cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14436581
title: Additional file 4 of Genome-wide inference of regulatory networks in Streptomyces coelicolor

description: Additional file 4: Network predictions. Rows represent network elements, columns indicate network modules and the cistron containing the regulatory gene. Numbers are MI values, higher MI values indicate higher correlation. (CSV 4 MB)
DOI: 10.6084/m9.figshare.14436581.v1
title: Additional file 4 of Genome-wide inference of regulatory networks in Streptomyces coelicolor

description: Additional file 4: Network predictions. Rows represent network elements, columns indicate network modules and the cistron containing the regulatory gene. Numbers are MI values, higher MI values indicate higher correlation. (CSV 4 MB)
DOI: 10.6084/m9.figshare.14436584
title: Additional file 5 of Genome-wide inference of regulatory networks in Streptomyces coelicolor

description: Additional file 5: Summary of the consensus sequences found in the networks. For each network the values E-valuethreshold and E-value are given. The number of motifs detected and if applicable its consensus sequence are given, together with the total number of elements in the module and the number of elements in which the consensus sequence was detected. (CSV 57 KB)
DOI: 10.6084/m9.figshare.14436584.v1
title: Additional file 5 of Genome-wide inference of regulatory networks in Streptomyces coelicolor

description: Additional file 5: Summary of the consensus sequences found in the networks. For each network the values E-valuethreshold and E-value are given. The number of motifs detected and if applicable its consensus sequence are given, together with the total number of elements in the module and the number of elements in which the consensus sequence was detected. (CSV 57 KB)
DOI: 10.6084/m9.figshare.14436587
title: Additional file 6 of Genome-wide inference of regulatory networks in Streptomyces coelicolor

description: Additional file 6: Enriched networks. Worksheet 1 contains the list of network modules enriched according to the protein classification scheme, and worksheet 2 those enriched according to GO terms. For each of the enriched network modules the p-value, q-value and the enriched class or term is given. All network modules are significant at an FDR = 0.01. (CSV 24 KB)
DOI: 10.6084/m9.figshare.14436578.v1
title: Additional file 3 of Genome-wide inference of regulatory networks in Streptomyces coelicolor

description: Additional file 3: Operon predictions. Column 1 contains genes, and column 2 contains the operon into which the gene was predicted. (CSV 105 KB)
DOI: 10.6084/m9.figshare.14436587.v1
title: Additional file 6 of Genome-wide inference of regulatory networks in Streptomyces coelicolor

description: Additional file 6: Enriched networks. Worksheet 1 contains the list of network modules enriched according to the protein classification scheme, and worksheet 2 those enriched according to GO terms. For each of the enriched network modules the p-value, q-value and the enriched class or term is given. All network modules are significant at an FDR = 0.01. (CSV 24 KB)
DOI: 10.6084/m9.figshare.14436590
title: Additional file 7 of Genome-wide inference of regulatory networks in Streptomyces coelicolor

description: Additional file 7: Details of the 20 network modules enriched in both a protein class and a GO term. The number of cistrons in the network module and the consensus sequence detected in all its members is given. (XLS 28 KB)
DOI: 10.6084/m9.figshare.14436590.v1
title: Additional file 7 of Genome-wide inference of regulatory networks in Streptomyces coelicolor

description: Additional file 7: Details of the 20 network modules enriched in both a protein class and a GO term. The number of cistrons in the network module and the consensus sequence detected in all its members is given. (XLS 28 KB)
DOI: 10.6084/m9.figshare.14436722.v7
title: Additional file of Deciphering the intracellular metabolism of Listeria monocytogenes by mutant screening and modelling

description: Additional file of Deciphering the intracellular metabolism of Listeria monocytogenes by mutant screening and modelling
DOI: 10.5281/zenodo.4697167
title: Data and code for the paper 'Trait-based responses to land use and canopy dynamics modify long-term diversity changes in forest understories'

