cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7096955.v1
title: Additional file 1: of Lignocellulose degradation at the holobiont level: teamwork in a keystone soil invertebrate

description: Table S1. List of primers used in RT-qPCR. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.7096952.v1
title: Additional file 3: of Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought

description: Summary of pairwise LD across the ten chromosomes of S. bicolor in our GWAS diversity panel. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.7096946
title: Additional file 3: of Constructions of alcohol consumption by non-problematised middle-aged drinkers: a qualitative systematic review

description: Metadata and paper summaries. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.7096946.v1
title: Additional file 3: of Constructions of alcohol consumption by non-problematised middle-aged drinkers: a qualitative systematic review

description: Metadata and paper summaries. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.7096925
title: Additional file 1: of Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought

description: Information about the lines used in this study. (XLSX 30 kb)
DOI: 10.6084/m9.figshare.7096925.v1
title: Additional file 1: of Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought

description: Information about the lines used in this study. (XLSX 30 kb)
DOI: 10.6084/m9.figshare.7096919
title: Additional file 2: of MicroRNA profiling associated with muscle growth in modern broilers compared to an unselected chicken breed

description: Target mRNAs of differentially expressed and qPCR validated miRNAs in PeM and BPR comparison. (XLSX 20Â kb)
DOI: 10.6084/m9.figshare.7096913
title: Additional file 14: of Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought

description: Potential evapotranspiration (ETo) and Irrigation water applications by treatment and date ranges in grain sorghum drought response study at the UC Kearney and UC Westside REC sites in 2016. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7096919.v1
title: Additional file 2: of MicroRNA profiling associated with muscle growth in modern broilers compared to an unselected chicken breed

description: Target mRNAs of differentially expressed and qPCR validated miRNAs in PeM and BPR comparison. (XLSX 20Â kb)
DOI: 10.6084/m9.figshare.7096913.v1
title: Additional file 14: of Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought

description: Potential evapotranspiration (ETo) and Irrigation water applications by treatment and date ranges in grain sorghum drought response study at the UC Kearney and UC Westside REC sites in 2016. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7096907
title: Additional file 1: of MicroRNA profiling associated with muscle growth in modern broilers compared to an unselected chicken breed

description: Read Per Million values of abundantly expressed miRNAs for indivial samples. (XLSX 22Â kb)
DOI: 10.6084/m9.figshare.7096907.v1
title: Additional file 1: of MicroRNA profiling associated with muscle growth in modern broilers compared to an unselected chicken breed

description: Read Per Million values of abundantly expressed miRNAs for indivial samples. (XLSX 22Â kb)
DOI: 10.6084/m9.figshare.7096895
title: Additional file 13: of Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought

description: Generalized comparison of recent Sorghum bicolor GWAS results. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7096892
title: Additional file 12: of Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought

description: Significantly enriched protein domains. (XLSX 43 kb)
DOI: 10.6084/m9.figshare.7096895.v1
title: Additional file 13: of Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought

description: Generalized comparison of recent Sorghum bicolor GWAS results. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7096892.v1
title: Additional file 12: of Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought

description: Significantly enriched protein domains. (XLSX 43 kb)
DOI: 10.6084/m9.figshare.7096880
title: Additional file 1: of Biomass burning history in East Asia during the last 4 million years recorded in elemental carbon variability at IODP site U1423

description: Table S1. The control points for the revised age model. (XLS 42 kb)
DOI: 10.6084/m9.figshare.7096880.v1
title: Additional file 1: of Biomass burning history in East Asia during the last 4 million years recorded in elemental carbon variability at IODP site U1423

description: Table S1. The control points for the revised age model. (XLS 42 kb)
DOI: 10.6084/m9.figshare.7096874
title: Additional file 11: of Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought

description: Significantly enriched gene ontologies. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7096874.v1
title: Additional file 11: of Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought

description: Significantly enriched gene ontologies. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7096868
title: Additional file 10: of Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought

description: Top candidate genes from PhytoMine and literature for 213 GWAS peaks. (XLSX 232 kb)
DOI: 10.6084/m9.figshare.7096868.v1
title: Additional file 10: of Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought

description: Top candidate genes from PhytoMine and literature for 213 GWAS peaks. (XLSX 232 kb)
DOI: 10.6084/m9.figshare.7096817
title: Additional file 5: of Role of AMPK signalling pathway during compensatory growth in pigs

description: Table S5. Principal functions represented in the biological networks identified in the list of differently expressed between animals subjected and not subjected to feed restriction. (XLS 149 kb)
DOI: 10.6084/m9.figshare.7096817.v1
title: Additional file 5: of Role of AMPK signalling pathway during compensatory growth in pigs

description: Table S5. Principal functions represented in the biological networks identified in the list of differently expressed between animals subjected and not subjected to feed restriction. (XLS 149 kb)
DOI: 10.6084/m9.figshare.7096808
title: Additional file 3: of Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis

description: sSNP and nSNP data for genes in clade 1 Nanoarchaeota SAGs and genome bins, organized in tabs by functional category. Genes highlighted in the discussion are separated into their own tab and highlighted in green within their respective functional category tabs. (XLSX 119 kb)
DOI: 10.6084/m9.figshare.7096802
title: Additional file 4: of Role of AMPK signalling pathway during compensatory growth in pigs

description: Table S4. List of canonical pathways identified at the list of 86 genes differentially expressed (Padj-value 1) between animals subjected and not subjected to a feed restriction period. (XLS 64 kb)
DOI: 10.6084/m9.figshare.7096808.v1
title: Additional file 3: of Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis

description: sSNP and nSNP data for genes in clade 1 Nanoarchaeota SAGs and genome bins, organized in tabs by functional category. Genes highlighted in the discussion are separated into their own tab and highlighted in green within their respective functional category tabs. (XLSX 119 kb)
DOI: 10.6084/m9.figshare.7096802.v1
title: Additional file 4: of Role of AMPK signalling pathway during compensatory growth in pigs

description: Table S4. List of canonical pathways identified at the list of 86 genes differentially expressed (Padj-value 1) between animals subjected and not subjected to a feed restriction period. (XLS 64 kb)
DOI: 10.6084/m9.figshare.7096796
title: Additional file 1: of Sex-related differences in coordination and variability among foot joints during running

description: Table S1. Complete results for joint coordination and variability. (XML 7 kb)
DOI: 10.6084/m9.figshare.7096793
title: Additional file 2: of Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis

description: Table S1. Read count, assembly statistics, completeness and contamination estimates from CheckM, and Nanoarchaeota-host pairing information for SAGs and selected Nanoarchaeota reference genomes. Table S2. Data identifiers for SAGs and reference genomes used in this study. Table S3. Assembly statistics, completeness and contamination estimates from CheckM, and additional information for reference genomes for comparison to putative host genome bins. Table S4. Assembly statistics, completeness and contamination estimates from CheckM, and additional information for Nanoarchaeota genome bins 95% ANI are highlighted. All cells with alignment lengths less than 20 kb have been set to 0% ANI. Table S7. Similarity of Nanoarchaeota 16S rRNA gene sequences extracted from genome bins and references. Sequences that are &gt; 98% similar are highlighted in green, sequence lengths are shown in parentheses. Table S8. Average nucleotide identity (ANI) of putative host genome bins and host reference genomes. Comparisons &gt; 95% ANI are highlighted. All cells with alignment lengths less than 20 kb have been set to 0% ANI. Table S9. Alignment results for proteins potentially horizontally transferred between hosts and Nanoarchaeota. Table S10. Within-SAG SNPs in single-sorted Nanoarchaeota SAGs and co-sorted Nanoarchaeota and putative host genome bins, at a MAF &gt; 10%. Table S11. Simulated within-SAG SNPs for pooled datasets of 1 to 6 SAGs, at a MAF &gt; 10%. Table S12. SNPs in all clade 1 Nanoarchaeota genome bins (&gt; 100 kb bin size), mean values shown for each site type. Table S13. Pairwise comparisons of mean non-synonymous SNPs per kb between functional categories of genes in clade 1 Nanoarchaeota SAGs and SAG bins, from post-hoc Tukey HSD tests. Significant comparisons are highlighted in green. (XLSX 65 kb)
DOI: 10.6084/m9.figshare.7096796.v1
title: Additional file 1: of Sex-related differences in coordination and variability among foot joints during running

