cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26988871
title: Additional file 1 of Microbe-driven elemental cycling enables microbial adaptation to deep-sea ferromanganese nodule sediment fields

description: Additional file 1: Fig. S1. Location of sampling sites in the CCFZ polymetallic nodule province in the eastern equatorial Pacific Ocean. Fig. S2. rpS3 species group classification and abundance. a, Relative abundance of all species groups (SGs) in each phylum. Red represent the most abundant SGs, whose combined average relative abundance was at least 25% of that of all SGs. ‘Other’ comprises phyla accounting for ≤ 5 SGs. ‘Unclassify’ indicates that some SGs could not be classified by phylogenetic methods. b, Relative abundance of members of the microbial community at the phylum level across seven samples. Fig. S3. Comparison of GTDB- and rpS3 gene-based classifications of the MAGs. The left side of the Sankey diagram represents the GTDB classification at the phylum level for MAGs containing rpS3 gene sequences. The right side represents rpS3 gene-based classification using NCBI taxonomy. Fig. S4. Schematic diagram of conserved domains of MnxG and MoxA proteins. Blue regions represent cupredoxin superfamily, and purple region represents LysM superfamily. Fig. S5. Flavin-based extracellular electron transfer (EET) in MAGs. a, EET model with iron as an electron acceptor. The process of electron transfer was drawn in accordance with [58]. In brief, the electron transfer path from NAD to Fe(III) includes Ndh2, DMK, EetB, EetA, and FMN groups on PplA, or free flavin shuttles. b, Synthesis of DMK via the proteins DmkB and DmkA. c, Post-translational modification of PplA. FAD is secreted via FmnA and RibU, and FmnB uses FAD to post-translationally modify PplA. The treemaps indicate the composition of MAGs which contained the genes encoding the proteins. DHNA, 1,4-dihydroxy-2-naphthoyl-CoA; DMK, demethylmenaquinone; FAD, flavin adenine dinucleotide; FMN, Flavin mononucleotide; IPP, isopentenyl pyrophosphate. Fig. S6. Functional roles of MAGs in the metabolism of small carbon compounds. The horizontal stacked histograms illustrate the distribution of genomes encoding each function. The numbers within parentheses correspond to the total number of genomes that exhibit each function. MaxF, calcium-dependent methanol dehydrogenase subunit 1 (K14028); FdhA, glutathione-independent formaldehyde dehydrogenase (K00148); Ldh, L-lactate dehydrogenase (K00016); LdhA, D-lactate dehydrogenase (K03778); Acs, acetyl-CoA synthetase (K01895); Pct, propionate CoA-transferase (K01026); CoxL, aerobic carbon monoxide dehydrogenase large subunit (K03520). Fig. S7. Functional profile of the remaining MAGs other than the dominant MAGs. We randomly selected 18 MAGs in 100 replicates among the remaining MAGs and calculated the number of gene types for each functional category including metal transport and redox, nitrogen and sulfur metabolism, and carbohydrate degradation. The box plots shows data distribution for 100 replicates based on a five number summary. The table on the right compares the number of gene types in each functional profile of dominant MAGs and remaining MAGs.
DOI: 10.6084/m9.figshare.26988871.v1
title: Additional file 1 of Microbe-driven elemental cycling enables microbial adaptation to deep-sea ferromanganese nodule sediment fields

