cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12880673.v1
title: Additional file of The genetic organisation of prokaryotic two-component system signalling pathways

description: Additional file of The genetic organisation of prokaryotic two-component system signalling pathways
DOI: 10.6084/m9.figshare.7943525
title: MOESM1 of Can conservation targets for imperilled freshwater fishes and mussels be achieved by captive breeding and release programs? A systematic map protocol to determine available evidence

description: Additional file 1. ROSES form for systematic map protocols.
DOI: 10.6084/m9.figshare.7943525.v1
title: MOESM1 of Can conservation targets for imperilled freshwater fishes and mussels be achieved by captive breeding and release programs? A systematic map protocol to determine available evidence

description: Additional file 1. ROSES form for systematic map protocols.
DOI: 10.6084/m9.figshare.12880706.v4
title: Additional file of Combining modularity, conservation, and interactions of proteins significantly increases precision and coverage of protein function prediction

description: Additional file of Combining modularity, conservation, and interactions of proteins significantly increases precision and coverage of protein function prediction
DOI: 10.6084/m9.figshare.12880706.v3
title: Additional file of Combining modularity, conservation, and interactions of proteins significantly increases precision and coverage of protein function prediction

description: Additional file of Combining modularity, conservation, and interactions of proteins significantly increases precision and coverage of protein function prediction
DOI: 10.6084/m9.figshare.12880685
title: Additional file 3 of Combining modularity, conservation, and interactions of proteins significantly increases precision and coverage of protein function prediction

description: Additional file 3:Complete results of the CCS-based function prediction approach. This file contains the complete results of the combined CCS-based function prediction approach for pairs of species and three, four, five and six species combinations. CCS from strict and relaxed network comparison are used depending on the species combinations. (XLS 52 KB)
DOI: 10.6084/m9.figshare.12880682
title: Additional file 2 of Combining modularity, conservation, and interactions of proteins significantly increases precision and coverage of protein function prediction

description: Additional file 2:Complete results of the strict and relaxed network comparisons. This files contains the complete results of the strict and relaxed network comparisons for pairs of species and three, four, five and six species combinations. The number of OrthoMCL groups, interologs from strict and relaxed definition as well as the total number of CCS and the size of the largest CCS are given. (XLS 40 KB)
DOI: 10.6084/m9.figshare.7943300
title: Additional file 3: of Temporal and spatial detection of Candidatus Liberibacter asiaticus putative effector transcripts during interaction with Huanglongbing-susceptible, â tolerant, and -resistant citrus hosts

description: Table S2. Primer sequences for reverse transcription and qPCR analysis of effector expression. The list of primers used in this study for reverse transcription and qPCR (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7943303
title: Additional file 4: of Temporal and spatial detection of Candidatus Liberibacter asiaticus putative effector transcripts during interaction with Huanglongbing-susceptible, â tolerant, and -resistant citrus hosts

description: Table S3. A time course study on the expression of Ca. L. asiaticus effectors in citron, Duncan and Cleopatra using the detached leaf assay. Three randomly selected Ca. L. asiaticus-infected samples were collected for each time point (Fig. 2) and were analyzed for expression by RT-qPCR. The data was presented as relative expression levels, based on normalization with citrus UPL7 (delta Ct), and transformed into 2-Î Ct. The table was formatted with color scales using Excel where values increase from green to red colors. The two highlighted columns were the two samples with high bacterial titer and larger number of detected candidate effectors. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.7943300.v1
title: Additional file 3: of Temporal and spatial detection of Candidatus Liberibacter asiaticus putative effector transcripts during interaction with Huanglongbing-susceptible, â tolerant, and -resistant citrus hosts

description: Table S2. Primer sequences for reverse transcription and qPCR analysis of effector expression. The list of primers used in this study for reverse transcription and qPCR (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7943303.v1
title: Additional file 4: of Temporal and spatial detection of Candidatus Liberibacter asiaticus putative effector transcripts during interaction with Huanglongbing-susceptible, â tolerant, and -resistant citrus hosts

