cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19351097
title: Additional file 16 of The expanded inhibitor of apoptosis gene family in oysters possesses novel domain architectures and may play diverse roles in apoptosis following immune challenge

description: Additional file 16: Additional File 1: C. virginica apoptosis genes, transcripts, and proteins. Text file containing GFF3 information about all identified apoptosis transcripts, genes, and proteins in the C. virginica reference genome annotation.
DOI: 10.6084/m9.figshare.19351097.v1
title: Additional file 16 of The expanded inhibitor of apoptosis gene family in oysters possesses novel domain architectures and may play diverse roles in apoptosis following immune challenge

description: Additional file 16: Additional File 1: C. virginica apoptosis genes, transcripts, and proteins. Text file containing GFF3 information about all identified apoptosis transcripts, genes, and proteins in the C. virginica reference genome annotation.
DOI: 10.6084/m9.figshare.19351100
title: Additional file 17 of The expanded inhibitor of apoptosis gene family in oysters possesses novel domain architectures and may play diverse roles in apoptosis following immune challenge

description: Additional file 17: Additional File 2: C. gigas apoptosis genes, transcripts, and proteins. Text file containing GFF3 information about all identified apoptosis transcripts, genes, and proteins in the C. gigas reference genome annotation.
DOI: 10.6084/m9.figshare.19351100.v1
title: Additional file 17 of The expanded inhibitor of apoptosis gene family in oysters possesses novel domain architectures and may play diverse roles in apoptosis following immune challenge

description: Additional file 17: Additional File 2: C. gigas apoptosis genes, transcripts, and proteins. Text file containing GFF3 information about all identified apoptosis transcripts, genes, and proteins in the C. gigas reference genome annotation.
DOI: 10.6084/m9.figshare.19351103
title: Additional file 18 of The expanded inhibitor of apoptosis gene family in oysters possesses novel domain architectures and may play diverse roles in apoptosis following immune challenge

description: Additional file 18: Additional File 3: Mollusc IAP Protein Multiple Sequence Alignment. FASTA file containing multiple sequence alignment of the full IAP amino acid sequences from all studied molluscs produced by MAFFT.
DOI: 10.6084/m9.figshare.19351103.v1
title: Additional file 18 of The expanded inhibitor of apoptosis gene family in oysters possesses novel domain architectures and may play diverse roles in apoptosis following immune challenge

description: Additional file 18: Additional File 3: Mollusc IAP Protein Multiple Sequence Alignment. FASTA file containing multiple sequence alignment of the full IAP amino acid sequences from all studied molluscs produced by MAFFT.
DOI: 10.6084/m9.figshare.19351106
title: Additional file 19 of The expanded inhibitor of apoptosis gene family in oysters possesses novel domain architectures and may play diverse roles in apoptosis following immune challenge

description: Additional file 19: Additional File 4: BIR domain Multiple Sequence Alignment. FASTA file containing Multiple Sequence alignment by MAFFT of individual BIR amino acid sequences from each protein. Sequences are named by their protein accession (XP), followed by which BIR domain the sequence was from (reading from 5′ to 3′), then ending with the gene accession (LOC). Species names for each are given in Supplementary Fig. 1b.
DOI: 10.6084/m9.figshare.19351106.v1
title: Additional file 19 of The expanded inhibitor of apoptosis gene family in oysters possesses novel domain architectures and may play diverse roles in apoptosis following immune challenge

description: Additional file 19: Additional File 4: BIR domain Multiple Sequence Alignment. FASTA file containing Multiple Sequence alignment by MAFFT of individual BIR amino acid sequences from each protein. Sequences are named by their protein accession (XP), followed by which BIR domain the sequence was from (reading from 5′ to 3′), then ending with the gene accession (LOC). Species names for each are given in Supplementary Fig. 1b.
DOI: 10.6084/m9.figshare.19351112.v1
title: Additional file 2 of The expanded inhibitor of apoptosis gene family in oysters possesses novel domain architectures and may play diverse roles in apoptosis following immune challenge

description: Additional file 2: Supplementary Table 2: IAP gene and transcript differential expression across experiments. The number of differentially expressed transcripts, and their total number of parent genes in each experiment, added across applicable multiple comparisons made within that experiment. *Distinct refers to unique “XM” ID in that experiment. Duplicates across multiple within-experiment comparisons not counted. **Uniquely refers to those only expressed in that experiment and not expressed in any other. (XLS 29 kb)
DOI: 10.6084/m9.figshare.19351109
title: Additional file 1 of The expanded inhibitor of apoptosis gene family in oysters possesses novel domain architectures and may play diverse roles in apoptosis following immune challenge

