cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5902966
title: Additional file 8: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

description: Table S8. Length thresholds used to identify (near) complete virus sequences in metagenomic datasets. Length thresholds used to exclude partial RNA virus sequences from metagenomic datasets. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.5902966.v1
title: Additional file 8: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

description: Table S8. Length thresholds used to identify (near) complete virus sequences in metagenomic datasets. Length thresholds used to exclude partial RNA virus sequences from metagenomic datasets. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.5902951
title: Additional file 7: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

description: Table S7. Classification of viruses from metagenomic data. A full listing of metagenomic sequences analysed by GRAViTy and their provisional assignments. (XLSX 110Â kb)
DOI: 10.6084/m9.figshare.5902951.v1
title: Additional file 7: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

description: Table S7. Classification of viruses from metagenomic data. A full listing of metagenomic sequences analysed by GRAViTy and their provisional assignments. (XLSX 110Â kb)
DOI: 10.6084/m9.figshare.5902945
title: TrewinThesis_HistoricalMarginalDetections.xlsx

description: Database of <i>Aedes aegypti </i>historical presence at cold range margins across all continents where present. Database was constructed for modelling by Brendan Trewin for his PhD thesis.
DOI: 10.6084/m9.figshare.5902936
title: Additional file 6: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

description: Table S6. Cross-validation analysis. Scoring table for cross-validation analysis used to test specificity and sensitivity of GRAViTy. (XLSX 586Â kb)
DOI: 10.6084/m9.figshare.5902936.v1
title: Additional file 6: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

description: Table S6. Cross-validation analysis. Scoring table for cross-validation analysis used to test specificity and sensitivity of GRAViTy. (XLSX 586Â kb)
DOI: 10.6084/m9.figshare.5902933
title: Additional file 1: of Diffuse microvascular C5b-9 deposition is a common feature in muscle and nerve biopsies from diabetic patients

description: Clinical, epidemiological and pathological features of nerve and muscle biopsies included in this study. (XLSX 43Â kb)
DOI: 10.6084/m9.figshare.5902933.v1
title: Additional file 1: of Diffuse microvascular C5b-9 deposition is a common feature in muscle and nerve biopsies from diabetic patients

description: Clinical, epidemiological and pathological features of nerve and muscle biopsies included in this study. (XLSX 43Â kb)
DOI: 10.6084/m9.figshare.5902930
title: Additional file 7: of A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera

description: Table S3. Complete list of significantly differentially abundant OTUs determined by metagenomeSeq. All differentially abundant OTUs between a) MEF and MEF; b) MEF and NPS; c) MER and NPS; d) ECS and MEF are shown with their log fold change, p-values and mean and median abundance. OTUs in bold/grey are those above the selected threshold of at least 0.35% mean or median abundance in at least one group, and were present in both sets of samples where applicable. Set 1 refers to the set of samples were the left or right ear was chosen at random; these numbers are reported in results. Set 2 refers to the set of samples where the opposite ear was chosen; these results were only used for validation of the differentially abundant OTUs from Set 1. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.5902930.v1
title: Additional file 7: of A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera

description: Table S3. Complete list of significantly differentially abundant OTUs determined by metagenomeSeq. All differentially abundant OTUs between a) MEF and MEF; b) MEF and NPS; c) MER and NPS; d) ECS and MEF are shown with their log fold change, p-values and mean and median abundance. OTUs in bold/grey are those above the selected threshold of at least 0.35% mean or median abundance in at least one group, and were present in both sets of samples where applicable. Set 1 refers to the set of samples were the left or right ear was chosen at random; these numbers are reported in results. Set 2 refers to the set of samples where the opposite ear was chosen; these results were only used for validation of the differentially abundant OTUs from Set 1. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.5902924
title: Additional file 4: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

description: Locations, gene identifiers, and tandem classifications for all discovered tandem NLRs in eight grass species. (XLSX 40 kb)
DOI: 10.6084/m9.figshare.5902924.v1
title: Additional file 4: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

