cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7109618
title: Additional file 14: of Exome scale map of genetic alterations promoting metastasis in colorectal cancer

description: Table S12. GO terms (molecular function branch) with the highest overrepresentation in the 10% of genes with the lowest p-value (“top genes”) in the comparison between normal vs PT (A) and PT vs MT (B). Count - number of genes associated to the given GO term in the “top genes” set according to p-value in a given comparison, expected count - number of genes expected to be associated to the given GO term by chance in the “top genes” set. (XLS 25 kb)
DOI: 10.6084/m9.figshare.7109615
title: MOESM3 of Systematic miRNome profiling reveals differential microRNAs in transgenic maize metabolism

description: Additional file 3. List of the primers used to amplify the differentially expressed conserved miRNAs and the putative novel miRNAs.
DOI: 10.6084/m9.figshare.7109618.v1
title: Additional file 14: of Exome scale map of genetic alterations promoting metastasis in colorectal cancer

description: Table S12. GO terms (molecular function branch) with the highest overrepresentation in the 10% of genes with the lowest p-value (“top genes”) in the comparison between normal vs PT (A) and PT vs MT (B). Count - number of genes associated to the given GO term in the “top genes” set according to p-value in a given comparison, expected count - number of genes expected to be associated to the given GO term by chance in the “top genes” set. (XLS 25 kb)
DOI: 10.6084/m9.figshare.7109615.v1
title: MOESM3 of Systematic miRNome profiling reveals differential microRNAs in transgenic maize metabolism

description: Additional file 3. List of the primers used to amplify the differentially expressed conserved miRNAs and the putative novel miRNAs.
DOI: 10.6084/m9.figshare.7109600
title: Additional file 2: of Is sperm morphology functionally related to sperm swimming ability? A case study in a wild passerine bird with male hierarchies

description: Table S1. Male social status manipulation. The manipulation was performed equally for each experimental block of 5 aviaries, and the net change reflects the number of social ranks that individual were expected to gain or lose (the net change adds up to zero). (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7109600.v1
title: Additional file 2: of Is sperm morphology functionally related to sperm swimming ability? A case study in a wild passerine bird with male hierarchies

description: Table S1. Male social status manipulation. The manipulation was performed equally for each experimental block of 5 aviaries, and the net change reflects the number of social ranks that individual were expected to gain or lose (the net change adds up to zero). (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7109597
title: Additional file 13: of Exome scale map of genetic alterations promoting metastasis in colorectal cancer

description: Table S11. Results of RNA expression comparison between normal colon tissue and primary tumours (A) and between primary tumours and metastases (B). Target - the producers (Life Technologies) id of respective amplicon; padj - p-value adjusted for multiple hypotheses testing with Benjamini-Hochberg algorithm. (XLSX 2856 kb)
DOI: 10.6084/m9.figshare.7109594
title: MOESM2 of Systematic miRNome profiling reveals differential microRNAs in transgenic maize metabolism

description: Additional file 2. Normalized read count of the sRNA libraries mapped to conserved Zea mays miRNAs.
DOI: 10.6084/m9.figshare.7109597.v1
title: Additional file 13: of Exome scale map of genetic alterations promoting metastasis in colorectal cancer

description: Table S11. Results of RNA expression comparison between normal colon tissue and primary tumours (A) and between primary tumours and metastases (B). Target - the producers (Life Technologies) id of respective amplicon; padj - p-value adjusted for multiple hypotheses testing with Benjamini-Hochberg algorithm. (XLSX 2856 kb)
DOI: 10.6084/m9.figshare.7109594.v1
title: MOESM2 of Systematic miRNome profiling reveals differential microRNAs in transgenic maize metabolism

description: Additional file 2. Normalized read count of the sRNA libraries mapped to conserved Zea mays miRNAs.
DOI: 10.6084/m9.figshare.7109579
title: MOESM1 of Systematic miRNome profiling reveals differential microRNAs in transgenic maize metabolism

description: Additional file 1. Read size distribution of all sequenced sRNA libraries.
DOI: 10.6084/m9.figshare.7109579.v1
title: MOESM1 of Systematic miRNome profiling reveals differential microRNAs in transgenic maize metabolism

description: Additional file 1. Read size distribution of all sequenced sRNA libraries.
DOI: 10.6084/m9.figshare.7109570
title: Additional file 11: of Exome scale map of genetic alterations promoting metastasis in colorectal cancer

description: Table S10. Sequencing summary for the transcriptome profiling. Valid read - fraction of reads meeting quality standard, on target - fraction of valid reads mapping to the part of genome targeted by employed primers. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7109570.v1
title: Additional file 11: of Exome scale map of genetic alterations promoting metastasis in colorectal cancer

description: Table S10. Sequencing summary for the transcriptome profiling. Valid read - fraction of reads meeting quality standard, on target - fraction of valid reads mapping to the part of genome targeted by employed primers. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7109558
title: Additional file 10: of Exome scale map of genetic alterations promoting metastasis in colorectal cancer

description: Table S9. GSEA results in which CHASM score for a gene was taken as a ranking metric where NAME – Reactome pathway name, SIZE – size of a dataset after substraction of genes not present in ranked set, ES/NES – enrichment score/normalized enrichment score, NOM p-value – nominal p-value, FDR – false discovery rate, LEADING EDGE – statistics used to define the leading edge subset (for details, please refer to http://software.broadinstitute.org/gsea/doc/GSEAUserGuideTEXT.htm#_GSEA_Report ). (XLSX 15 kb)
DOI: 10.6084/m9.figshare.7109558.v1
title: Additional file 10: of Exome scale map of genetic alterations promoting metastasis in colorectal cancer

description: Table S9. GSEA results in which CHASM score for a gene was taken as a ranking metric where NAME – Reactome pathway name, SIZE – size of a dataset after substraction of genes not present in ranked set, ES/NES – enrichment score/normalized enrichment score, NOM p-value – nominal p-value, FDR – false discovery rate, LEADING EDGE – statistics used to define the leading edge subset (for details, please refer to http://software.broadinstitute.org/gsea/doc/GSEAUserGuideTEXT.htm#_GSEA_Report ). (XLSX 15 kb)
DOI: 10.6084/m9.figshare.7109549
title: Additional file 1: of The gut of the finch: uniqueness of the gut microbiome of the Galápagos vampire finch

description: Table S1. Taxonomic composition of Galápagos finch gut microbial communities, from Illumina 16S rRNA gene surveys, based on OTU clustering at 97% identity trimmed to at least 1% relative abundance in at least one finch. (XLSX 196 kb)
DOI: 10.6084/m9.figshare.7109549.v1
title: Additional file 1: of The gut of the finch: uniqueness of the gut microbiome of the Galápagos vampire finch

description: Table S1. Taxonomic composition of Galápagos finch gut microbial communities, from Illumina 16S rRNA gene surveys, based on OTU clustering at 97% identity trimmed to at least 1% relative abundance in at least one finch. (XLSX 196 kb)
DOI: 10.6084/m9.figshare.7109510
title: Additional file 2: of Microhabitat change drives diversification in pholcid spiders

description: (comma separated value table [.csv]): All specimensâ leg-ratio and assigned microhabitat. The metatarsus to tibia ratio of the first leg and the assigned microhabitat (ground, leaf, or space) is given for all pholcid specimens included in the phylogeny. (CSV 10 kb)
DOI: 10.6084/m9.figshare.7109510.v1
title: Additional file 2: of Microhabitat change drives diversification in pholcid spiders

description: (comma separated value table [.csv]): All specimensâ leg-ratio and assigned microhabitat. The metatarsus to tibia ratio of the first leg and the assigned microhabitat (ground, leaf, or space) is given for all pholcid specimens included in the phylogeny. (CSV 10 kb)
DOI: 10.6084/m9.figshare.7109480
title: Additional file 2: of Genome-wide SNP analyses reveal high gene flow and signatures of local adaptation among the scalloped spiny lobster (Panulirus homarus) along the Omani coastline

description: A plot of the Discriminant Analysis of Principal Components (DAPC) against the discriminant function retained. The plot is indicating presence of two genetic clusters of P. homarus in Oman. The plot was generated using the most informative 13 PCs identified from all 7988 SNPs dataset across 164 P. homarus individuals in the R package adegenet. (TXT 9105Â kb)
DOI: 10.6084/m9.figshare.7109480.v1
title: Additional file 2: of Genome-wide SNP analyses reveal high gene flow and signatures of local adaptation among the scalloped spiny lobster (Panulirus homarus) along the Omani coastline

description: A plot of the Discriminant Analysis of Principal Components (DAPC) against the discriminant function retained. The plot is indicating presence of two genetic clusters of P. homarus in Oman. The plot was generated using the most informative 13 PCs identified from all 7988 SNPs dataset across 164 P. homarus individuals in the R package adegenet. (TXT 9105Â kb)
DOI: 10.6084/m9.figshare.7109468
title: Additional file 1: of Genome-wide SNP analyses reveal high gene flow and signatures of local adaptation among the scalloped spiny lobster (Panulirus homarus) along the Omani coastline

description: Genotypic data of P. homarus for 164 individuals from Oman using 7988 SNPs. Genotypes are in genetix format. (TXT 576Â kb)
DOI: 10.6084/m9.figshare.7109468.v1
title: Additional file 1: of Genome-wide SNP analyses reveal high gene flow and signatures of local adaptation among the scalloped spiny lobster (Panulirus homarus) along the Omani coastline

description: Genotypic data of P. homarus for 164 individuals from Oman using 7988 SNPs. Genotypes are in genetix format. (TXT 576Â kb)
DOI: 10.6084/m9.figshare.7109453
title: Additional file 3: of Surveying knowledge, practice and attitudes towards intervention fidelity within trials of complex healthcare interventions

description: Dataset: anonymized raw data. (XLS 419 kb)
DOI: 10.6084/m9.figshare.7109453.v1
title: Additional file 3: of Surveying knowledge, practice and attitudes towards intervention fidelity within trials of complex healthcare interventions

description: Dataset: anonymized raw data. (XLS 419 kb)
DOI: 10.6084/m9.figshare.7109441
title: Additional file 2: of Surveying knowledge, practice and attitudes towards intervention fidelity within trials of complex healthcare interventions

description: Open-ended questions from survey. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.7109441.v1
title: Additional file 2: of Surveying knowledge, practice and attitudes towards intervention fidelity within trials of complex healthcare interventions

description: Open-ended questions from survey. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.7109339
title: Additional file 9: of A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments

description: Dataset 6. Sheet 1 shows the MAGs positive for the marker gene acsB (K14138) encoding an acetyl-CoA synthase (ACS). The basis for Fig. 6, namely presence and absence of key genes involved in the Wood-Ljungdahly pathway, acetogenesis, methanogenesis, glycolysis and pyruvate to CO2 conversion is shown for each MAG. Sheet 2 shows the MAGs positive for the marker gene cdhC (K00193) encoding for the beta subunit of an acetyl-CoA decarboxylase synthase complex. While acsB and cdhC correspond roughly to the Bacterial-type and Archaeal-type (methanogens) enzymes with the same function, we found few discrepancies between marker gene and genome phylogeny within the Methanomassiliicoccaceae and Chloroflexi. (XLSX 52 kb)
DOI: 10.6084/m9.figshare.7109339.v1
title: Additional file 9: of A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments

description: Dataset 6. Sheet 1 shows the MAGs positive for the marker gene acsB (K14138) encoding an acetyl-CoA synthase (ACS). The basis for Fig. 6, namely presence and absence of key genes involved in the Wood-Ljungdahly pathway, acetogenesis, methanogenesis, glycolysis and pyruvate to CO2 conversion is shown for each MAG. Sheet 2 shows the MAGs positive for the marker gene cdhC (K00193) encoding for the beta subunit of an acetyl-CoA decarboxylase synthase complex. While acsB and cdhC correspond roughly to the Bacterial-type and Archaeal-type (methanogens) enzymes with the same function, we found few discrepancies between marker gene and genome phylogeny within the Methanomassiliicoccaceae and Chloroflexi. (XLSX 52 kb)
DOI: 10.6084/m9.figshare.7109318
title: Additional file 7: of A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments

description: Dataset S5. Sheet 1 Presence and absence of marker genes and putative carbohydrate-active enzymes in the MAGs to infer putative roles in C, N and S element cycles based on K-number assignments and CAZy annotations. Sheet 2 Summary basis for Fig. 4. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.7109318.v1
title: Additional file 7: of A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments

description: Dataset S5. Sheet 1 Presence and absence of marker genes and putative carbohydrate-active enzymes in the MAGs to infer putative roles in C, N and S element cycles based on K-number assignments and CAZy annotations. Sheet 2 Summary basis for Fig. 4. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.7109312
title: Additional file 9: of Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don

description: Table S6. Annotation for adventitious root formation related genes included in list 2â ˛ for â base and middleâ . Gene names are given by DAVID. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7109312.v1
title: Additional file 9: of Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don

description: Table S6. Annotation for adventitious root formation related genes included in list 2â ˛ for â base and middleâ . Gene names are given by DAVID. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7109300
title: Additional file 6: of A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments

description: Dataset S4. Average Nucleotide Identity (ANI) and conserved DNA (condna) matrices to determine species delineation between the most abundant MAGs shown in Fig. 4, closely related (less abundant) MAGs and NCBI reference genomes. Decision matrix shows: 1 = same species, − 1 = might be same species, 0 = different species (see Methods section). (XLSX 1161 kb)
DOI: 10.6084/m9.figshare.7109297
title: Additional file 8: of Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don

description: Table S5. Functional enrichment annotations for the top 100 genes with the largest PC1. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7109297.v1
title: Additional file 8: of Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don

description: Table S5. Functional enrichment annotations for the top 100 genes with the largest PC1. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7109300.v1
title: Additional file 6: of A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments

description: Dataset S4. Average Nucleotide Identity (ANI) and conserved DNA (condna) matrices to determine species delineation between the most abundant MAGs shown in Fig. 4, closely related (less abundant) MAGs and NCBI reference genomes. Decision matrix shows: 1 = same species, − 1 = might be same species, 0 = different species (see Methods section). (XLSX 1161 kb)
DOI: 10.6084/m9.figshare.7109285
title: Additional file 5: of A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments

description: Dataset S3. Estimated abundance and derived salinity preference from each MAG in each metagenomic dataset expressed as Reads per Kilobase of MAG per Gigabase of mapped reads (RPKG) and â salinity preference scoreâ (see Methods section), basis for Fig. 4. (XLSX 143 kb)
DOI: 10.6084/m9.figshare.7109285.v1
title: Additional file 5: of A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments

description: Dataset S3. Estimated abundance and derived salinity preference from each MAG in each metagenomic dataset expressed as Reads per Kilobase of MAG per Gigabase of mapped reads (RPKG) and â salinity preference scoreâ (see Methods section), basis for Fig. 4. (XLSX 143 kb)
DOI: 10.6084/m9.figshare.7109282
title: Additional file 7: of Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don

description: Table S4. Annotation of the top 100 genes with the largest principal component 1 (PC1) coefficients. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.7109282.v1
title: Additional file 7: of Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don

description: Table S4. Annotation of the top 100 genes with the largest principal component 1 (PC1) coefficients. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.7109276
title: Additional file 4: of A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments

description: Dataset S2. Organism names, statistics and general description incl. Completeness and contamination estimates, phylogeny and DDBJ/EMBL/Genbank accession numbers of the metagenome assembled genomes (MAGs) described in this paper. All submitted versions described in this paper are version XXXX01000000. Sizeâ =â recovered genome size, Completeness (Compl1), contamination (Cont), strain heterogenity (Str het) and Taxon CheckM were inferred from lineage-specific marker sets and a reference tree build with CheckM [74]. Additional completeness (compl2) and redundancy (red) estimates were inferred based on the presence of universal single copy genes for Bacteria and Archaea [75]. Decision and confidence intervals from the Candidate Phyla Radiation (CPR) scan [75] are given, as well as the taxonomy of the besthit in SILVA when 16S rRNA genes were present. Phylum/class 16 ribosomal proteins is the taxonomy derived from our ribosomal protein trees (see main text: Figs. 2 and 3). OTU gives the inferred link of a population genome with our 16S rRNA gene amplicon dataset (Additional file 3). (XLSX 253 kb)
DOI: 10.6084/m9.figshare.7109276.v1
title: Additional file 4: of A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments

description: Dataset S2. Organism names, statistics and general description incl. Completeness and contamination estimates, phylogeny and DDBJ/EMBL/Genbank accession numbers of the metagenome assembled genomes (MAGs) described in this paper. All submitted versions described in this paper are version XXXX01000000. Sizeâ =â recovered genome size, Completeness (Compl1), contamination (Cont), strain heterogenity (Str het) and Taxon CheckM were inferred from lineage-specific marker sets and a reference tree build with CheckM [74]. Additional completeness (compl2) and redundancy (red) estimates were inferred based on the presence of universal single copy genes for Bacteria and Archaea [75]. Decision and confidence intervals from the Candidate Phyla Radiation (CPR) scan [75] are given, as well as the taxonomy of the besthit in SILVA when 16S rRNA genes were present. Phylum/class 16 ribosomal proteins is the taxonomy derived from our ribosomal protein trees (see main text: Figs. 2 and 3). OTU gives the inferred link of a population genome with our 16S rRNA gene amplicon dataset (Additional file 3). (XLSX 253 kb)
DOI: 10.6084/m9.figshare.7109267
title: Additional file 6: of Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don

description: Table S3. Functional annotation in clusters in (A) “all”, (B) “base and middle” and (C) “needles”. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.7109267.v1
title: Additional file 6: of Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don

description: Table S3. Functional annotation in clusters in (A) “all”, (B) “base and middle” and (C) “needles”. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.7109261
title: Additional file 3: of A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments

description: Dataset S1. Relative abundance of the OTUs assigned to the genus-level within the Archaea, Bacteria and organelles from Eukaryota detected by 16S rRNA gene amplicon sequencing. The OTUs with less than 0.1% abundance accross all five datasets are not shown. The names of highly abundant genera (â Ľ1% in at least one of the datasets) are shown in bold. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.7109261.v1
title: Additional file 3: of A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments

description: Dataset S1. Relative abundance of the OTUs assigned to the genus-level within the Archaea, Bacteria and organelles from Eukaryota detected by 16S rRNA gene amplicon sequencing. The OTUs with less than 0.1% abundance accross all five datasets are not shown. The names of highly abundant genera (â Ľ1% in at least one of the datasets) are shown in bold. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.7109252
title: Additional file 5: of Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don

description: Table S2. Annotation of genes in clusters in (A) “all”, (B) “base and middle” and (C) “needles”. (XLSX 1006 kb)
DOI: 10.6084/m9.figshare.7109252.v1
title: Additional file 5: of Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don

description: Table S2. Annotation of genes in clusters in (A) “all”, (B) “base and middle” and (C) “needles”. (XLSX 1006 kb)
DOI: 10.6084/m9.figshare.7109240
title: Additional file 4: of Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don

description: Table S1. Primers for qRT-PCR analyses. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7109240.v1
title: Additional file 4: of Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don

description: Table S1. Primers for qRT-PCR analyses. (XLSX 10 kb)