description: Additional file 1: Supplementary Table 1: IAP genes and transcripts with each domain architecture manually identified in oysters (Cv = C. virginica, Cg = C. gigas). Domain architecture classification for IAPs in well supported clusters (&gt; 90% bootstrap support) (see Fig. 4). Genes often coded for multiple IAP transcripts in each reference annotation. * = BIR Domain Identified by Interproscan and not CDD search. (XLS 28 kb)
DOI: 10.6084/m9.figshare.19351109.v1
title: Additional file 1 of The expanded inhibitor of apoptosis gene family in oysters possesses novel domain architectures and may play diverse roles in apoptosis following immune challenge

description: Additional file 1: Supplementary Table 1: IAP genes and transcripts with each domain architecture manually identified in oysters (Cv = C. virginica, Cg = C. gigas). Domain architecture classification for IAPs in well supported clusters (&gt; 90% bootstrap support) (see Fig. 4). Genes often coded for multiple IAP transcripts in each reference annotation. * = BIR Domain Identified by Interproscan and not CDD search. (XLS 28 kb)
DOI: 10.6084/m9.figshare.19351112
title: Additional file 2 of The expanded inhibitor of apoptosis gene family in oysters possesses novel domain architectures and may play diverse roles in apoptosis following immune challenge

description: Additional file 2: Supplementary Table 2: IAP gene and transcript differential expression across experiments. The number of differentially expressed transcripts, and their total number of parent genes in each experiment, added across applicable multiple comparisons made within that experiment. *Distinct refers to unique “XM” ID in that experiment. Duplicates across multiple within-experiment comparisons not counted. **Uniquely refers to those only expressed in that experiment and not expressed in any other. (XLS 29 kb)
DOI: 10.6084/m9.figshare.19351115
title: Additional file 3 of The expanded inhibitor of apoptosis gene family in oysters possesses novel domain architectures and may play diverse roles in apoptosis following immune challenge

description: Additional file 3: Supplementary Table 3: Domain architectures of significantly differentially expressed and constitutively expressed IAP transcripts in oysters. The total significantly differentially expressed and constitutively expressed transcripts per species with each domain architecture type, and the percent of the total IAPs in that species represented by that type. The total unique significantly differentially expressed transcripts with each domain architecture type in each experiment are also displayed. DEG = significantly differentially expressed genes, CEG = constitutively expressed genes. *Distinct refers to unique “XM” ID in that experiment. Duplicates across multiple within-experiment comparisons not counted. BIR* = BIR Domain Identified by Interproscan and not CDD search. (XLS 34 kb)
DOI: 10.6084/m9.figshare.19351118
title: Additional file 4 of The expanded inhibitor of apoptosis gene family in oysters possesses novel domain architectures and may play diverse roles in apoptosis following immune challenge

description: Additional file 4: Supplementary Table 4: Apoptosis and regulated cell death products identified in C. gigas and C. virginica reference annotations. Representative members of each apoptosis pathway-related gene product identified in C. gigas (Ostreida) and C. virginica (Ostreida) for viewing the breadth of identified products. The full list of identified apoptosis pathway related genes and transcripts for each species is presented in Additional Files 1 and 2. IAP* = Genes putatively identified as IAPs in this research based on HMMER and Interproscan analysis. (XLS 100 kb)
DOI: 10.6084/m9.figshare.19351115.v1
title: Additional file 3 of The expanded inhibitor of apoptosis gene family in oysters possesses novel domain architectures and may play diverse roles in apoptosis following immune challenge

description: Additional file 3: Supplementary Table 3: Domain architectures of significantly differentially expressed and constitutively expressed IAP transcripts in oysters. The total significantly differentially expressed and constitutively expressed transcripts per species with each domain architecture type, and the percent of the total IAPs in that species represented by that type. The total unique significantly differentially expressed transcripts with each domain architecture type in each experiment are also displayed. DEG = significantly differentially expressed genes, CEG = constitutively expressed genes. *Distinct refers to unique “XM” ID in that experiment. Duplicates across multiple within-experiment comparisons not counted. BIR* = BIR Domain Identified by Interproscan and not CDD search. (XLS 34 kb)
DOI: 10.6084/m9.figshare.19351118.v1
title: Additional file 4 of The expanded inhibitor of apoptosis gene family in oysters possesses novel domain architectures and may play diverse roles in apoptosis following immune challenge