description: <strong>Data and code for the paper 'Trait-based responses to forestry and reindeer husbandry modify long-term changes in forest understories'</strong> See the preprint. The R markdown document (containing R code) docs/new_figures.Rmd can be used to reproduce all figures and modelling results of the paper. The models themselves are described and fitted in the R markdown document spatial_confounds.Rmd. Among other variables, this repository contains ready-calculated community characteristics (results/clean_data/data_for_analyses/kaik.csv: species richness, Shannon diversity, species evenness, height, LDMC, SLA) and their temporal changes along with temporal Jaccard distance between 1968–1975 and 2013–2019 (results/clean_data/data_for_analyses/erot.csv) for 245 5 m x 5 m plots of field-layer vegetation. Information is also included on tree-layer SLA and canopy cover for 10 m x 10 m plots directly above them. Each plot also has information on reindeer densities in their reindeer herding district, and on the level of management intensity. For more information, see the paper. Original community and trait data and are not included to avoid data duplication. Community data are available upon request, and will be submitted to an open repository at a later date. Original trait data are from TRY and LEDA, supplemented with our own measurements, references to trait sources are listed in docs/trait_references.txt. Climate data are from TerraClimate. ## References<br> Abatzoglou, John T., Solomon Z. Dobrowski, Sean A. Parks, and Katherine C. Hegewisch. 2018. “TerraClimate, a High-Resolution Global Dataset of Monthly Climate and Climatic Water Balance from 1958-2015.” Scientific Data 5 (January): 170191. Kattge, Jens, S. Díaz, S. Lavorel, I. C. Prentice, P. Leadley, G. Bönisch, E. Garnier, et al. 2011. “TRY - a Global Database of Plant Traits.” Global Change Biology 17 (9): 2905–35. Kleyer, M., R. M. Bekker, I. C. Knevel, J. P. Bakker, K. Thompson, M. Sonnenschein, P. Poschlod, et al. 2008. “The LEDA Traitbase: A Database of Life-History Traits of the Northwest European Flora.” The Journal of Ecology 96 (6): 1266–74.
DOI: 10.5281/zenodo.3784332
title: Data and code for the paper 'Trait-based responses to land use and canopy dynamics modify long-term diversity changes in forest understories'

description: <strong>Data and code for the paper 'Trait-based responses to forestry and reindeer husbandry modify long-term changes in forest understories'</strong> See the preprint. The R markdown document (containing R code) docs/new_figures.Rmd can be used to reproduce all figures and modelling results of the paper. The models themselves are described and fitted in the R markdown document spatial_confounds.Rmd. Among other variables, this repository contains ready-calculated community characteristics (results/clean_data/data_for_analyses/kaik.csv: species richness, Shannon diversity, species evenness, height, LDMC, SLA) and their temporal changes along with temporal Jaccard distance between 1968–1975 and 2013–2019 (results/clean_data/data_for_analyses/erot.csv) for 245 5 m x 5 m plots of field-layer vegetation. Information is also included on tree-layer SLA and canopy cover for 10 m x 10 m plots directly above them. Each plot also has information on reindeer densities in their reindeer herding district, and on the level of management intensity. For more information, see the paper. Original community and trait data and are not included to avoid data duplication. Community data are available upon request, and will be submitted to an open repository at a later date. Original trait data are from TRY and LEDA, supplemented with our own measurements, references to trait sources are listed in docs/trait_references.txt. Climate data are from TerraClimate. ## References<br> Abatzoglou, John T., Solomon Z. Dobrowski, Sean A. Parks, and Katherine C. Hegewisch. 2018. “TerraClimate, a High-Resolution Global Dataset of Monthly Climate and Climatic Water Balance from 1958-2015.” Scientific Data 5 (January): 170191. Kattge, Jens, S. Díaz, S. Lavorel, I. C. Prentice, P. Leadley, G. Bönisch, E. Garnier, et al. 2011. “TRY - a Global Database of Plant Traits.” Global Change Biology 17 (9): 2905–35. Kleyer, M., R. M. Bekker, I. C. Knevel, J. P. Bakker, K. Thompson, M. Sonnenschein, P. Poschlod, et al. 2008. “The LEDA Traitbase: A Database of Life-History Traits of the Northwest European Flora.” The Journal of Ecology 96 (6): 1266–74.
DOI: 10.6084/m9.figshare.14436743
title: Additional file 6 of Deciphering the intracellular metabolism of Listeria monocytogenes by mutant screening and modelling

description: Additional file 6: Total cell number of mutants after invasion and after 7 hours of intracellular replication; the generation time is indicated. (XLS 62 KB)
DOI: 10.6084/m9.figshare.14436743.v1
title: Additional file 6 of Deciphering the intracellular metabolism of Listeria monocytogenes by mutant screening and modelling

description: Additional file 6: Total cell number of mutants after invasion and after 7 hours of intracellular replication; the generation time is indicated. (XLS 62 KB)
DOI: 10.6084/m9.figshare.14436755.v1
title: Additional file of Identification of expression QTL (eQTL) of genes expressed in porcine M. longissimus dorsi and associated with meat quality traits