description: Table S3. A time course study on the expression of Ca. L. asiaticus effectors in citron, Duncan and Cleopatra using the detached leaf assay. Three randomly selected Ca. L. asiaticus-infected samples were collected for each time point (Fig. 2) and were analyzed for expression by RT-qPCR. The data was presented as relative expression levels, based on normalization with citrus UPL7 (delta Ct), and transformed into 2-Î Ct. The table was formatted with color scales using Excel where values increase from green to red colors. The two highlighted columns were the two samples with high bacterial titer and larger number of detected candidate effectors. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.7943282
title: MOESM1 of A genetical metabolomics approach for bioprospecting plant biosynthetic gene clusters

description: Additional file 1. List of predicted BGCs, list of mQTLs, list of BGCs with mQTLs, list of matches for mQTL genes with profile Hidden Markov Models related to scaffold biosynthesis, overview of LCMS clusters.
DOI: 10.6084/m9.figshare.7943288
title: Additional file 1: of Temporal and spatial detection of Candidatus Liberibacter asiaticus putative effector transcripts during interaction with Huanglongbing-susceptible, â tolerant, and -resistant citrus hosts

description: Table S1. The list of putative effectors identified by filtering Ca. L. asiaticus genome using bioinformatics. Supplemental TableÂ 1-A contains the list of Ca. L. asiaticus genes with a signal peptide predicted by SignalP. Supplemental TableÂ 1-B contains the list of Ca. L. asiaticus genes having signal peptide but not transmembrane domain, with the protein size smaller than 200 amino acids. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.7943288.v1
title: Additional file 1: of Temporal and spatial detection of Candidatus Liberibacter asiaticus putative effector transcripts during interaction with Huanglongbing-susceptible, â tolerant, and -resistant citrus hosts

description: Table S1. The list of putative effectors identified by filtering Ca. L. asiaticus genome using bioinformatics. Supplemental TableÂ 1-A contains the list of Ca. L. asiaticus genes with a signal peptide predicted by SignalP. Supplemental TableÂ 1-B contains the list of Ca. L. asiaticus genes having signal peptide but not transmembrane domain, with the protein size smaller than 200 amino acids. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.7943282.v1
title: MOESM1 of A genetical metabolomics approach for bioprospecting plant biosynthetic gene clusters

description: Additional file 1. List of predicted BGCs, list of mQTLs, list of BGCs with mQTLs, list of matches for mQTL genes with profile Hidden Markov Models related to scaffold biosynthesis, overview of LCMS clusters.
DOI: 10.6084/m9.figshare.12880748.v6
title: Additional file of miRNeye: a microRNA expression atlas of the mouse eye

description: Additional file of miRNeye: a microRNA expression atlas of the mouse eye
DOI: 10.6084/m9.figshare.12880748.v9
title: Additional file of miRNeye: a microRNA expression atlas of the mouse eye

description: Additional file of miRNeye: a microRNA expression atlas of the mouse eye
DOI: 10.6084/m9.figshare.12880748.v8
title: Additional file of miRNeye: a microRNA expression atlas of the mouse eye

description: Additional file of miRNeye: a microRNA expression atlas of the mouse eye
DOI: 10.6084/m9.figshare.12880724
title: Additional file 2 of miRNeye: a microRNA expression atlas of the mouse eye

description: Additional file 2:Complete dataset of the Gene Ontology analysis. The worksheet 'gsea_results_intersection' includes all the enriched GO/KEGG terms in biological processes and pathways for each of the predicted targets of the miRNAs present within each selected sub-cluster. The worksheet 'gsea_results_occurencies' summarizes the occurrence of each GO/KEGG term among the miRNA members of each selected node. The number of the miRNA members of each sub-cluster considered in the analysis is given in the last column. (XLS 2 MB)
DOI: 10.6084/m9.figshare.12880724.v1
title: Additional file 2 of miRNeye: a microRNA expression atlas of the mouse eye