description: Additional file 1: Fig. S1. Location of sampling sites in the CCFZ polymetallic nodule province in the eastern equatorial Pacific Ocean. Fig. S2. rpS3 species group classification and abundance. a, Relative abundance of all species groups (SGs) in each phylum. Red represent the most abundant SGs, whose combined average relative abundance was at least 25% of that of all SGs. ‘Other’ comprises phyla accounting for ≤ 5 SGs. ‘Unclassify’ indicates that some SGs could not be classified by phylogenetic methods. b, Relative abundance of members of the microbial community at the phylum level across seven samples. Fig. S3. Comparison of GTDB- and rpS3 gene-based classifications of the MAGs. The left side of the Sankey diagram represents the GTDB classification at the phylum level for MAGs containing rpS3 gene sequences. The right side represents rpS3 gene-based classification using NCBI taxonomy. Fig. S4. Schematic diagram of conserved domains of MnxG and MoxA proteins. Blue regions represent cupredoxin superfamily, and purple region represents LysM superfamily. Fig. S5. Flavin-based extracellular electron transfer (EET) in MAGs. a, EET model with iron as an electron acceptor. The process of electron transfer was drawn in accordance with [58]. In brief, the electron transfer path from NAD to Fe(III) includes Ndh2, DMK, EetB, EetA, and FMN groups on PplA, or free flavin shuttles. b, Synthesis of DMK via the proteins DmkB and DmkA. c, Post-translational modification of PplA. FAD is secreted via FmnA and RibU, and FmnB uses FAD to post-translationally modify PplA. The treemaps indicate the composition of MAGs which contained the genes encoding the proteins. DHNA, 1,4-dihydroxy-2-naphthoyl-CoA; DMK, demethylmenaquinone; FAD, flavin adenine dinucleotide; FMN, Flavin mononucleotide; IPP, isopentenyl pyrophosphate. Fig. S6. Functional roles of MAGs in the metabolism of small carbon compounds. The horizontal stacked histograms illustrate the distribution of genomes encoding each function. The numbers within parentheses correspond to the total number of genomes that exhibit each function. MaxF, calcium-dependent methanol dehydrogenase subunit 1 (K14028); FdhA, glutathione-independent formaldehyde dehydrogenase (K00148); Ldh, L-lactate dehydrogenase (K00016); LdhA, D-lactate dehydrogenase (K03778); Acs, acetyl-CoA synthetase (K01895); Pct, propionate CoA-transferase (K01026); CoxL, aerobic carbon monoxide dehydrogenase large subunit (K03520). Fig. S7. Functional profile of the remaining MAGs other than the dominant MAGs. We randomly selected 18 MAGs in 100 replicates among the remaining MAGs and calculated the number of gene types for each functional category including metal transport and redox, nitrogen and sulfur metabolism, and carbohydrate degradation. The box plots shows data distribution for 100 replicates based on a five number summary. The table on the right compares the number of gene types in each functional profile of dominant MAGs and remaining MAGs.
DOI: 10.6084/m9.figshare.26988874
title: Additional file 2 of Microbe-driven elemental cycling enables microbial adaptation to deep-sea ferromanganese nodule sediment fields

description: Additional file 2: Table S1. Sampling sites and elemental composition of the sediment samples. Table S2. Assembly statistics for the seven sediment samples. Table S3. All identified SGs and their relative abundance across each sample. Table S4. All nonredundant MAGs identified in the study, and associated information. Table S5. The relative abundance of MAGs across each sample. Table S6. Information of TCDB's annotation in the 179 MAGs. Table S7. Information of metal redox annotation in the 179 MAGs. Table S8. The list of proteins involved in iron oxidation and iron reduction. Table S9. The matrix for the presence or absence of CAZymes in the 179 MAGs. Table S10. The proportion of MAGs which contained CAZymes within each phylum. Table S11. The matrix for the presence or absence of enzymes involved in the metabolism of small carbon compounds in the 179 MAGs. Table S12. The matrix for the presence or absence of nitrogen and sulfur metabolic genes in the 179 MAGs. Table S13. Checked annotations involved in metal transport and redox reactions. Table S14. Checked annotations involved in nitrogen and sulfur metabolism.
DOI: 10.6084/m9.figshare.26988874.v1
title: Additional file 2 of Microbe-driven elemental cycling enables microbial adaptation to deep-sea ferromanganese nodule sediment fields