description: Additional file of Identification of expression QTL (eQTL) of genes expressed in porcine M. longissimus dorsi and associated with meat quality traits
DOI: 10.6084/m9.figshare.14436758
title: Additional file 1 of Identification of expression QTL (eQTL) of genes expressed in porcine M. longissimus dorsi and associated with meat quality traits

description: Additional file 1: eQTL detected for probe-sets representing transcripts that are expressed in porcine M. longissimus dorsi. All 9,180 eQTL (at LOD score &gt; 2) estimated for probe-sets of the Affymetrix Porcine Genome Array, their position in cM on linkage groups, corresponding gene names and chromosomal positions according to the current porcine genome sequence assembly (Sscrofa9 assembly, April 2009) [6](XLS 3 MB)
DOI: 10.6084/m9.figshare.14436758.v1
title: Additional file 1 of Identification of expression QTL (eQTL) of genes expressed in porcine M. longissimus dorsi and associated with meat quality traits

description: Additional file 1: eQTL detected for probe-sets representing transcripts that are expressed in porcine M. longissimus dorsi. All 9,180 eQTL (at LOD score &gt; 2) estimated for probe-sets of the Affymetrix Porcine Genome Array, their position in cM on linkage groups, corresponding gene names and chromosomal positions according to the current porcine genome sequence assembly (Sscrofa9 assembly, April 2009) [6](XLS 3 MB)
DOI: 10.6084/m9.figshare.14436779.v2
title: Additional file of Comparing de novo assemblers for 454 transcriptome data

description: Additional file of Comparing de novo assemblers for 454 transcriptome data
DOI: 10.6084/m9.figshare.14436785.v1
title: Additional file 2 of Comparing de novo assemblers for 454 transcriptome data

description: Additional file 2: Results of merging three assemblies. Assembly metrics as a result of merging three first-order assemblies. Alignments of merged assemblies to reference sequences. (XLS 62 KB)
DOI: 10.6084/m9.figshare.14436785
title: Additional file 2 of Comparing de novo assemblers for 454 transcriptome data

description: Additional file 2: Results of merging three assemblies. Assembly metrics as a result of merging three first-order assemblies. Alignments of merged assemblies to reference sequences. (XLS 62 KB)
DOI: 10.6084/m9.figshare.14436794.v1
title: Additional file of Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.)

description: Additional file of Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.)
DOI: 10.6084/m9.figshare.14436794.v2
title: Additional file of Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.)

description: Additional file of Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.)
DOI: 10.6084/m9.figshare.14436794.v3
title: Additional file of Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.)

description: Additional file of Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.)
DOI: 10.6084/m9.figshare.14436797
title: Additional file 1 of Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.)

description: Additional file 1: This MS Excel file includes supplemental Tables S1 to S4. Supplement Table S1. Characteristics of genomic and EST sequence databases used. Supplement Table S2a. Distribution of di-, tri-, and tetranucleotide repeats in genomic and EST sequences of cucumber. Supplement Table S2b. Distribution of the most frequent penta-, hexa-, hepta- and octanucleotide repeats in genomic and EST sequences of cucumber. Supplement Table S3a. Distribution of di-, tri-, and tetranucleotide repeats in genomic and EST sequences of reference plant species. Supplement Table S3b. Distribution of the most frequent penta-, hexa-, hepta- and octanucleotide repeats in genomic and EST sequences of reference species. Supplement S4. Information of 1,006 SSRs used in silico PCR analysis (XLS )
DOI: 10.6084/m9.figshare.14436800
title: Additional file 2 of Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.)

description: Additional file 2: Supplement Table S5a: list of primers for 83,472 microsatellites found in Cucumis sativus Gy14 genome sequences (# 000001 to 063346)(XLS )
DOI: 10.6084/m9.figshare.14436803
title: Additional file 3 of Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.)

description: Additional file 3: Supplement Table S5b: list of primers for 83,472 microsatellites found in Cucumis sativus Gy14 genome sequences (#063347 to 083472). (XLS )
DOI: 10.6084/m9.figshare.14436803.v1
title: Additional file 3 of Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.)

description: Additional file 3: Supplement Table S5b: list of primers for 83,472 microsatellites found in Cucumis sativus Gy14 genome sequences (#063347 to 083472). (XLS )
DOI: 10.6084/m9.figshare.14436800.v1
title: Additional file 2 of Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.)