description: Additional file 4: Supplementary Table 4: Apoptosis and regulated cell death products identified in C. gigas and C. virginica reference annotations. Representative members of each apoptosis pathway-related gene product identified in C. gigas (Ostreida) and C. virginica (Ostreida) for viewing the breadth of identified products. The full list of identified apoptosis pathway related genes and transcripts for each species is presented in Additional Files 1 and 2. IAP* = Genes putatively identified as IAPs in this research based on HMMER and Interproscan analysis. (XLS 100 kb)
DOI: 10.6084/m9.figshare.19351121
title: Additional file 5 of The expanded inhibitor of apoptosis gene family in oysters possesses novel domain architectures and may play diverse roles in apoptosis following immune challenge

description: Additional file 5: Supplementary Table 5: C. virginica and C. gigas immune challenge apoptosis differential expression. The total number of differentially expressed transcripts and apoptosis-related transcripts identified in each experimental group in each experiment, and the proportion of the total differentially expressed transcripts represented by apoptosis-related transcripts. (XLS 33 kb)
DOI: 10.6084/m9.figshare.19351121.v1
title: Additional file 5 of The expanded inhibitor of apoptosis gene family in oysters possesses novel domain architectures and may play diverse roles in apoptosis following immune challenge

description: Additional file 5: Supplementary Table 5: C. virginica and C. gigas immune challenge apoptosis differential expression. The total number of differentially expressed transcripts and apoptosis-related transcripts identified in each experimental group in each experiment, and the proportion of the total differentially expressed transcripts represented by apoptosis-related transcripts. (XLS 33 kb)
DOI: 10.6084/m9.figshare.19351124.v1
title: Additional file 6 of The expanded inhibitor of apoptosis gene family in oysters possesses novel domain architectures and may play diverse roles in apoptosis following immune challenge

description: Additional file 6: Supplementary Table 6: C. virginica and C. gigas immune challenge apoptosis co-expression. Results from Weighted Gene Correlation Network Analysis (WGCNA) for each experiment regarding: the number of significant modules, how many apoptosis-related genes and transcripts were identified across significant modules, and how many IAP genes, transcripts, and domain architectures were identified across significant modules. * = No significant modules identified by WGCNA. (XLS 29 kb)
DOI: 10.6084/m9.figshare.19351127
title: Additional file 7 of The expanded inhibitor of apoptosis gene family in oysters possesses novel domain architectures and may play diverse roles in apoptosis following immune challenge

description: Additional file 7: Supplementary Table 7: Domain architectures of IAP transcripts significantly co-expressed with apoptosis for each immune challenge. The number of IAP transcripts significantly co-expressed with each immune challenge. * = BIR Domain Identified by Interproscan and not CDD search. (XLS 29 kb)
DOI: 10.6084/m9.figshare.19351127.v1
title: Additional file 7 of The expanded inhibitor of apoptosis gene family in oysters possesses novel domain architectures and may play diverse roles in apoptosis following immune challenge

description: Additional file 7: Supplementary Table 7: Domain architectures of IAP transcripts significantly co-expressed with apoptosis for each immune challenge. The number of IAP transcripts significantly co-expressed with each immune challenge. * = BIR Domain Identified by Interproscan and not CDD search. (XLS 29 kb)
DOI: 10.6084/m9.figshare.19351130
title: Additional file 8 of The expanded inhibitor of apoptosis gene family in oysters possesses novel domain architectures and may play diverse roles in apoptosis following immune challenge

description: Additional file 8: Supplementary Table 8: C. virginica IAP haplotigs identified. C. virginica IAP proteins identified as likely assembly artifacts (haplotigs). Read counts for IAP proteins resulting from these assembly errors were combined with their most similar protein (“Protein Haplotig Collapsed Into”) for differential expression and WGCNA analysis (see Methods). Due to lack of a chromosome-based assembly for C. gigas at the time this analysis was conducted, manual haplotig analysis was not performed in this species. (XLS 29 kb)
DOI: 10.6084/m9.figshare.19351133
title: Additional file 9 of The expanded inhibitor of apoptosis gene family in oysters possesses novel domain architectures and may play diverse roles in apoptosis following immune challenge