description: Additional file 2: Table S1. Sampling sites and elemental composition of the sediment samples. Table S2. Assembly statistics for the seven sediment samples. Table S3. All identified SGs and their relative abundance across each sample. Table S4. All nonredundant MAGs identified in the study, and associated information. Table S5. The relative abundance of MAGs across each sample. Table S6. Information of TCDB's annotation in the 179 MAGs. Table S7. Information of metal redox annotation in the 179 MAGs. Table S8. The list of proteins involved in iron oxidation and iron reduction. Table S9. The matrix for the presence or absence of CAZymes in the 179 MAGs. Table S10. The proportion of MAGs which contained CAZymes within each phylum. Table S11. The matrix for the presence or absence of enzymes involved in the metabolism of small carbon compounds in the 179 MAGs. Table S12. The matrix for the presence or absence of nitrogen and sulfur metabolic genes in the 179 MAGs. Table S13. Checked annotations involved in metal transport and redox reactions. Table S14. Checked annotations involved in nitrogen and sulfur metabolism.
DOI: 10.6084/m9.figshare.26988922
title: Additional file 16 of Phages are unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis

description: Additional file 16: Supplementary Data 01. Overview of bacterial and phage genome information.
DOI: 10.6084/m9.figshare.26988922.v1
title: Additional file 16 of Phages are unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis

description: Additional file 16: Supplementary Data 01. Overview of bacterial and phage genome information.
DOI: 10.6084/m9.figshare.26988925
title: Additional file 17 of Phages are unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis

description: Additional file 17: Supplementary Data 02. Virulence.
DOI: 10.6084/m9.figshare.26988925.v1
title: Additional file 17 of Phages are unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis

description: Additional file 17: Supplementary Data 02. Virulence.
DOI: 10.6084/m9.figshare.26988928
title: Additional file 18 of Phages are unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis

description: Additional file 18: Supplementary Data 03. vConTACT2, VirClust, and VICTOR analyses.
DOI: 10.6084/m9.figshare.26988928.v1
title: Additional file 18 of Phages are unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis

description: Additional file 18: Supplementary Data 03. vConTACT2, VirClust, and VICTOR analyses.
DOI: 10.6084/m9.figshare.26988931.v1
title: Additional file 19 of Phages are unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis

description: Additional file 19: Supplementary Data 04. Phage protein coding gene annotations.
DOI: 10.6084/m9.figshare.26988931
title: Additional file 19 of Phages are unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis

description: Additional file 19: Supplementary Data 04. Phage protein coding gene annotations.
DOI: 10.6084/m9.figshare.26988934
title: Additional file 20 of Phages are unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis

description: Additional file 20: Supplementary Data 05. CRISPR-Cas system annotations.
DOI: 10.6084/m9.figshare.26988940
title: Additional file 22 of Phages are unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis

description: Additional file 22: Supplementary Data 07. SpacePHARER CRISPR spacer hits to phages.
DOI: 10.6084/m9.figshare.26988943
title: Additional file 23 of Phages are unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis

description: Additional file 23: Supplementary Data 08. CRISPROpenDB CRISPR spacer hits to phages.
DOI: 10.6084/m9.figshare.26988934.v1
title: Additional file 20 of Phages are unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis

description: Additional file 20: Supplementary Data 05. CRISPR-Cas system annotations.
DOI: 10.6084/m9.figshare.26988937
title: Additional file 21 of Phages are unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis

description: Additional file 21: Supplementary Data 06. CCtyper CRISPR spacer hits to phages.
DOI: 10.6084/m9.figshare.26988937.v1
title: Additional file 21 of Phages are unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis

description: Additional file 21: Supplementary Data 06. CCtyper CRISPR spacer hits to phages.
DOI: 10.6084/m9.figshare.26988940.v1
title: Additional file 22 of Phages are unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis

description: Additional file 22: Supplementary Data 07. SpacePHARER CRISPR spacer hits to phages.
DOI: 10.6084/m9.figshare.26988943.v1
title: Additional file 23 of Phages are unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis

description: Additional file 23: Supplementary Data 08. CRISPROpenDB CRISPR spacer hits to phages.
DOI: 10.6084/m9.figshare.26988946
title: Additional file 24 of Phages are unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis

description: Additional file 24: Supplementary Data 09. Bacterial protein coding gene annotations.
DOI: 10.6084/m9.figshare.26988946.v1
title: Additional file 24 of Phages are unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis

description: Additional file 24: Supplementary Data 09. Bacterial protein coding gene annotations.
DOI: 10.6084/m9.figshare.26988949
title: Additional file 25 of Phages are unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis

description: Additional file 25: Supplementary Data 10. Transposases.
DOI: 10.6084/m9.figshare.26988949.v1
title: Additional file 25 of Phages are unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis

description: Additional file 25: Supplementary Data 10. Transposases.
DOI: 10.6084/m9.figshare.26988952
title: Additional file 26 of Phages are unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis

description: Additional file 26: Supplementary Data 11. Mapping of cell-free nuclease-protected DNA to Pg ATCC 49417.
DOI: 10.6084/m9.figshare.26988952.v1
title: Additional file 26 of Phages are unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis

description: Additional file 26: Supplementary Data 11. Mapping of cell-free nuclease-protected DNA to Pg ATCC 49417.
DOI: 10.6084/m9.figshare.26988967
title: Additional file 3 of Morphological and transcriptomic analyses of stem cell-derived cortical neurons reveal mechanisms underlying synaptic dysfunction in schizophrenia

description: Additional file 3. DEG analysis.
DOI: 10.5281/zenodo.2645664
title: (06)-He2019A-DS0003 – Tribolium castaneum AGOC #6 subline × foxQ2-5' line long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

description: (06)-He2019A-DS0003 – Tribolium castaneum AGOC #6 subline × foxQ2-5' line long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy
DOI: 10.5281/zenodo.2645665
title: (06)-He2019A-DS0003 – Tribolium castaneum AGOC #6 subline × foxQ2-5' line long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

description: (06)-He2019A-DS0003 – Tribolium castaneum AGOC #6 subline × foxQ2-5' line long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy
DOI: 10.6084/m9.figshare.26988967.v1
title: Additional file 3 of Morphological and transcriptomic analyses of stem cell-derived cortical neurons reveal mechanisms underlying synaptic dysfunction in schizophrenia

description: Additional file 3. DEG analysis.
DOI: 10.6084/m9.figshare.26988979
title: Additional file 1 of A meta-analysis of immune-cell fractions at high resolution reveals novel associations with common phenotypes and health outcomes

description: Additional file 1. An excel spreadsheet containing all Supplementary Tables.
DOI: 10.6084/m9.figshare.26988979.v1
title: Additional file 1 of A meta-analysis of immune-cell fractions at high resolution reveals novel associations with common phenotypes and health outcomes

description: Additional file 1. An excel spreadsheet containing all Supplementary Tables.
DOI: 10.6084/m9.figshare.26988991
title: Additional file 2 of Genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton

description: Additional file 2: Table S1. Summary of DNase-seq data sets.
DOI: 10.6084/m9.figshare.26988991.v1
title: Additional file 2 of Genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton

description: Additional file 2: Table S1. Summary of DNase-seq data sets.
DOI: 10.6084/m9.figshare.26988994
title: Additional file 3 of Genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton

description: Additional file 3: Table S2. Summary of functional validation of DHSs using a fluorescence reporting assay.
DOI: 10.6084/m9.figshare.26988994.v1
title: Additional file 3 of Genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton

description: Additional file 3: Table S2. Summary of functional validation of DHSs using a fluorescence reporting assay.
DOI: 10.6084/m9.figshare.26988997
title: Additional file 4 of Genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton

description: Additional file 4: Table S3. Summary of gene expression and epigenetic modification in centromere regions.
DOI: 10.6084/m9.figshare.26988997.v1
title: Additional file 4 of Genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton

description: Additional file 4: Table S3. Summary of gene expression and epigenetic modification in centromere regions.
DOI: 10.6084/m9.figshare.26989000
title: Additional file 5 of Genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton

description: Additional file 5: Table S4. Summary of DEGs and DOCRs.
DOI: 10.6084/m9.figshare.26989000.v1
title: Additional file 5 of Genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton

description: Additional file 5: Table S4. Summary of DEGs and DOCRs.
DOI: 10.6084/m9.figshare.26989003
title: Additional file 6 of Genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton

description: Additional file 6: Table S5. Summary of unique links between DNase-seq peaks and genes.
DOI: 10.6084/m9.figshare.26989003.v1
title: Additional file 6 of Genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton

description: Additional file 6: Table S5. Summary of unique links between DNase-seq peaks and genes.
DOI: 10.6084/m9.figshare.26989006
title: Additional file 7 of Genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton

description: Additional file 7: Table S6. Summary of activated and repressed DOCRs and its related DEGs at ovule and fiber elongation.
DOI: 10.6084/m9.figshare.26989006.v1
title: Additional file 7 of Genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton

description: Additional file 7: Table S6. Summary of activated and repressed DOCRs and its related DEGs at ovule and fiber elongation.
DOI: 10.6084/m9.figshare.26989009.v1
title: Additional file 8 of Genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton

description: Additional file 8: Table S7. Summary of hormones related genes from cottonfgd.
DOI: 10.6084/m9.figshare.26989012
title: Additional file 9 of Genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton

description: Additional file 9: Table S8. TF regulatory networks during fiber development.
DOI: 10.6084/m9.figshare.26989009
title: Additional file 8 of Genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton

description: Additional file 8: Table S7. Summary of hormones related genes from cottonfgd.
DOI: 10.6084/m9.figshare.26989012.v1
title: Additional file 9 of Genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton

description: Additional file 9: Table S8. TF regulatory networks during fiber development.
DOI: 10.6084/m9.figshare.26989015
title: Additional file 10 of Genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton

description: Additional file 10: Table S9. Cotton TFs and their corresponding motifs.
DOI: 10.6084/m9.figshare.26989015.v1
title: Additional file 10 of Genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton

description: Additional file 10: Table S9. Cotton TFs and their corresponding motifs.
DOI: 10.6084/m9.figshare.26989018
title: Additional file 1 of Population transcriptogenomics highlights impaired metabolism and small population sizes in tree frogs living in the Chernobyl Exclusion Zone

description: Additional file 1: Table S1. Sampling sites, doses and individual parameters measured in 87 sampled frogs including weight, length, width, BCI (Ri), Individual Total Dose Rate (ITDR) and Average Total Dose Rate (ATDR).
DOI: 10.6084/m9.figshare.26989018.v1
title: Additional file 1 of Population transcriptogenomics highlights impaired metabolism and small population sizes in tree frogs living in the Chernobyl Exclusion Zone

description: Additional file 1: Table S1. Sampling sites, doses and individual parameters measured in 87 sampled frogs including weight, length, width, BCI (Ri), Individual Total Dose Rate (ITDR) and Average Total Dose Rate (ATDR).
DOI: 10.6084/m9.figshare.26989027
title: Additional file 4 of Population transcriptogenomics highlights impaired metabolism and small population sizes in tree frogs living in the Chernobyl Exclusion Zone

description: Additional file 4: Table S2. NGS quality control of RNAseq 87 individuals, including RNA index Number (RIN), read coverage and read quality (Phred score as Q30).
DOI: 10.6084/m9.figshare.26989027.v1
title: Additional file 4 of Population transcriptogenomics highlights impaired metabolism and small population sizes in tree frogs living in the Chernobyl Exclusion Zone

description: Additional file 4: Table S2. NGS quality control of RNAseq 87 individuals, including RNA index Number (RIN), read coverage and read quality (Phred score as Q30).
DOI: 10.6084/m9.figshare.26989030
title: Additional file 5 of Population transcriptogenomics highlights impaired metabolism and small population sizes in tree frogs living in the Chernobyl Exclusion Zone

description: Additional file 5: Table S3. Summary of SNPs correlated with ITDR in the CEZ. The result of tblastx giving the closest human Uniprot orthologue is indicated, as well as the results from SNP calling with GATK, variant prediction from SnpEff and the DEG obtained by DESeq2.