description: Table S1. Complete results for joint coordination and variability. (XML 7 kb)
DOI: 10.6084/m9.figshare.7096793.v1
title: Additional file 2: of Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis

description: Table S1. Read count, assembly statistics, completeness and contamination estimates from CheckM, and Nanoarchaeota-host pairing information for SAGs and selected Nanoarchaeota reference genomes. Table S2. Data identifiers for SAGs and reference genomes used in this study. Table S3. Assembly statistics, completeness and contamination estimates from CheckM, and additional information for reference genomes for comparison to putative host genome bins. Table S4. Assembly statistics, completeness and contamination estimates from CheckM, and additional information for Nanoarchaeota genome bins 95% ANI are highlighted. All cells with alignment lengths less than 20 kb have been set to 0% ANI. Table S7. Similarity of Nanoarchaeota 16S rRNA gene sequences extracted from genome bins and references. Sequences that are &gt; 98% similar are highlighted in green, sequence lengths are shown in parentheses. Table S8. Average nucleotide identity (ANI) of putative host genome bins and host reference genomes. Comparisons &gt; 95% ANI are highlighted. All cells with alignment lengths less than 20 kb have been set to 0% ANI. Table S9. Alignment results for proteins potentially horizontally transferred between hosts and Nanoarchaeota. Table S10. Within-SAG SNPs in single-sorted Nanoarchaeota SAGs and co-sorted Nanoarchaeota and putative host genome bins, at a MAF &gt; 10%. Table S11. Simulated within-SAG SNPs for pooled datasets of 1 to 6 SAGs, at a MAF &gt; 10%. Table S12. SNPs in all clade 1 Nanoarchaeota genome bins (&gt; 100 kb bin size), mean values shown for each site type. Table S13. Pairwise comparisons of mean non-synonymous SNPs per kb between functional categories of genes in clade 1 Nanoarchaeota SAGs and SAG bins, from post-hoc Tukey HSD tests. Significant comparisons are highlighted in green. (XLSX 65 kb)
DOI: 10.6084/m9.figshare.7096790
title: Additional file 3: of Role of AMPK signalling pathway during compensatory growth in pigs

description: Table S3. List of genes differentially expressed (p-value adjusted for multiple testing 2 (i.e. ǀlog2FCǀ &gt; 1); and b) FC &gt; 1.8 (i.e. ǀlog2FCǀ &gt; 0.85). (XLSX 38 kb)
DOI: 10.6084/m9.figshare.7096790.v1
title: Additional file 3: of Role of AMPK signalling pathway during compensatory growth in pigs

description: Table S3. List of genes differentially expressed (p-value adjusted for multiple testing 2 (i.e. ǀlog2FCǀ &gt; 1); and b) FC &gt; 1.8 (i.e. ǀlog2FCǀ &gt; 0.85). (XLSX 38 kb)
DOI: 10.6084/m9.figshare.7096754
title: Additional file 1: of Neuropharmacological and antibacterial effects of the ethyl acetate extract of Diospyros malabarica (Ebenaceae) seeds

description: Zone of inhibition produced by D. malabarica seed extract. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.7096757
title: Additional file 1: of Role of AMPK signalling pathway during compensatory growth in pigs

description: Table S1. Composition of the fed used. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7096754.v1
title: Additional file 1: of Neuropharmacological and antibacterial effects of the ethyl acetate extract of Diospyros malabarica (Ebenaceae) seeds

description: Zone of inhibition produced by D. malabarica seed extract. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.7096757.v1
title: Additional file 1: of Role of AMPK signalling pathway during compensatory growth in pigs