description: Additional file 9: Supplementary Table 9: C. virginica and C. gigas transcriptome experiment metadata. SRA (NCBI) database information for each transcriptome analyzed in each experiment. (XLS 50 kb)
DOI: 10.6084/m9.figshare.19351124
title: Additional file 6 of The expanded inhibitor of apoptosis gene family in oysters possesses novel domain architectures and may play diverse roles in apoptosis following immune challenge

description: Additional file 6: Supplementary Table 6: C. virginica and C. gigas immune challenge apoptosis co-expression. Results from Weighted Gene Correlation Network Analysis (WGCNA) for each experiment regarding: the number of significant modules, how many apoptosis-related genes and transcripts were identified across significant modules, and how many IAP genes, transcripts, and domain architectures were identified across significant modules. * = No significant modules identified by WGCNA. (XLS 29 kb)
DOI: 10.6084/m9.figshare.19351130.v1
title: Additional file 8 of The expanded inhibitor of apoptosis gene family in oysters possesses novel domain architectures and may play diverse roles in apoptosis following immune challenge

description: Additional file 8: Supplementary Table 8: C. virginica IAP haplotigs identified. C. virginica IAP proteins identified as likely assembly artifacts (haplotigs). Read counts for IAP proteins resulting from these assembly errors were combined with their most similar protein (“Protein Haplotig Collapsed Into”) for differential expression and WGCNA analysis (see Methods). Due to lack of a chromosome-based assembly for C. gigas at the time this analysis was conducted, manual haplotig analysis was not performed in this species. (XLS 29 kb)
DOI: 10.6084/m9.figshare.19351133.v1
title: Additional file 9 of The expanded inhibitor of apoptosis gene family in oysters possesses novel domain architectures and may play diverse roles in apoptosis following immune challenge

description: Additional file 9: Supplementary Table 9: C. virginica and C. gigas transcriptome experiment metadata. SRA (NCBI) database information for each transcriptome analyzed in each experiment. (XLS 50 kb)
DOI: 10.6084/m9.figshare.19351158
title: Additional file 1 of Herpesviruses and their genetic diversity in the blood virome of healthy individuals: effect of aging

description: Additional file 1. Supplementary tables of virus genes. The file contains information on what viral genes are present in the reference sequences and the read counts attributed to each viral gene.
DOI: 10.6084/m9.figshare.19351158.v1
title: Additional file 1 of Herpesviruses and their genetic diversity in the blood virome of healthy individuals: effect of aging

description: Additional file 1. Supplementary tables of virus genes. The file contains information on what viral genes are present in the reference sequences and the read counts attributed to each viral gene.
DOI: 10.6084/m9.figshare.19351167
title: Additional file 1 of Existing evidence on antibiotic resistance exposure and transmission to humans from the environment: a systematic map

description: Additional file 1. ROSES for Systematic Map Reports.
DOI: 10.6084/m9.figshare.19351167.v1
title: Additional file 1 of Existing evidence on antibiotic resistance exposure and transmission to humans from the environment: a systematic map

description: Additional file 1. ROSES for Systematic Map Reports.
DOI: 10.6084/m9.figshare.19351170
title: Additional file 2 of Existing evidence on antibiotic resistance exposure and transmission to humans from the environment: a systematic map

description: Additional file 2. Map 1 supplementary articles.
DOI: 10.6084/m9.figshare.19351170.v1
title: Additional file 2 of Existing evidence on antibiotic resistance exposure and transmission to humans from the environment: a systematic map

description: Additional file 2. Map 1 supplementary articles.
DOI: 10.6084/m9.figshare.19351185.v1
title: Additional file 7 of Existing evidence on antibiotic resistance exposure and transmission to humans from the environment: a systematic map

description: Additional file 7. Extraction sheets.
DOI: 10.6084/m9.figshare.19351185
title: Additional file 7 of Existing evidence on antibiotic resistance exposure and transmission to humans from the environment: a systematic map

description: Additional file 7. Extraction sheets.
DOI: 10.6084/m9.figshare.19351188
title: Additional file 8 of Existing evidence on antibiotic resistance exposure and transmission to humans from the environment: a systematic map

description: Additional file 8. Map 1 interactive geographical map of studies.
DOI: 10.6084/m9.figshare.19351188.v1
title: Additional file 8 of Existing evidence on antibiotic resistance exposure and transmission to humans from the environment: a systematic map