description: Locations, gene identifiers, and tandem classifications for all discovered tandem NLRs in eight grass species. (XLSX 40 kb)
DOI: 10.6084/m9.figshare.5902921
title: Additional file 5: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

description: Table S5. Mutual information scores. Informativeness of different PPHMMs in the assignment of sequences to ICTV taxa expressed as a mutual information score. (XLSX 538Â kb)
DOI: 10.6084/m9.figshare.5902921.v1
title: Additional file 5: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

description: Table S5. Mutual information scores. Informativeness of different PPHMMs in the assignment of sequences to ICTV taxa expressed as a mutual information score. (XLSX 538Â kb)
DOI: 10.6084/m9.figshare.5902912
title: Additional file 5: of Mouse chromocenters DNA content: sequencing and in silico analysis

description: Table S3. Contigs from mouse WGS with TRPC-21A and ERV fragments. (XLS 32Â kb)
DOI: 10.6084/m9.figshare.5902912.v1
title: Additional file 5: of Mouse chromocenters DNA content: sequencing and in silico analysis

description: Table S3. Contigs from mouse WGS with TRPC-21A and ERV fragments. (XLS 32Â kb)
DOI: 10.6084/m9.figshare.5902894
title: Additional file 4: of Mouse chromocenters DNA content: sequencing and in silico analysis

description: Table S2. Contigs from mouse WGS with MiSat and ERV fragments. (XLS 31Â kb)
DOI: 10.6084/m9.figshare.5902894.v1
title: Additional file 4: of Mouse chromocenters DNA content: sequencing and in silico analysis

description: Table S2. Contigs from mouse WGS with MiSat and ERV fragments. (XLS 31Â kb)
DOI: 10.6084/m9.figshare.5902891
title: Additional file 2: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

description: Clade memberships of all NLRs present in the tree in Fig.Â 1 and corresponding integrated domains present in NLR-IDsÂ (evalue &lt;= 0.05). (TSV 157 kb)
DOI: 10.6084/m9.figshare.5902891.v1
title: Additional file 2: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

description: Clade memberships of all NLRs present in the tree in Fig.Â 1 and corresponding integrated domains present in NLR-IDsÂ (evalue &lt;= 0.05). (TSV 157 kb)
DOI: 10.6084/m9.figshare.5902885
title: Additional file 3: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

description: Table S3. Summary of protein profile hidden Markov model databases. Complete list and description of PPHMMs assigned from viral genome sequences. (XLSX 1181Â kb)
DOI: 10.6084/m9.figshare.5902885.v1
title: Additional file 3: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

description: Table S3. Summary of protein profile hidden Markov model databases. Complete list and description of PPHMMs assigned from viral genome sequences. (XLSX 1181Â kb)
DOI: 10.6084/m9.figshare.5902873
title: Additional file 1: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

description: Quality assessment of the gene datasets used for phylogenetic analysis: N50 and size of the corresponding genome assembly, number of NLR genes with incomplete coverage (&lt; 70%) across the NB-ARC1_ARC2 domain and BUSCO analysis of the primary genes in the protein annotation. (XLSX 33 kb)
DOI: 10.6084/m9.figshare.5902873.v1
title: Additional file 1: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

description: Quality assessment of the gene datasets used for phylogenetic analysis: N50 and size of the corresponding genome assembly, number of NLR genes with incomplete coverage (&lt; 70%) across the NB-ARC1_ARC2 domain and BUSCO analysis of the primary genes in the protein annotation. (XLSX 33 kb)
DOI: 10.6084/m9.figshare.5902861
title: Additional file 16: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

description: The HMM trained from alignment of NB, ARC1, and ARC2 for NLR proteins used for phylogenetic analysis. (HMM 154 kb)
DOI: 10.6084/m9.figshare.5902861.v1
title: Additional file 16: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