description: Additional file 2:Complete dataset of the Gene Ontology analysis. The worksheet 'gsea_results_intersection' includes all the enriched GO/KEGG terms in biological processes and pathways for each of the predicted targets of the miRNAs present within each selected sub-cluster. The worksheet 'gsea_results_occurencies' summarizes the occurrence of each GO/KEGG term among the miRNA members of each selected node. The number of the miRNA members of each sub-cluster considered in the analysis is given in the last column. (XLS 2 MB)
DOI: 10.6084/m9.figshare.12880730
title: Additional file 4 of miRNeye: a microRNA expression atlas of the mouse eye

description: Additional file 4:Detailed annotation of the miRNA expression patterns obtained at all developmental stages analyzed. The table presents the overall pattern of expression (e.g. ubiquitous, ubiquitous with pattern, regional, not detected) at each developmental stage and a brief annotation of the structures that were positive for miRNA expression at each stage. Abbreviations are as follows: Developmental stage: E = Embryonic day; P = Postnatal day. Overall signal: nd = not detected; reg/1-2-3 = regional; ubi/1-2-3 = ubiquitous; uwp/1-2-3 = ubiquitous with pattern; 1-2-3 = signal intensity level Anatomical structures: BR = Brain; CB = Ciliary body; EOM = Extraocular muscles; GCL = Ganglion Cell Layer; INBL = Inner Neuroblastic Layer; INL = Inner Nuclear Layer; IR = Iris; OLF = Olfactory epithelium; ONBL = Outer Neuroblastic Layer; ONL = Outer Nuclear Layer; PHOT = Photoreceptors; RPE = Retinal Pigment Epithelium. (XLS 72 KB)
DOI: 10.6084/m9.figshare.12880733
title: Additional file 5 of miRNeye: a microRNA expression atlas of the mouse eye

description: Additional file 5:Complete list of differential expression values [Log2 median ratios and Delta Log2 median ratios between each sample group (average) versus EYE1 sample]. This page contains an expression matrix for all 9 samples analyzed by microarray. Only miRNAs with 9 values (no 'NA's accepted) across samples have been included in the analysis (see column named 'count'). In column 'M' to 'P' the difference in Log2 median ratios (ΔLMR) between each sample group (average) has been calculated to the 'entire eye' common reference sample named 'EYE1'. The miRNAs have been sorted on the basis of the values in column 'Q' with the highest differential expression on top (see column named MAX). The acronym 'NA' indicates miRNAs that did not yield reliable read-outs (see Methods for further details). The numbers are all log2(Hy3/Hy5) ratios. (XLS 144 KB)
DOI: 10.6084/m9.figshare.12880733.v1
title: Additional file 5 of miRNeye: a microRNA expression atlas of the mouse eye

description: Additional file 5:Complete list of differential expression values [Log2 median ratios and Delta Log2 median ratios between each sample group (average) versus EYE1 sample]. This page contains an expression matrix for all 9 samples analyzed by microarray. Only miRNAs with 9 values (no 'NA's accepted) across samples have been included in the analysis (see column named 'count'). In column 'M' to 'P' the difference in Log2 median ratios (ΔLMR) between each sample group (average) has been calculated to the 'entire eye' common reference sample named 'EYE1'. The miRNAs have been sorted on the basis of the values in column 'Q' with the highest differential expression on top (see column named MAX). The acronym 'NA' indicates miRNAs that did not yield reliable read-outs (see Methods for further details). The numbers are all log2(Hy3/Hy5) ratios. (XLS 144 KB)
DOI: 10.6084/m9.figshare.12880748.v10
title: Additional file of miRNeye: a microRNA expression atlas of the mouse eye

description: Additional file of miRNeye: a microRNA expression atlas of the mouse eye
DOI: 10.6084/m9.figshare.12880736
title: Additional file 6 of miRNeye: a microRNA expression atlas of the mouse eye

