cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17799143
title: Additional file 6 of Increased expression of six-large extracellular vesicle-derived miRNAs signature for nonvalvular atrial fibrillation

description: Additional file 6: Table S5. Putative targets of 6 highly expressed lEV miRNAs in atrial fibrillation (AF) patients.
DOI: 10.6084/m9.figshare.17799143.v1
title: Additional file 6 of Increased expression of six-large extracellular vesicle-derived miRNAs signature for nonvalvular atrial fibrillation

description: Additional file 6: Table S5. Putative targets of 6 highly expressed lEV miRNAs in atrial fibrillation (AF) patients.
DOI: 10.6084/m9.figshare.17799117
title: Additional file 10 of Performance of distinct microbial based solutions in a Campylobacter infection challenge model in poultry

description: Additional file 10. Table S10. Significance of the distribution of samples grouped by treatment. Results from pairwise PERMDISP analyses of the Bray–Curtis distances. Conducted in parallel to pairwise PERMANOVA analyses to place confidence in a significant result.
DOI: 10.6084/m9.figshare.17799117.v1
title: Additional file 10 of Performance of distinct microbial based solutions in a Campylobacter infection challenge model in poultry

description: Additional file 10. Table S10. Significance of the distribution of samples grouped by treatment. Results from pairwise PERMDISP analyses of the Bray–Curtis distances. Conducted in parallel to pairwise PERMANOVA analyses to place confidence in a significant result.
DOI: 10.6084/m9.figshare.17799120
title: Additional file 11 of Performance of distinct microbial based solutions in a Campylobacter infection challenge model in poultry

description: Additional file 11. Table S11. Influence of days post-hatch on microbiome structure within each treatment group. Results from PERMANOVA and PERMDISP analyses of the Bray–Curtis distances conducted in parallel.
DOI: 10.6084/m9.figshare.17799120.v1
title: Additional file 11 of Performance of distinct microbial based solutions in a Campylobacter infection challenge model in poultry

description: Additional file 11. Table S11. Influence of days post-hatch on microbiome structure within each treatment group. Results from PERMANOVA and PERMDISP analyses of the Bray–Curtis distances conducted in parallel.
DOI: 10.6084/m9.figshare.17799135
title: Additional file 1 of Performance of distinct microbial based solutions in a Campylobacter infection challenge model in poultry

description: Additional file 1. Table S1. Results from differential abundance analyses with DESeq2 of 39-day samples, comparing treated groups to the untreated group under C. jejuni challenge.
DOI: 10.6084/m9.figshare.17799135.v1
title: Additional file 1 of Performance of distinct microbial based solutions in a Campylobacter infection challenge model in poultry

description: Additional file 1. Table S1. Results from differential abundance analyses with DESeq2 of 39-day samples, comparing treated groups to the untreated group under C. jejuni challenge.
DOI: 10.6084/m9.figshare.17799138
title: Additional file 2 of Performance of distinct microbial based solutions in a Campylobacter infection challenge model in poultry

description: Additional file 2. Table S2. Results from differential abundance analyses with DESeq2 of 30-day samples, comparing treated groups to the untreated group under C. jejuni challenge.
DOI: 10.6084/m9.figshare.17799138.v1
title: Additional file 2 of Performance of distinct microbial based solutions in a Campylobacter infection challenge model in poultry

description: Additional file 2. Table S2. Results from differential abundance analyses with DESeq2 of 30-day samples, comparing treated groups to the untreated group under C. jejuni challenge.
DOI: 10.6084/m9.figshare.17799144
title: Additional file 3 of Performance of distinct microbial based solutions in a Campylobacter infection challenge model in poultry

description: Additional file 3. Table S3. Results from differential abundance analyses with DESeq2, comparing the bacitracin group to the untreated group in the absence of C. jejuni challenge.
DOI: 10.6084/m9.figshare.17799144.v1
title: Additional file 3 of Performance of distinct microbial based solutions in a Campylobacter infection challenge model in poultry

description: Additional file 3. Table S3. Results from differential abundance analyses with DESeq2, comparing the bacitracin group to the untreated group in the absence of C. jejuni challenge.
DOI: 10.6084/m9.figshare.17799147
title: Additional file 4 of Performance of distinct microbial based solutions in a Campylobacter infection challenge model in poultry

description: Additional file 4. Table S4. Results from differential abundance analyses with DESeq2, comparing samples at 39 days to samples at 30 days post-hatch within each of the 8 treatment groups.
DOI: 10.6084/m9.figshare.17799147.v1
title: Additional file 4 of Performance of distinct microbial based solutions in a Campylobacter infection challenge model in poultry

