-associated ARGs, and MGE-associated VAGs.
DOI: 10.6084/m9.figshare.19386624
title: Additional file 9 of Comparative analysis of Streptococcus suis genomes identifies novel candidate virulence-associated genes in North American isolates

description: Additional file 9: Identification and predicted location of phages in S. suis genomes (n = 208). List of intact, questionable, and incomplete phages identified by PHASTER and their location (chromosome, plasmid) as predicted by viralVerify.
DOI: 10.6084/m9.figshare.19386624.v1
title: Additional file 9 of Comparative analysis of Streptococcus suis genomes identifies novel candidate virulence-associated genes in North American isolates

description: Additional file 9: Identification and predicted location of phages in S. suis genomes (n = 208). List of intact, questionable, and incomplete phages identified by PHASTER and their location (chromosome, plasmid) as predicted by viralVerify.
DOI: 10.6084/m9.figshare.19386672
title: Additional file 6 of Optimizing the integration of family caregivers in the delivery of person-centered care: evaluation of an educational program for the healthcare workforce

description: Additional file 6.
DOI: 10.6084/m9.figshare.19386672.v1
title: Additional file 6 of Optimizing the integration of family caregivers in the delivery of person-centered care: evaluation of an educational program for the healthcare workforce

description: Additional file 6.
DOI: 10.6084/m9.figshare.19386688.v1
title: Additional file 1 of Self-reported symptoms and health complaints associated with exposure to Ixodes ricinus-borne pathogens

description: Additional file 1. Data and statistical analyses.
DOI: 10.6084/m9.figshare.19386688
title: Additional file 1 of Self-reported symptoms and health complaints associated with exposure to Ixodes ricinus-borne pathogens

description: Additional file 1. Data and statistical analyses.
DOI: 10.6084/m9.figshare.19386705
title: Additional file 1 of Identifying genes with conserved splicing structure and orthologous isoforms in human, mouse and dog

description: Additional file 1 Full gene information in human with known and predicted transcripts for the 253 gene set. The additional file is an excel spreadsheet consisting of a sheet which describes all the information of a standard GTF file.
DOI: 10.6084/m9.figshare.19386705.v1
title: Additional file 1 of Identifying genes with conserved splicing structure and orthologous isoforms in human, mouse and dog

description: Additional file 1 Full gene information in human with known and predicted transcripts for the 253 gene set. The additional file is an excel spreadsheet consisting of a sheet which describes all the information of a standard GTF file.
DOI: 10.6084/m9.figshare.19386711.v1
title: Additional file 3 of Identifying genes with conserved splicing structure and orthologous isoforms in human, mouse and dog

description: Additional file 3 Full gene information in dog with known and predicted transcripts for the 253 gene set. The additional file is an excel spreadsheet consisting of a sheet which describes all the information of a standard GTF file.
DOI: 10.6084/m9.figshare.19386708
title: Additional file 2 of Identifying genes with conserved splicing structure and orthologous isoforms in human, mouse and dog

description: Additional file 2 Full gene information in mouse with known and predicted transcripts for the 253 gene set. The additional file is an excel spreadsheet consisting of a sheet which describes all the information of a standard GTF file.
DOI: 10.6084/m9.figshare.19386708.v1
title: Additional file 2 of Identifying genes with conserved splicing structure and orthologous isoforms in human, mouse and dog

description: Additional file 2 Full gene information in mouse with known and predicted transcripts for the 253 gene set. The additional file is an excel spreadsheet consisting of a sheet which describes all the information of a standard GTF file.
DOI: 10.6084/m9.figshare.19386711
title: Additional file 3 of Identifying genes with conserved splicing structure and orthologous isoforms in human, mouse and dog

description: Additional file 3 Full gene information in dog with known and predicted transcripts for the 253 gene set. The additional file is an excel spreadsheet consisting of a sheet which describes all the information of a standard GTF file.
DOI: 10.6084/m9.figshare.19386714
title: Additional file 4 of Identifying genes with conserved splicing structure and orthologous isoforms in human, mouse and dog

description: Additional file 4 List of the 879 orthologous CDS groups with their transcript identifiers. The additional file is an excel spreadsheet consisting of a sheet with, for each orthologous CDS group, its transcript identifiers in the three species.
DOI: 10.6084/m9.figshare.19386714.v1
title: Additional file 4 of Identifying genes with conserved splicing structure and orthologous isoforms in human, mouse and dog

description: Additional file 4 List of the 879 orthologous CDS groups with their transcript identifiers. The additional file is an excel spreadsheet consisting of a sheet with, for each orthologous CDS group, its transcript identifiers in the three species.
DOI: 10.6084/m9.figshare.19386717.v1
title: Additional file 5 of Identifying genes with conserved splicing structure and orthologous isoforms in human, mouse and dog

description: Additional file 5 Size of each CDS orthology group concerning the 118 gene set (alternative UTRs). The additional file is an excel spreadsheet consisting of a sheet with, for each orthologous gene triplet and each CDS orthology group, the number of transcripts encoding a same CDS per species.
DOI: 10.6084/m9.figshare.19386720
title: Additional file 6 of Identifying genes with conserved splicing structure and orthologous isoforms in human, mouse and dog

description: Additional file 6 List of the 1,029 predicted transcripts and their associated evidence found in external databases. The additional file is an excel spreadsheet consisting of a sheet with, for each predicted transcript, its evidence tag (see “Methods”).
DOI: 10.6084/m9.figshare.19386717
title: Additional file 5 of Identifying genes with conserved splicing structure and orthologous isoforms in human, mouse and dog

description: Additional file 5 Size of each CDS orthology group concerning the 118 gene set (alternative UTRs). The additional file is an excel spreadsheet consisting of a sheet with, for each orthologous gene triplet and each CDS orthology group, the number of transcripts encoding a same CDS per species.
DOI: 10.6084/m9.figshare.19386720.v1
title: Additional file 6 of Identifying genes with conserved splicing structure and orthologous isoforms in human, mouse and dog

description: Additional file 6 List of the 1,029 predicted transcripts and their associated evidence found in external databases. The additional file is an excel spreadsheet consisting of a sheet with, for each predicted transcript, its evidence tag (see “Methods”).
DOI: 10.6084/m9.figshare.19386709
title: Additional file 1 of Quantitative glycoproteomics analysis identifies novel FUT8 targets and signaling networks critical for breast cancer cell invasiveness

description: Additional file 1: Table S1. Core fucosylated FUT8 target proteins identified by comparative quantitative glycoproteomics.
DOI: 10.6084/m9.figshare.19386709.v1
title: Additional file 1 of Quantitative glycoproteomics analysis identifies novel FUT8 targets and signaling networks critical for breast cancer cell invasiveness

description: Additional file 1: Table S1. Core fucosylated FUT8 target proteins identified by comparative quantitative glycoproteomics.
DOI: 10.6084/m9.figshare.19386718
title: Additional file 4 of Quantitative glycoproteomics analysis identifies novel FUT8 targets and signaling networks critical for breast cancer cell invasiveness

description: Additional file 4: Table S2. Prognostic value of FUT8 target proteins.
DOI: 10.6084/m9.figshare.19386718.v1
title: Additional file 4 of Quantitative glycoproteomics analysis identifies novel FUT8 targets and signaling networks critical for breast cancer cell invasiveness

description: Additional file 4: Table S2. Prognostic value of FUT8 target proteins.
DOI: 10.6084/m9.figshare.19386727
title: Additional file 7 of Quantitative glycoproteomics analysis identifies novel FUT8 targets and signaling networks critical for breast cancer cell invasiveness

description: Additional file 7: Table S3. List of identified core fucosylated glycopeptides for IL6ST, integrin αv, and integrin β5.
DOI: 10.6084/m9.figshare.19386727.v1
title: Additional file 7 of Quantitative glycoproteomics analysis identifies novel FUT8 targets and signaling networks critical for breast cancer cell invasiveness

description: Additional file 7: Table S3. List of identified core fucosylated glycopeptides for IL6ST, integrin αv, and integrin β5.
DOI: 10.6084/m9.figshare.19386748
title: Additional file 1 of Prevalence of lifetime self-injurious thoughts and behaviors in a global sample of 599 patients reporting prospectively confirmed diagnosis with premenstrual dysphoric disorder

description: Additional file 1: Table 1. Nonparametric correlations among all study variables.
DOI: 10.6084/m9.figshare.19386748.v1
title: Additional file 1 of Prevalence of lifetime self-injurious thoughts and behaviors in a global sample of 599 patients reporting prospectively confirmed diagnosis with premenstrual dysphoric disorder

description: Additional file 1: Table 1. Nonparametric correlations among all study variables.
DOI: 10.6084/m9.figshare.19386760
title: Additional file 2 of In silico evaluation of a targeted metaproteomics strategy for broad screening of cellulolytic enzyme capacities in anaerobic microbiome bioreactors

description: Additional file 2: Table S1. List of 1401 high quality and medium–high quality metagenome-assembled genomes (MAGs) from Campanaro et al. (2020) used for this study.
DOI: 10.6084/m9.figshare.19386760.v1
title: Additional file 2 of In silico evaluation of a targeted metaproteomics strategy for broad screening of cellulolytic enzyme capacities in anaerobic microbiome bioreactors

description: Additional file 2: Table S1. List of 1401 high quality and medium–high quality metagenome-assembled genomes (MAGs) from Campanaro et al. (2020) used for this study.
DOI: 10.6084/m9.figshare.19386763
title: Additional file 3 of In silico evaluation of a targeted metaproteomics strategy for broad screening of cellulolytic enzyme capacities in anaerobic microbiome bioreactors

description: Additional file 3: Table S2. CAZy annotation results from the proteome of 1399 high quality and medium–high quality MAGs using the carbohydrate-active enzyme Annotation (dbCAN2) meta server. dbCAN2 searches were performed using HMMER, DIAMOND, and Hotpep tools.