description: The HMM trained from alignment of NB, ARC1, and ARC2 for NLR proteins used for phylogenetic analysis. (HMM 154 kb)
DOI: 10.6084/m9.figshare.5902855
title: Additional file 3: of A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera

description: Table S1. Full taxonomy of all OTUs identified in this study. Taxonomy is from the SILVA database, v123 for QIIME. Taxonomy assigned to OTUs by UCLUST v1.2.22q within QIIME v1.9.1 (assign_taxonomy.py). (XLSX 13 kb)
DOI: 10.6084/m9.figshare.5902855.v1
title: Additional file 3: of A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera

description: Table S1. Full taxonomy of all OTUs identified in this study. Taxonomy is from the SILVA database, v123 for QIIME. Taxonomy assigned to OTUs by UCLUST v1.2.22q within QIIME v1.9.1 (assign_taxonomy.py). (XLSX 13 kb)
DOI: 10.6084/m9.figshare.5902849
title: Additional file 1: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

description: Table S1. Viruses used in this study and their associated information. Listing of classified virus sequences used in the analysis. (XLSX 381Â kb)
DOI: 10.6084/m9.figshare.5902849.v1
title: Additional file 1: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

description: Table S1. Viruses used in this study and their associated information. Listing of classified virus sequences used in the analysis. (XLSX 381Â kb)
DOI: 10.6084/m9.figshare.5902846
title: Additional file 5: of The slowdown of Y chromosome expansion in dioecious Silene latifolia due to DNA loss and male-specific silencing of retrotransposons

description: Primers used for fluorescent in situ hybridization (FISH). (XLSX 8 kb)
DOI: 10.6084/m9.figshare.5902843
title: Additional file 4: of CEMiTool: a Bioconductor package for performing comprehensive modular co-expression analyses

description: html report. CEMiTool output html file using the RNA-seq data of Leishmania-infected patients. (ZIP 14736 kb)
DOI: 10.6084/m9.figshare.5902846.v1
title: Additional file 5: of The slowdown of Y chromosome expansion in dioecious Silene latifolia due to DNA loss and male-specific silencing of retrotransposons

description: Primers used for fluorescent in situ hybridization (FISH). (XLSX 8 kb)
DOI: 10.6084/m9.figshare.5902843.v1
title: Additional file 4: of CEMiTool: a Bioconductor package for performing comprehensive modular co-expression analyses

description: html report. CEMiTool output html file using the RNA-seq data of Leishmania-infected patients. (ZIP 14736 kb)
DOI: 10.6084/m9.figshare.5902840
title: Additional file 1: of Mouse chromocenters DNA content: sequencing and in silico analysis

description: Table S1. Contig annotation. (XLS 13Â kb)
DOI: 10.6084/m9.figshare.5902840.v1
title: Additional file 1: of Mouse chromocenters DNA content: sequencing and in silico analysis

description: Table S1. Contig annotation. (XLS 13Â kb)
DOI: 10.6084/m9.figshare.5902831
title: Additional file 15: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

description: The alignment of NB, ARC1, and ARC2 used to train the HMM for NLR proteins used for phylogenetic analysis. (FASTA 3 kb)
DOI: 10.6084/m9.figshare.5902831.v1
title: Additional file 15: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

description: The alignment of NB, ARC1, and ARC2 used to train the HMM for NLR proteins used for phylogenetic analysis. (FASTA 3 kb)
DOI: 10.6084/m9.figshare.5902819
title: Additional file 12: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

description: Figures S16–S19. Dendrograms of individual virus sequences of classified and metagenomic viruses in Baltimore groups II, III, IVa and IVb. Full dendrograms that correspond to the collapsed dendrograms shown in Figs. 5, 6, 7, 8 and 9 (lower panels). (ZIP 417 kb)
DOI: 10.6084/m9.figshare.5902819.v1
title: Additional file 12: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