description: Additional file 2: Supplement Table S5a: list of primers for 83,472 microsatellites found in Cucumis sativus Gy14 genome sequences (# 000001 to 063346)(XLS )
DOI: 10.6084/m9.figshare.14436797.v1
title: Additional file 1 of Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.)

description: Additional file 1: This MS Excel file includes supplemental Tables S1 to S4. Supplement Table S1. Characteristics of genomic and EST sequence databases used. Supplement Table S2a. Distribution of di-, tri-, and tetranucleotide repeats in genomic and EST sequences of cucumber. Supplement Table S2b. Distribution of the most frequent penta-, hexa-, hepta- and octanucleotide repeats in genomic and EST sequences of cucumber. Supplement Table S3a. Distribution of di-, tri-, and tetranucleotide repeats in genomic and EST sequences of reference plant species. Supplement Table S3b. Distribution of the most frequent penta-, hexa-, hepta- and octanucleotide repeats in genomic and EST sequences of reference species. Supplement S4. Information of 1,006 SSRs used in silico PCR analysis (XLS )
DOI: 10.6084/m9.figshare.14436821.v7
title: Additional file of Units of plasticity in bacterial genomes: new insight from the comparative genomics of two bacteria interacting with invertebrates, Photorhabdus and Xenorhabdus

description: Additional file of Units of plasticity in bacterial genomes: new insight from the comparative genomics of two bacteria interacting with invertebrates, Photorhabdus and Xenorhabdus
DOI: 10.6084/m9.figshare.14436821.v10
title: Additional file of Units of plasticity in bacterial genomes: new insight from the comparative genomics of two bacteria interacting with invertebrates, Photorhabdus and Xenorhabdus

description: Additional file of Units of plasticity in bacterial genomes: new insight from the comparative genomics of two bacteria interacting with invertebrates, Photorhabdus and Xenorhabdus
DOI: 10.6084/m9.figshare.14436842
title: Additional file 2 of Units of plasticity in bacterial genomes: new insight from the comparative genomics of two bacteria interacting with invertebrates, Photorhabdus and Xenorhabdus

description: Additional file 2: List of regions of genomic plasticity (RGPs) in the P. luminescens TT01 (Pl), P. asymbiotica ATCC43949 (Pa), X. nematophila ATCC19061 (Xn) and X. bovienii SS- 2004 (Xb) genomes. A table listing the RGPs. (XLS 96 KB)
DOI: 10.6084/m9.figshare.14436842.v1
title: Additional file 2 of Units of plasticity in bacterial genomes: new insight from the comparative genomics of two bacteria interacting with invertebrates, Photorhabdus and Xenorhabdus

description: Additional file 2: List of regions of genomic plasticity (RGPs) in the P. luminescens TT01 (Pl), P. asymbiotica ATCC43949 (Pa), X. nematophila ATCC19061 (Xn) and X. bovienii SS- 2004 (Xb) genomes. A table listing the RGPs. (XLS 96 KB)
DOI: 10.6084/m9.figshare.14436851
title: Additional file 5 of Units of plasticity in bacterial genomes: new insight from the comparative genomics of two bacteria interacting with invertebrates, Photorhabdus and Xenorhabdus

description: Additional file 5: List of modules in the P. luminescens TT01 (Pl), P. asymbiotica ATCC43949 (Pa), X. nematophila ATCC19061 (Xn) and X. bovienii SS-2004 (Xb) genomes and their distribution in the Yersinia pestis CO92 (Yp), Salmonella enterica subsp. enterica Typhi CT18 (St), Erwinia carotovora subsp. atroseptica SCRI1043 (Eca) and E. coli K12 (Eco) genomes. A table listing the modules. (XLS 882 KB)
DOI: 10.6084/m9.figshare.14436851.v1
title: Additional file 5 of Units of plasticity in bacterial genomes: new insight from the comparative genomics of two bacteria interacting with invertebrates, Photorhabdus and Xenorhabdus

description: Additional file 5: List of modules in the P. luminescens TT01 (Pl), P. asymbiotica ATCC43949 (Pa), X. nematophila ATCC19061 (Xn) and X. bovienii SS-2004 (Xb) genomes and their distribution in the Yersinia pestis CO92 (Yp), Salmonella enterica subsp. enterica Typhi CT18 (St), Erwinia carotovora subsp. atroseptica SCRI1043 (Eca) and E. coli K12 (Eco) genomes. A table listing the modules. (XLS 882 KB)
DOI: 10.6084/m9.figshare.14436887.v1
title: Additional file of Transcriptomic and functional analysis of the Anopheles gambiae salivary gland in relation to blood feeding

description: Additional file of Transcriptomic and functional analysis of the Anopheles gambiae salivary gland in relation to blood feeding
DOI: 10.6084/m9.figshare.14436887.v2
title: Additional file of Transcriptomic and functional analysis of the Anopheles gambiae salivary gland in relation to blood feeding

description: Additional file of Transcriptomic and functional analysis of the Anopheles gambiae salivary gland in relation to blood feeding
DOI: 10.6084/m9.figshare.14436890
title: Additional file 1 of Transcriptomic and functional analysis of the Anopheles gambiae salivary gland in relation to blood feeding

description: Additional file 1: List of genes expressed in the female salivary gland of A. gambiae, along with their previous (ENSANGT) and recent (AGAP-R) transcript IDs. Note that the recent AGAP-R IDs for some transcripts are missing in VectorBase and have therefore been left blank in column B. The fluorescent values at 635 nm (Cy-5 dye) and 532 nm (Cy-3 dye) for each gene are shown in column E and F respectively. The excel file has three sheets: Sheet 1 lists the genes that are highly expressed, with fluorescent values (at 635 nm) from 5,000 to the maximum threshold of 65,000, Sheet 2 lists the moderately expressed genes with fluorescent values (at 635 nm) between 1,000 to 4,999 and Sheet 3 lists the weakly expressed genes with fluorescent values (at 635 nm) between 100 to 999. The gene list is further sorted into different functional groups, according to the predicted function of the genes [CS: cytoskeletal and structural; CIR: circadian; CSR: chemosensory; PROT/DIG: proteolytic digestion; IMM: immunity; MET/ENZ: metabolism and enzymes; RED/STR: redox/stress; R/T/T: replication/transcription and translation; TRP: transport]. The list of genes in each group is further sorted into descending order of the fluorescent value at 635 nm (column E). (XLS 846 KB)
DOI: 10.6084/m9.figshare.14436890.v1
title: Additional file 1 of Transcriptomic and functional analysis of the Anopheles gambiae salivary gland in relation to blood feeding

description: Additional file 1: List of genes expressed in the female salivary gland of A. gambiae, along with their previous (ENSANGT) and recent (AGAP-R) transcript IDs. Note that the recent AGAP-R IDs for some transcripts are missing in VectorBase and have therefore been left blank in column B. The fluorescent values at 635 nm (Cy-5 dye) and 532 nm (Cy-3 dye) for each gene are shown in column E and F respectively. The excel file has three sheets: Sheet 1 lists the genes that are highly expressed, with fluorescent values (at 635 nm) from 5,000 to the maximum threshold of 65,000, Sheet 2 lists the moderately expressed genes with fluorescent values (at 635 nm) between 1,000 to 4,999 and Sheet 3 lists the weakly expressed genes with fluorescent values (at 635 nm) between 100 to 999. The gene list is further sorted into different functional groups, according to the predicted function of the genes [CS: cytoskeletal and structural; CIR: circadian; CSR: chemosensory; PROT/DIG: proteolytic digestion; IMM: immunity; MET/ENZ: metabolism and enzymes; RED/STR: redox/stress; R/T/T: replication/transcription and translation; TRP: transport]. The list of genes in each group is further sorted into descending order of the fluorescent value at 635 nm (column E). (XLS 846 KB)
DOI: 10.6084/m9.figshare.14436893
title: Additional file 2 of Transcriptomic and functional analysis of the Anopheles gambiae salivary gland in relation to blood feeding

description: Additional file 2: List of genes that are regulated upon blood-feeding in the female A. gambiae salivary gland, along with their ENSANGT and more recent AGAP-R transcript IDs. Transcripts lacking AGAP-R IDs are only indicated with the ENSANT transcript ID. Genes are only listed if they display significant differential regulation between fed and unfed mosquitoes, at a log2 fold ratio above or below the ± 0.75 threshold. Predicted functional groups classification for genes are also presented [CS: cytoskeletal and structural; CIR: circadian; CSR: chemosensory; PROT/DIG: proteolytic digestion; IMM: immunity; MET/ENZ: metabolism and enzymes; RED/STR: redox/stress; R/T/T: replication/transcription and translation; TRP: transport]. (XLS 31 KB)