description: Additional file 4. Table S4. Results from differential abundance analyses with DESeq2, comparing samples at 39 days to samples at 30 days post-hatch within each of the 8 treatment groups.
DOI: 10.6084/m9.figshare.17799150.v1
title: Additional file 5 of Performance of distinct microbial based solutions in a Campylobacter infection challenge model in poultry

description: Additional file 5. Table S5. Results from Kruskal–Wallis rank sum tests comparing the alpha diversity indices (Observed, Chao1, Shannon, Simpson) of samples grouped according to treatment at each time point.
DOI: 10.6084/m9.figshare.17799150
title: Additional file 5 of Performance of distinct microbial based solutions in a Campylobacter infection challenge model in poultry

description: Additional file 5. Table S5. Results from Kruskal–Wallis rank sum tests comparing the alpha diversity indices (Observed, Chao1, Shannon, Simpson) of samples grouped according to treatment at each time point.
DOI: 10.6084/m9.figshare.17799153
title: Additional file 6 of Performance of distinct microbial based solutions in a Campylobacter infection challenge model in poultry

description: Additional file 6. Table S6. P-values from post-hoc pairwise Wilcoxon rank sum tests comparing the alpha diversity indices (Observed, Chao1, Shannon, Simpson) of samples grouped according to treatment at each time point.
DOI: 10.6084/m9.figshare.17799153.v1
title: Additional file 6 of Performance of distinct microbial based solutions in a Campylobacter infection challenge model in poultry

description: Additional file 6. Table S6. P-values from post-hoc pairwise Wilcoxon rank sum tests comparing the alpha diversity indices (Observed, Chao1, Shannon, Simpson) of samples grouped according to treatment at each time point.
DOI: 10.6084/m9.figshare.17799156
title: Additional file 7 of Performance of distinct microbial based solutions in a Campylobacter infection challenge model in poultry

description: Additional file 7. Table S7. P-values from Wilcoxon rank sum tests comparing the alpha diversity indices (Observed, Chao1, Shannon, Simpson) of samples grouped according to days post-hatch within each treatment group.
DOI: 10.6084/m9.figshare.17799156.v1
title: Additional file 7 of Performance of distinct microbial based solutions in a Campylobacter infection challenge model in poultry

description: Additional file 7. Table S7. P-values from Wilcoxon rank sum tests comparing the alpha diversity indices (Observed, Chao1, Shannon, Simpson) of samples grouped according to days post-hatch within each treatment group.
DOI: 10.6084/m9.figshare.17799159
title: Additional file 8 of Performance of distinct microbial based solutions in a Campylobacter infection challenge model in poultry

description: Additional file 8. Table S8. Influence of treatment on microbiome structure at each time point. Results from PERMANOVA and PERMDISP analyses of the Bray–Curtis distances conducted in parallel.
DOI: 10.6084/m9.figshare.17799159.v1
title: Additional file 8 of Performance of distinct microbial based solutions in a Campylobacter infection challenge model in poultry

description: Additional file 8. Table S8. Influence of treatment on microbiome structure at each time point. Results from PERMANOVA and PERMDISP analyses of the Bray–Curtis distances conducted in parallel.
DOI: 10.6084/m9.figshare.17799162
title: Additional file 9 of Performance of distinct microbial based solutions in a Campylobacter infection challenge model in poultry

description: Additional file 9. Table S9. Significance of separation between centroids of samples grouped by treatment. Results from pairwise PERMANOVA analyses of the Bray–Curtis distances.
DOI: 10.6084/m9.figshare.17799162.v1
title: Additional file 9 of Performance of distinct microbial based solutions in a Campylobacter infection challenge model in poultry

description: Additional file 9. Table S9. Significance of separation between centroids of samples grouped by treatment. Results from pairwise PERMANOVA analyses of the Bray–Curtis distances.
DOI: 10.6084/m9.figshare.17799231
title: Additional file 1 of Optimal surgical treatment for paratesticular leiomyosarcoma: retrospective analysis of 217 reported cases

description: Additional file 1.
DOI: 10.6084/m9.figshare.17799231.v1
title: Additional file 1 of Optimal surgical treatment for paratesticular leiomyosarcoma: retrospective analysis of 217 reported cases

description: Additional file 1.
DOI: 10.6084/m9.figshare.17799413
title: Additional file 2 of A proteomics informed by transcriptomics insight into the proteome of Ornithodoros erraticus adult tick saliva

description: Additional file 2: Dataset S1. ProteinPilot report of female saliva digested in gel.
DOI: 10.6084/m9.figshare.17799413.v1
title: Additional file 2 of A proteomics informed by transcriptomics insight into the proteome of Ornithodoros erraticus adult tick saliva

description: Additional file 2: Dataset S1. ProteinPilot report of female saliva digested in gel.
DOI: 10.6084/m9.figshare.17799419
title: Additional file 3 of A proteomics informed by transcriptomics insight into the proteome of Ornithodoros erraticus adult tick saliva

description: Additional file 3: Dataset S2. ProteinPilot report of male saliva digested in solution.
DOI: 10.6084/m9.figshare.17799419.v1
title: Additional file 3 of A proteomics informed by transcriptomics insight into the proteome of Ornithodoros erraticus adult tick saliva

description: Additional file 3: Dataset S2. ProteinPilot report of male saliva digested in solution.
DOI: 10.6084/m9.figshare.17799431.v1
title: Additional file 4 of A proteomics informed by transcriptomics insight into the proteome of Ornithodoros erraticus adult tick saliva

description: Additional file 4: Dataset S3. ProteinPilot report of the spectral library.
DOI: 10.6084/m9.figshare.17799449
title: Additional file 6 of A proteomics informed by transcriptomics insight into the proteome of Ornithodoros erraticus adult tick saliva

description: Additional file 6: Figure S1. Gene ontology (GO) distribution of O. erraticus saliva proteome. Level 2 GO terms of cellular components, molecular functions and biological processes were visualised using WEGO (Web Gene Ontology Annotation Plot).
DOI: 10.6084/m9.figshare.17799431
title: Additional file 4 of A proteomics informed by transcriptomics insight into the proteome of Ornithodoros erraticus adult tick saliva

description: Additional file 4: Dataset S3. ProteinPilot report of the spectral library.
DOI: 10.6084/m9.figshare.17799449.v1
title: Additional file 6 of A proteomics informed by transcriptomics insight into the proteome of Ornithodoros erraticus adult tick saliva

description: Additional file 6: Figure S1. Gene ontology (GO) distribution of O. erraticus saliva proteome. Level 2 GO terms of cellular components, molecular functions and biological processes were visualised using WEGO (Web Gene Ontology Annotation Plot).
DOI: 10.6084/m9.figshare.17701573
title: Additional file 10 of Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia

description: Additional file 10. Archive S7: The tree with QS identifiers and quartet fidelity (qf) score resulting from the quartet sampling method (NEWICK format).
DOI: 10.6084/m9.figshare.17701579
title: Additional file 12 of Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia

description: Additional file 12. Archive S9: Data used for Four-cluster Likelihood Mapping (FcLM). This archive includes two directories [one per approach, with (a) 19 species included in Group 4 and (b) 15 species included in Group 4; see Additional file 1]. Each directory includes four subdirectories: original, permutationI, permutationII, and permutationIII. In each subdirectory, the following files that served as input for the FcLM with IQ-TREE are provided: superalignment (FASTA format) of the strict data set, partition file with gene boundaries and respective models, and the group file (NEXUS format) listing the species included in the defined groups (see Additional file 2: Table S13).
DOI: 10.6084/m9.figshare.17701573.v1
title: Additional file 10 of Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia

description: Additional file 10. Archive S7: The tree with QS identifiers and quartet fidelity (qf) score resulting from the quartet sampling method (NEWICK format).
DOI: 10.6084/m9.figshare.17701576
title: Additional file 11 of Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia

description: Additional file 11. Archive S8: The tree topologies displaying the different positions of Embletonia pulchra that were tested using the approximately unbiased (AU) test with IQ-TREE. This archive contains four directories: intermediate, strict partitioned, strict unpartitioned, and strict SOS. Each directory contains the tree topologies that were tested for this specific data set (see Additional file 2: Table S15).
DOI: 10.6084/m9.figshare.17701576.v1
title: Additional file 11 of Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia

description: Additional file 11. Archive S8: The tree topologies displaying the different positions of Embletonia pulchra that were tested using the approximately unbiased (AU) test with IQ-TREE. This archive contains four directories: intermediate, strict partitioned, strict unpartitioned, and strict SOS. Each directory contains the tree topologies that were tested for this specific data set (see Additional file 2: Table S15).
DOI: 10.6084/m9.figshare.17701579.v1
title: Additional file 12 of Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia

description: Additional file 12. Archive S9: Data used for Four-cluster Likelihood Mapping (FcLM). This archive includes two directories [one per approach, with (a) 19 species included in Group 4 and (b) 15 species included in Group 4; see Additional file 1]. Each directory includes four subdirectories: original, permutationI, permutationII, and permutationIII. In each subdirectory, the following files that served as input for the FcLM with IQ-TREE are provided: superalignment (FASTA format) of the strict data set, partition file with gene boundaries and respective models, and the group file (NEXUS format) listing the species included in the defined groups (see Additional file 2: Table S13).
DOI: 10.6084/m9.figshare.17701585
title: Additional file 2 of Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia

description: Additional file 2. Table S1: Sampling information for the species collected for this study. Table S2: NCBI accession numbers for all species used in this study. Table S3: Statistics of raw sequence reads before and after trimming. Table S4: Assembly statistics. Table S5: BUSCO results. Table S6: Results of the Quality Checker script and selection of the best assembly. Table S7: Information on sequences removed during contamination filtering. Table S8: Number of removed outlier sequences per species. Table S9: Group definitions to compile the intermediate data set. Table S10: Information content and evolutionary rates of the orthologs included in the strict data set. Table S11: Supermatrix diagnostics of data sets used in this study. Table S12: Results of the Quartet Sampling analysis. Table S13: Group definitions used for Four-cluster Likelihood Mapping (FcLM) analyses. Table S14: FcLM results testing the position of Embletonia. Table S15: AU test results on the intermediate and strict (partitioned, unpartitioned, SOS) data sets.
DOI: 10.6084/m9.figshare.17701591
title: Additional file 4 of Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia

description: Additional file 4. Archive S1: Illumina adapters used for adapter trimming.
DOI: 10.6084/m9.figshare.17701585.v1
title: Additional file 2 of Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia

description: Additional file 2. Table S1: Sampling information for the species collected for this study. Table S2: NCBI accession numbers for all species used in this study. Table S3: Statistics of raw sequence reads before and after trimming. Table S4: Assembly statistics. Table S5: BUSCO results. Table S6: Results of the Quality Checker script and selection of the best assembly. Table S7: Information on sequences removed during contamination filtering. Table S8: Number of removed outlier sequences per species. Table S9: Group definitions to compile the intermediate data set. Table S10: Information content and evolutionary rates of the orthologs included in the strict data set. Table S11: Supermatrix diagnostics of data sets used in this study. Table S12: Results of the Quartet Sampling analysis. Table S13: Group definitions used for Four-cluster Likelihood Mapping (FcLM) analyses. Table S14: FcLM results testing the position of Embletonia. Table S15: AU test results on the intermediate and strict (partitioned, unpartitioned, SOS) data sets.
DOI: 10.6084/m9.figshare.17701591.v1
title: Additional file 4 of Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia

description: Additional file 4. Archive S1: Illumina adapters used for adapter trimming.
DOI: 10.6084/m9.figshare.17701594
title: Additional file 5 of Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia

description: Additional file 5. Archive S2: Included in this archive are the five alternative assemblies for each sample that has been sequenced in the frame of this study (FASTA format). Note that the best selected assembly has been deposited at the NCBI TSA database. Pseudobornella orientalis (HW08) has been removed from the NCBI TSA database due to exceptionally low sequence quality. Its alternative assemblies are therefore also not part of this archive.
DOI: 10.6084/m9.figshare.17701636.v1
title: Additional file 6 of Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia

description: Additional file 6. Archive S3: This archive includes official gene sets of the three reference species Biomphalaria glabrata, Crassostrea gigas, and Lottia gigantea on translational and transcriptional level, the list of all orthologous sequence clusters (OGs) as required for Orthograph, and an exemplary Orthograph config file.
DOI: 10.6084/m9.figshare.17701639
title: Additional file 7 of Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia

description: Additional file 7. Archive S4: Unmasked multiple sequence alignments on amino acid level including Doris kerguelenensis and Calmella cavolini prior to the removal of outliers.
DOI: 10.6084/m9.figshare.17701639.v1
title: Additional file 7 of Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia

description: Additional file 7. Archive S4: Unmasked multiple sequence alignments on amino acid level including Doris kerguelenensis and Calmella cavolini prior to the removal of outliers.
DOI: 10.6084/m9.figshare.17701636
title: Additional file 6 of Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia

description: Additional file 6. Archive S3: This archive includes official gene sets of the three reference species Biomphalaria glabrata, Crassostrea gigas, and Lottia gigantea on translational and transcriptional level, the list of all orthologous sequence clusters (OGs) as required for Orthograph, and an exemplary Orthograph config file.
DOI: 10.6084/m9.figshare.17701642
title: Additional file 8 of Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia

description: Additional file 8. Archive S5: 1,767 multiple sequence alignments (FASTA format) on amino acid level, from which sequences belonging to Doris kerguelenensis and Calmella cavolini as well as ambiguously aligned sections and gap-only sites were removed. These served as the basis for compiling the final unreduced supermatrix.
DOI: 10.6084/m9.figshare.17701642.v1
title: Additional file 8 of Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia

description: Additional file 8. Archive S5: 1,767 multiple sequence alignments (FASTA format) on amino acid level, from which sequences belonging to Doris kerguelenensis and Calmella cavolini as well as ambiguously aligned sections and gap-only sites were removed. These served as the basis for compiling the final unreduced supermatrix.