description: Figures S16–S19. Dendrograms of individual virus sequences of classified and metagenomic viruses in Baltimore groups II, III, IVa and IVb. Full dendrograms that correspond to the collapsed dendrograms shown in Figs. 5, 6, 7, 8 and 9 (lower panels). (ZIP 417 kb)
DOI: 10.6084/m9.figshare.5902816
title: Additional file 3: of CEMiTool: a Bioconductor package for performing comprehensive modular co-expression analyses

description: Table S2. List of 1000 microarray studies utilized in Fig. 6. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.5902816.v1
title: Additional file 3: of CEMiTool: a Bioconductor package for performing comprehensive modular co-expression analyses

description: Table S2. List of 1000 microarray studies utilized in Fig. 6. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.5902807
title: Additional file 14: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

description: All NLR-IDs found in nine grasses (e-value at relaxed cut-offâ
DOI: 10.6084/m9.figshare.5902807.v1
title: Additional file 14: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

description: All NLR-IDs found in nine grasses (e-value at relaxed cut-offâ
DOI: 10.6084/m9.figshare.5902801
title: Additional file 3: of The slowdown of Y chromosome expansion in dioecious Silene latifolia due to DNA loss and male-specific silencing of retrotransposons

description: Information about studied LTR retrotransposons. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.5902801.v1
title: Additional file 3: of The slowdown of Y chromosome expansion in dioecious Silene latifolia due to DNA loss and male-specific silencing of retrotransposons

description: Information about studied LTR retrotransposons. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.5902783
title: Additional file 2: of CEMiTool: a Bioconductor package for performing comprehensive modular co-expression analyses

description: Table S1. List of 300 microarray studies utilized in Fig. 3. (XLSX 99 kb)
DOI: 10.6084/m9.figshare.5902783.v1
title: Additional file 2: of CEMiTool: a Bioconductor package for performing comprehensive modular co-expression analyses

description: Table S1. List of 300 microarray studies utilized in Fig. 3. (XLSX 99 kb)
DOI: 10.6084/m9.figshare.5902780
title: Additional file 10: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

description: Figures S7–S12. Dendrograms of individual virus sequences of classified viruses in Baltimore groups I–V and VI/VII. Full dendrograms that correspond to the collapsed dendrograms shown in Fig. 2. (ZIP 425 kb)
DOI: 10.6084/m9.figshare.5902780.v1
title: Additional file 10: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

description: Figures S7–S12. Dendrograms of individual virus sequences of classified viruses in Baltimore groups I–V and VI/VII. Full dendrograms that correspond to the collapsed dendrograms shown in Fig. 2. (ZIP 425 kb)
DOI: 10.6084/m9.figshare.5902777
title: Additional file 2: of The slowdown of Y chromosome expansion in dioecious Silene latifolia due to DNA loss and male-specific silencing of retrotransposons

description: Title: Information about analyzed data. Table S1 Geographical locations of wild S. latifolia populations used in this study. Table S2 Genome size of individual samples estimated by flow cytometry. Table S3 Detailed information about sequencing libraries of individual samples. Table S4 Number of preprocessed reads used in analyses. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.5902777.v1
title: Additional file 2: of The slowdown of Y chromosome expansion in dioecious Silene latifolia due to DNA loss and male-specific silencing of retrotransposons

description: Title: Information about analyzed data. Table S1 Geographical locations of wild S. latifolia populations used in this study. Table S2 Genome size of individual samples estimated by flow cytometry. Table S3 Detailed information about sequencing libraries of individual samples. Table S4 Number of preprocessed reads used in analyses. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.5902768
title: Additional file 11: of A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera

description: Table S4. All correlations between OTUs determined by SparCC. Correlations within each sample type are listed in separate sheets. This includes correlations between all possible pairs of OTUs found in the samples. P-values are non-parametric and were calculated as the proportion of times a correlation coefficient more extreme than the observed correlation coefficient occurred in 100 simulated datasets. (XLSX 443 kb)
DOI: 10.6084/m9.figshare.5902768.v1
title: Additional file 11: of A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera

description: Table S4. All correlations between OTUs determined by SparCC. Correlations within each sample type are listed in separate sheets. This includes correlations between all possible pairs of OTUs found in the samples. P-values are non-parametric and were calculated as the proportion of times a correlation coefficient more extreme than the observed correlation coefficient occurred in 100 simulated datasets. (XLSX 443 kb)
DOI: 10.6084/m9.figshare.5902747
title: Additional file 11: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

description: Potential donor - NLR acceptor gene sets, as observed from phylogenetic trees of the donor ID genes. High bootstrap support (&gt; 85) was used to determine likely donor ID and acceptor NLR-ID gene clades. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.5902747.v1
title: Additional file 11: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

description: Potential donor - NLR acceptor gene sets, as observed from phylogenetic trees of the donor ID genes. High bootstrap support (&gt; 85) was used to determine likely donor ID and acceptor NLR-ID gene clades. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.5902690
title: Measurements of 4 seasonal surveys of pCO2, radon, DO, temperature, salinity and Chl a for Lake Batur, Bali.

description: Georeferenced (WGS84) measurements of pCO2, 222Rn, dissolved oxygen, temperature, salinity and chlorophyll a, in 4 seasonal underway surveys in Lake Batur, Bali.
DOI: 10.6084/m9.figshare.5902516.v1
title: Docking scores for suitable candidates from top 100

description: All docking scores (Fred ChemGauss4) for those compounds examined from the top 100 matches for candidate ligands.<br><br>Some compounds were excluded based on general incompatibility (i.e. non-druglikeness)<br>
DOI: 10.6084/m9.figshare.5902453
title: eliza data - raw data of the amount of experience of first 20 ants

description: this is the raw data of the amount of experience of the first 20 ants to enter the experimental apparatus. L = leftR = rightM1 = marked once, therefore 1 training tripM2 = marked twice, 2 training tripsM3 = marked thrice, 3 training tripsM4 = marked four times, 4 training tripsU = unmarked, likely no training trips. <br>Time in seconds is at what time from the beginning of filming of the experiment did the individual arrive. <br>Treatments are as recorded for chris data raw file.
DOI: 10.6084/m9.figshare.5902453.v1
title: eliza data - raw data of the amount of experience of first 20 ants

description: this is the raw data of the amount of experience of the first 20 ants to enter the experimental apparatus. L = leftR = rightM1 = marked once, therefore 1 training tripM2 = marked twice, 2 training tripsM3 = marked thrice, 3 training tripsM4 = marked four times, 4 training tripsU = unmarked, likely no training trips. <br>Time in seconds is at what time from the beginning of filming of the experiment did the individual arrive. <br>Treatments are as recorded for chris data raw file.
DOI: 10.6084/m9.figshare.5902399
title: chris data - raw data of the ants from the 3 different treatments

description: raw data of the first 20 ants choosing the left or right side of the experimental setup, and whether they were marked or unmarked. p stay is the pheromone trail was allowed to build up during training and was left exactly where it was for the experimentp flip is the pheromone trail was built up and the swapped sides to the opposite arm during the experimentno p is the pheromone trail was built up during training and then removed and new clean paper was placed on the apparatus.
DOI: 10.6084/m9.figshare.5902399.v1
title: chris data - raw data of the ants from the 3 different treatments

description: raw data of the first 20 ants choosing the left or right side of the experimental setup, and whether they were marked or unmarked. p stay is the pheromone trail was allowed to build up during training and was left exactly where it was for the experimentp flip is the pheromone trail was built up and the swapped sides to the opposite arm during the experimentno p is the pheromone trail was built up during training and then removed and new clean paper was placed on the apparatus.