description: Table S1. Composition of the fed used. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7096748
title: Additional file 1: of HIV partner services in Kenya: a cost and budget impact analysis study

description: Cost and Budget Impact Model Parameters and their outputs. (ZIP 1380 kb)
DOI: 10.6084/m9.figshare.7096748.v1
title: Additional file 1: of HIV partner services in Kenya: a cost and budget impact analysis study

description: Cost and Budget Impact Model Parameters and their outputs. (ZIP 1380 kb)
DOI: 10.6084/m9.figshare.7096742
title: Additional file 1: of Data-driven human transcriptomic modules determined by independent component analysis

description: Text S1. Axis labels for Figures in Paper. Table S1. MeSH Annotations of Representative Compendium Samples. Figure S1. KNN-kneeplots from Full Compendium. Figure S2. Tanglegram of FC and Gene space dendrograms (MAQC data). Figure S3. Heatmap of all samples in nervous system (GSE3536). Figure S4. Clustering of GSE71370 samples using 6636 DE genes. Figure S5. Reanalysis of GSE7538 (Parthenolide study used by Engreitz et al.). Figure S6. Number of unique GO terms versus number of leading principal components from PCA. Table S2. Full GO annotations for DE FCs in E-MTAB-3162. Table S3. Full GO annotations for DE FCs in GSE71370. (ZIP 1335 kb)
DOI: 10.6084/m9.figshare.7096742.v1
title: Additional file 1: of Data-driven human transcriptomic modules determined by independent component analysis

description: Text S1. Axis labels for Figures in Paper. Table S1. MeSH Annotations of Representative Compendium Samples. Figure S1. KNN-kneeplots from Full Compendium. Figure S2. Tanglegram of FC and Gene space dendrograms (MAQC data). Figure S3. Heatmap of all samples in nervous system (GSE3536). Figure S4. Clustering of GSE71370 samples using 6636 DE genes. Figure S5. Reanalysis of GSE7538 (Parthenolide study used by Engreitz et al.). Figure S6. Number of unique GO terms versus number of leading principal components from PCA. Table S2. Full GO annotations for DE FCs in E-MTAB-3162. Table S3. Full GO annotations for DE FCs in GSE71370. (ZIP 1335 kb)
DOI: 10.6084/m9.figshare.7096640
title: Additional file 6: of Phylogenomic analysis reveals splicing as a mechanism of parallel evolution of non-canonical SVAs in hominine primates

description: pt_SVA_D6 â a subfamily of non-canonical SVA elements in chimpanzees. Positions, target site duplications, length of the STK40-derived sequence and details on additional 5â ˛ transductions are provided. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.7096640.v1
title: Additional file 6: of Phylogenomic analysis reveals splicing as a mechanism of parallel evolution of non-canonical SVAs in hominine primates

description: pt_SVA_D6 â a subfamily of non-canonical SVA elements in chimpanzees. Positions, target site duplications, length of the STK40-derived sequence and details on additional 5â ˛ transductions are provided. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.7096619
title: Additional file 7: of Heterogeneous combinatorial expression of Hoxd genes in single cells during limb development

description: Table S2. List of the 343 differentially expressed genes between the six main groups of cells as shown in Fig. 4. Tab-delimited file. The first three columns indicate the coordinates of the genomic segments; all other columns represent values of individual cells. NA, no data available. (TXT 50 kb)
DOI: 10.6084/m9.figshare.7096619.v1
title: Additional file 7: of Heterogeneous combinatorial expression of Hoxd genes in single cells during limb development

description: Table S2. List of the 343 differentially expressed genes between the six main groups of cells as shown in Fig. 4. Tab-delimited file. The first three columns indicate the coordinates of the genomic segments; all other columns represent values of individual cells. NA, no data available. (TXT 50 kb)
DOI: 10.6084/m9.figshare.7096595
title: Additional file 3: of Phylogenomic analysis reveals splicing as a mechanism of parallel evolution of non-canonical SVAs in hominine primates

description: Consensus sequences of the SINE-R domains of SVA_D subfamilies in gorilla (gg), chimpanzee (pt) and humans (hs). (TXT 31 kb)
DOI: 10.6084/m9.figshare.7096595.v1
title: Additional file 3: of Phylogenomic analysis reveals splicing as a mechanism of parallel evolution of non-canonical SVAs in hominine primates

description: Consensus sequences of the SINE-R domains of SVA_D subfamilies in gorilla (gg), chimpanzee (pt) and humans (hs). (TXT 31 kb)
DOI: 10.6084/m9.figshare.7096583
title: Additional file 2: of Phylogenomic analysis reveals splicing as a mechanism of parallel evolution of non-canonical SVAs in hominine primates

description: Genomic coordinates, subfamily affiliation and species-specificity of SVA_D elements in hominine primates. (XLSX 182 kb)
DOI: 10.6084/m9.figshare.7096583.v1
title: Additional file 2: of Phylogenomic analysis reveals splicing as a mechanism of parallel evolution of non-canonical SVAs in hominine primates

description: Genomic coordinates, subfamily affiliation and species-specificity of SVA_D elements in hominine primates. (XLSX 182 kb)
DOI: 10.6084/m9.figshare.7096574
title: Additional file 1: of Phylogenomic analysis reveals splicing as a mechanism of parallel evolution of non-canonical SVAs in hominine primates

description: SVA_D elements in gorilla, chimpanzee and humans. Subfamily denominations, total number of elements in the respective subfamily and numbers of elements shared between lineages are provided for gorilla, chimpanzee and humans. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.7096574.v1
title: Additional file 1: of Phylogenomic analysis reveals splicing as a mechanism of parallel evolution of non-canonical SVAs in hominine primates

description: SVA_D elements in gorilla, chimpanzee and humans. Subfamily denominations, total number of elements in the respective subfamily and numbers of elements shared between lineages are provided for gorilla, chimpanzee and humans. (XLSX 16 kb)
DOI: 10.5281/zenodo.4005643
title: PacBio amplicon re-sequencing of 62 P. tricornutum genomic loci – processed datasets

description: Processed datasets from PacBio amplicon re-sequencing of 62 P. tricornutum genomic loci. Raw data are available at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA658511. Available datasets: - reference file for regions selected for amplicon sequencing: <em>Phaeodactylum_tricornutum_amplicon_sequencing_loci.fa</em> - final .bam files containing processed PacBio sequencing reads aligned to the reference: <em>PacBio_amplicon_seq_T1.bam</em> and <em>PacBio_amplicon_seq_T6.bam</em> - . table files with the position, reference and alternative allele for reliable biallelic SNPs selected in ILLUMINA sequencing of the culture at T1: <em>P_tricornutum_PacBio_amplicon_sequencing_T1_SNPs.table</em> and <em>P_tricornutum_PacBio_amplicon_sequencing_T6_SNPs.table</em> Re-sequencing of 62 endogenous P. tricornutum loci selected in a genome-wide analysis of haplotype diversity. The goal was to determine the number of haplotypes per locus and the appearance of new haplotypes over time. The length of the sequenced loci was 2kb (+/- 5%). Loci were amplified by emulsion PCR on the same culture harvested in two time points: five loci were amplified one month (T1) and all loci were amplified 6 months (T6) after the start of the culture from a single cell. Plasmids containing cloned GFP or YFP were amplified separately as a control for random errors. Control reactions for artificial haplotypes detection consisted of mixed CFP with YFP or CFP with GFP. Amplicons were pooled together into two samples. Sample PacBio_AS_T1 contained five P. tricornutum endogenous amplicons from DNA harvested at T1 time point, GFP amplified separately and CFP+YFP amplified in one reaction. Sample PacBio_AS_T6 contained 63 P. tricornutum endogenous amplicons from DNA harvested at T6 time point, YFP amplified separately and CFP+GFP amplified in one reaction. Samples were mixed in 1:9 PacBio_AS_T1: PacBio_AS_T6 ratio before sequencing on one PacBio Sequel SMRT cell.