description: Additional file 6:Probes used for RNA in situ hybridization. The table summarizes information on probe sequence, miRBase accession number and hybridization (Thyb) temperatures. (XLS 48 KB)
DOI: 10.6084/m9.figshare.12880736.v1
title: Additional file 6 of miRNeye: a microRNA expression atlas of the mouse eye

description: Additional file 6:Probes used for RNA in situ hybridization. The table summarizes information on probe sequence, miRBase accession number and hybridization (Thyb) temperatures. (XLS 48 KB)
DOI: 10.6084/m9.figshare.12880730.v1
title: Additional file 4 of miRNeye: a microRNA expression atlas of the mouse eye

description: Additional file 4:Detailed annotation of the miRNA expression patterns obtained at all developmental stages analyzed. The table presents the overall pattern of expression (e.g. ubiquitous, ubiquitous with pattern, regional, not detected) at each developmental stage and a brief annotation of the structures that were positive for miRNA expression at each stage. Abbreviations are as follows: Developmental stage: E = Embryonic day; P = Postnatal day. Overall signal: nd = not detected; reg/1-2-3 = regional; ubi/1-2-3 = ubiquitous; uwp/1-2-3 = ubiquitous with pattern; 1-2-3 = signal intensity level Anatomical structures: BR = Brain; CB = Ciliary body; EOM = Extraocular muscles; GCL = Ganglion Cell Layer; INBL = Inner Neuroblastic Layer; INL = Inner Nuclear Layer; IR = Iris; OLF = Olfactory epithelium; ONBL = Outer Neuroblastic Layer; ONL = Outer Nuclear Layer; PHOT = Photoreceptors; RPE = Retinal Pigment Epithelium. (XLS 72 KB)
DOI: 10.6084/m9.figshare.7943150
title: MOESM5 of What are the effects of even-aged and uneven-aged forest management on boreal forest biodiversity in Fennoscandia and European Russia? A systematic review protocol

description: Additional file 5. Data extraction spreadsheet.
DOI: 10.6084/m9.figshare.7943141
title: MOESM4 of What are the effects of even-aged and uneven-aged forest management on boreal forest biodiversity in Fennoscandia and European Russia? A systematic review protocol

description: Additional file 4. The performance of the search string.
DOI: 10.6084/m9.figshare.7943150.v1
title: MOESM5 of What are the effects of even-aged and uneven-aged forest management on boreal forest biodiversity in Fennoscandia and European Russia? A systematic review protocol

description: Additional file 5. Data extraction spreadsheet.
DOI: 10.6084/m9.figshare.7943141.v1
title: MOESM4 of What are the effects of even-aged and uneven-aged forest management on boreal forest biodiversity in Fennoscandia and European Russia? A systematic review protocol

description: Additional file 4. The performance of the search string.
DOI: 10.6084/m9.figshare.7943126
title: MOESM2 of What are the effects of even-aged and uneven-aged forest management on boreal forest biodiversity in Fennoscandia and European Russia? A systematic review protocol

description: Additional file 2. ROSES form.
DOI: 10.6084/m9.figshare.7943126.v1
title: MOESM2 of What are the effects of even-aged and uneven-aged forest management on boreal forest biodiversity in Fennoscandia and European Russia? A systematic review protocol

description: Additional file 2. ROSES form.
DOI: 10.6084/m9.figshare.7943090
title: Additional file 1 of OMICfpp: a fuzzy approach for paired RNA-Seq counts

description: All procedures and data needed to reproduce the whole study have been included in the file SupplementaryMaterial.tar.gz. Once decompressed the file SupplementaryMaterialMethods.pdf contains a detailed description of the methods used and the results obtained. The whole paper can be reproduced reading this file. Other data files generated during the analysis are included in the folder Methods. The detailed html reports with the results can be found in the folder Results. (GZ 118,244 kb)
DOI: 10.6084/m9.figshare.7943090.v1
title: Additional file 1 of OMICfpp: a fuzzy approach for paired RNA-Seq counts