description: Additional file 8. Map 1 interactive geographical map of studies.
DOI: 10.6084/m9.figshare.19351191
title: Additional file 9 of Existing evidence on antibiotic resistance exposure and transmission to humans from the environment: a systematic map

description: Additional file 9. Map 2 interactive geographical map of studies.
DOI: 10.6084/m9.figshare.19351191.v1
title: Additional file 9 of Existing evidence on antibiotic resistance exposure and transmission to humans from the environment: a systematic map

description: Additional file 9. Map 2 interactive geographical map of studies.
DOI: 10.6084/m9.figshare.19351187
title: Additional file 10 of SprayNPray: user-friendly taxonomic profiling of genome and metagenome contigs

description: Additional file 10: Supplemental File 8. FASTA file generated by SprayNPray, representing a subset of contigs from the simulated metagenome that match Ferrovum.
DOI: 10.6084/m9.figshare.19351187.v1
title: Additional file 10 of SprayNPray: user-friendly taxonomic profiling of genome and metagenome contigs

description: Additional file 10: Supplemental File 8. FASTA file generated by SprayNPray, representing a subset of contigs from the simulated metagenome that match Ferrovum.
DOI: 10.6084/m9.figshare.19351190
title: Additional file 11 of SprayNPray: user-friendly taxonomic profiling of genome and metagenome contigs

description: Additional file 11: Supplemental File 9. FASTA file generated by SprayNPray, representing a subset of contigs from the simulated metagenome that match Gallionellales.
DOI: 10.6084/m9.figshare.19351190.v1
title: Additional file 11 of SprayNPray: user-friendly taxonomic profiling of genome and metagenome contigs

description: Additional file 11: Supplemental File 9. FASTA file generated by SprayNPray, representing a subset of contigs from the simulated metagenome that match Gallionellales.
DOI: 10.6084/m9.figshare.19351193
title: Additional file 12 of SprayNPray: user-friendly taxonomic profiling of genome and metagenome contigs

description: Additional file 12: Supplemental File 10. FASTA file generated by SprayNPray, representing a subset of contigs from the simulated metagenome that match Ignavibacteria.
DOI: 10.6084/m9.figshare.19351196
title: Additional file 13 of SprayNPray: user-friendly taxonomic profiling of genome and metagenome contigs

description: Additional file 13: Supplemental File 11. FASTA file generated by SprayNPray, representing a subset of contigs from thesimulated metagenome that match Nitrospira.
DOI: 10.6084/m9.figshare.19351196.v1
title: Additional file 13 of SprayNPray: user-friendly taxonomic profiling of genome and metagenome contigs

description: Additional file 13: Supplemental File 11. FASTA file generated by SprayNPray, representing a subset of contigs from thesimulated metagenome that match Nitrospira.
DOI: 10.6084/m9.figshare.19351199
title: Additional file 14 of SprayNPray: user-friendly taxonomic profiling of genome and metagenome contigs

description: Additional file 14: Supplemental File 12. FASTA file generated by SprayNPray, representing a subset of contigs from the simulated metagenome that match Rickettsiales.
DOI: 10.6084/m9.figshare.19351199.v1
title: Additional file 14 of SprayNPray: user-friendly taxonomic profiling of genome and metagenome contigs

description: Additional file 14: Supplemental File 12. FASTA file generated by SprayNPray, representing a subset of contigs from the simulated metagenome that match Rickettsiales.
DOI: 10.6084/m9.figshare.19351202
title: Additional file 15 of SprayNPray: user-friendly taxonomic profiling of genome and metagenome contigs

description: Additional file 15: Supplemental File 13. FASTA file generated by SprayNPray, representing a subset of contigs from the simulated metagenome that match Sulfuricella.
DOI: 10.6084/m9.figshare.19351202.v1
title: Additional file 15 of SprayNPray: user-friendly taxonomic profiling of genome and metagenome contigs

description: Additional file 15: Supplemental File 13. FASTA file generated by SprayNPray, representing a subset of contigs from the simulated metagenome that match Sulfuricella.
DOI: 10.6084/m9.figshare.19351193.v1
title: Additional file 12 of SprayNPray: user-friendly taxonomic profiling of genome and metagenome contigs

description: Additional file 12: Supplemental File 10. FASTA file generated by SprayNPray, representing a subset of contigs from the simulated metagenome that match Ignavibacteria.