description: All procedures and data needed to reproduce the whole study have been included in the file SupplementaryMaterial.tar.gz. Once decompressed the file SupplementaryMaterialMethods.pdf contains a detailed description of the methods used and the results obtained. The whole paper can be reproduced reading this file. Other data files generated during the analysis are included in the folder Methods. The detailed html reports with the results can be found in the folder Results. (GZ 118,244 kb)
DOI: 10.6084/m9.figshare.7943018
title: gVCF_NA12873

description: 1000 Genomes gVCF mapped to hs37d5 for NA12873. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.12880821
title: Additional file 8 of Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure

description: Additional file 8:Table S4. Detailed information about SNP markers highly significant in the analysis of interactions in the CAP Core. (XLS 29 KB)
DOI: 10.6084/m9.figshare.12880821.v1
title: Additional file 8 of Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure

description: Additional file 8:Table S4. Detailed information about SNP markers highly significant in the analysis of interactions in the CAP Core. (XLS 29 KB)
DOI: 10.6084/m9.figshare.12880824.v1
title: Additional file 9 of Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure

description: Additional file 9:Table S5. POPA SNP markers developed from re-sequencing of loci related to vernalization sensitivity and inflorescence type. (XLS 31 KB)
DOI: 10.6084/m9.figshare.12880800.v1
title: Additional file 1 of Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure

description: Additional file 1:Table S1. Passport information and phenotypic characterization of the CAP Core for flowering time and inflorescence type and genotypic characterization for the main loci controlling these traits. (XLS 59 KB)
DOI: 10.6084/m9.figshare.7942949
title: gVCF_NA20764

description: 1000 Genomes gVCF mapped to hs37d5 for NA20764. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7943018.v1
title: gVCF_NA12873

description: 1000 Genomes gVCF mapped to hs37d5 for NA12873. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.12880824
title: Additional file 9 of Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure

description: Additional file 9:Table S5. POPA SNP markers developed from re-sequencing of loci related to vernalization sensitivity and inflorescence type. (XLS 31 KB)
DOI: 10.6084/m9.figshare.7942949.v1
title: gVCF_NA20764

description: 1000 Genomes gVCF mapped to hs37d5 for NA20764. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.12880800
title: Additional file 1 of Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure

description: Additional file 1:Table S1. Passport information and phenotypic characterization of the CAP Core for flowering time and inflorescence type and genotypic characterization for the main loci controlling these traits. (XLS 59 KB)
DOI: 10.6084/m9.figshare.7942904
title: gVCF_NA12872

description: 1000 Genomes gVCF mapped to hs37d5 for NA12872. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.12880803.v1
title: Additional file 2 of Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure

description: Additional file 2:Table S2. Accession numbers of the sequences deposited with GenBank. (XLS 43 KB)
DOI: 10.6084/m9.figshare.7942784
title: gVCF_NA20763

description: 1000 Genomes gVCF mapped to hs37d5 for NA20763. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7942781
title: gVCF_NA12843

description: 1000 Genomes gVCF mapped to hs37d5 for NA12843. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.12880827.v12
title: Additional file of Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure

description: Additional file of Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure
DOI: 10.6084/m9.figshare.12880827.v6
title: Additional file of Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure

description: Additional file of Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure
DOI: 10.6084/m9.figshare.7942778
title: gVCF_NA20762

description: 1000 Genomes gVCF mapped to hs37d5 for NA20762. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7942784.v1
title: gVCF_NA20763

description: 1000 Genomes gVCF mapped to hs37d5 for NA20763. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7942904.v1
title: gVCF_NA12872

description: 1000 Genomes gVCF mapped to hs37d5 for NA12872. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.12880806
title: Additional file 3 of Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure

description: Additional file 3:Table S3. Primers used for genotyping and/or re-sequencing VRN-H, PPD-H, FR-H, and VRS1 specific genes in the CAP Core. (XLS 20 KB)
DOI: 10.6084/m9.figshare.12880827.v5
title: Additional file of Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure

description: Additional file of Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure
DOI: 10.6084/m9.figshare.12880827
title: Additional file of Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure

description: Additional file of Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure