cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10264781
title: The leucine biosynthetic pathway is crucial for adaptation to iron starvation and virulence in <i>Aspergillus fumigatus</i>

description: In contrast to mammalia, fungi are able to synthesize the branched-chain amino acid leucine <i>de novo</i>. Recently, the transcription factor LeuB has been shown to cross-regulate leucine biosynthesis, nitrogen metabolism and iron homeostasis in <i>Aspergillus fumigatus</i>, the most common human mold pathogen. Moreover, the leucine biosynthetic pathway intermediate α-isopropylmalate (α-IPM) has previously been shown to posttranslationally activate LeuB homologs in <i>S. cerevisiae</i> and <i>A. nidulans</i>. Here, we demonstrate that in <i>A. fumigatus</i> inactivation of both leucine biosynthetic enzymes α-IPM synthase (LeuC), which disrupts α-IPM synthesis, and α-IPM isomerase (LeuA), which causes cellular α-IPM accumulation, results in leucine auxotrophy. However, compared to lack of LeuA, lack of LeuC resulted in increased leucine dependence, a growth defect during iron starvation and decreased expression of LeuB-regulated genes including genes involved in iron acquisition. Lack of either LeuA or LeuC decreased virulence in an insect infection model, and inactivation of LeuC rendered <i>A. fumigatus</i> avirulent in a pulmonary aspergillosis mouse model. Taken together, we demonstrate that the lack of two leucine biosynthetic enzymes, LeuA and LeuC, results in significant phenotypic consequences indicating that the regulator LeuB is activated by α-IPM in <i>A. fumigatus</i> and that the leucine biosynthetic pathway is an attractive target for the development of antifungal drugs.
DOI: 10.6084/m9.figshare.10264790
title: Integrated Capital Shares - Data

description: The data can be used to reproduce the analysis on the cross-country inter-dependencies between capital shares of total national income.
DOI: 10.6084/m9.figshare.10264832.v3
title: Transcriptome profiling of abiotic responses to heat, cold, salt, and osmotic stress of Capsicum annuum L.

description: Additional files generated upon qualification and validation of pepper transcriptome under abiotic stresses Statistical summary of RNA-seq for each sample.xlsx --- Detailed pepper RNA-seq information used in this study DEG result for each stress.zip --- DEG information from four abiotic stresses Normalized TMM.zip --- Expression profiling of TMM normalized data from four abiotic stresses GO enrichment analysis result.zip --- Results of GO enrichment analysis from four abiotic stresses Programs and code information.docx --- Programs and codes used in the RNA-seq data processing‬<br>
DOI: 10.6084/m9.figshare.10264790.v1
title: Integrated Capital Shares - Data

description: The data can be used to reproduce the analysis on the cross-country inter-dependencies between capital shares of total national income.
DOI: 10.6084/m9.figshare.10264832.v4
title: Transcriptome profiling of abiotic responses to heat, cold, salt, and osmotic stress of Capsicum annuum L.

description: Additional files generated upon qualification and validation of pepper transcriptome under abiotic stresses Statistical summary of RNA-seq for each sample.xlsx --- Detailed pepper RNA-seq information used in this study DEG result for each stress.zip --- DEG information from four abiotic stresses Normalized TMM.zip --- Expression profiling of TMM normalized data from four abiotic stresses GO enrichment analysis result.zip --- Results of GO enrichment analysis from four abiotic stresses Programs and code information.docx --- Programs and codes used in the RNA-seq data processing‬<br>
DOI: 10.6084/m9.figshare.10264781.v1
title: The leucine biosynthetic pathway is crucial for adaptation to iron starvation and virulence in <i>Aspergillus fumigatus</i>

description: In contrast to mammalia, fungi are able to synthesize the branched-chain amino acid leucine <i>de novo</i>. Recently, the transcription factor LeuB has been shown to cross-regulate leucine biosynthesis, nitrogen metabolism and iron homeostasis in <i>Aspergillus fumigatus</i>, the most common human mold pathogen. Moreover, the leucine biosynthetic pathway intermediate α-isopropylmalate (α-IPM) has previously been shown to posttranslationally activate LeuB homologs in <i>S. cerevisiae</i> and <i>A. nidulans</i>. Here, we demonstrate that in <i>A. fumigatus</i> inactivation of both leucine biosynthetic enzymes α-IPM synthase (LeuC), which disrupts α-IPM synthesis, and α-IPM isomerase (LeuA), which causes cellular α-IPM accumulation, results in leucine auxotrophy. However, compared to lack of LeuA, lack of LeuC resulted in increased leucine dependence, a growth defect during iron starvation and decreased expression of LeuB-regulated genes including genes involved in iron acquisition. Lack of either LeuA or LeuC decreased virulence in an insect infection model, and inactivation of LeuC rendered <i>A. fumigatus</i> avirulent in a pulmonary aspergillosis mouse model. Taken together, we demonstrate that the lack of two leucine biosynthetic enzymes, LeuA and LeuC, results in significant phenotypic consequences indicating that the regulator LeuB is activated by α-IPM in <i>A. fumigatus</i> and that the leucine biosynthetic pathway is an attractive target for the development of antifungal drugs.
DOI: 10.6084/m9.figshare.10264721
title: MOESM8 of Genome-wide analysis, transcription factor network approach and gene expression profile of GH3 genes over early somatic embryogenesis in Coffea spp

description: Additional file 8: Table S2 Concentration and quality assessment of RNA samples used for RT-qPCR analysis.
DOI: 10.6084/m9.figshare.10264727
title: MOESM9 of Genome-wide analysis, transcription factor network approach and gene expression profile of GH3 genes over early somatic embryogenesis in Coffea spp

description: Additional file 9: Table S3 Primers used in RT-qPCR experiments.
DOI: 10.6084/m9.figshare.10264727.v1
title: MOESM9 of Genome-wide analysis, transcription factor network approach and gene expression profile of GH3 genes over early somatic embryogenesis in Coffea spp

description: Additional file 9: Table S3 Primers used in RT-qPCR experiments.
DOI: 10.6084/m9.figshare.10264721.v1
title: MOESM8 of Genome-wide analysis, transcription factor network approach and gene expression profile of GH3 genes over early somatic embryogenesis in Coffea spp

description: Additional file 8: Table S2 Concentration and quality assessment of RNA samples used for RT-qPCR analysis.
DOI: 10.6084/m9.figshare.10264709
title: MOESM6 of Genome-wide analysis, transcription factor network approach and gene expression profile of GH3 genes over early somatic embryogenesis in Coffea spp

description: Additional file 6: Table S1 Number of binding possibilities for each transcription factor in selected GH3 promoter regions.
DOI: 10.6084/m9.figshare.10264715
title: MOESM7 of Genome-wide analysis, transcription factor network approach and gene expression profile of GH3 genes over early somatic embryogenesis in Coffea spp

description: Additional file 7: Table S1 Appendix. Description of binding possibilities for each transcription factor in selected GH3 genes promoter regions.
DOI: 10.6084/m9.figshare.10264715.v1
title: MOESM7 of Genome-wide analysis, transcription factor network approach and gene expression profile of GH3 genes over early somatic embryogenesis in Coffea spp

description: Additional file 7: Table S1 Appendix. Description of binding possibilities for each transcription factor in selected GH3 genes promoter regions.
DOI: 10.6084/m9.figshare.10264709.v1
title: MOESM6 of Genome-wide analysis, transcription factor network approach and gene expression profile of GH3 genes over early somatic embryogenesis in Coffea spp

description: Additional file 6: Table S1 Number of binding possibilities for each transcription factor in selected GH3 promoter regions.
DOI: 10.6084/m9.figshare.10264667
title: MOESM12 of Genome-wide analysis, transcription factor network approach and gene expression profile of GH3 genes over early somatic embryogenesis in Coffea spp

description: Additional file 12: Table S5 Gene expression profile correlations between CaGH3s and CaBBM. Scores were obtained by Spearman’s correlation.
DOI: 10.6084/m9.figshare.10264667.v1
title: MOESM12 of Genome-wide analysis, transcription factor network approach and gene expression profile of GH3 genes over early somatic embryogenesis in Coffea spp

description: Additional file 12: Table S5 Gene expression profile correlations between CaGH3s and CaBBM. Scores were obtained by Spearman’s correlation.
DOI: 10.6084/m9.figshare.10264661
title: MOESM4 of Accelerated evolution at chaperone promoters among Antarctic notothenioid fishes

description: Additional file 4. phastCons scores across chaperone promoters derived from (i) a substitution model fitted to all species and (ii) a substitution model fitted to Notothenioidei. bp numbers negatively descend in 3' - 5' order across promoters beginning at 5' end of 1st exons.
DOI: 10.6084/m9.figshare.10264655
title: MOESM3 of Accelerated evolution at chaperone promoters among Antarctic notothenioid fishes

description: Additional file 3. CONACC output of base-by-base conservation/acceleration scores and p-values for each gene and clade. bp number ascends in 5' - 3' order across promoters toward 1st exons.
DOI: 10.6084/m9.figshare.10264658
title: MOESM11 of Genome-wide analysis, transcription factor network approach and gene expression profile of GH3 genes over early somatic embryogenesis in Coffea spp

description: Additional file 11: Table S4 Appendix. Primer pairs used into analysis of expression stability for endogenous genes (Freitas et al. 2017).
DOI: 10.6084/m9.figshare.10264652
title: MOESM10 of Genome-wide analysis, transcription factor network approach and gene expression profile of GH3 genes over early somatic embryogenesis in Coffea spp

description: Additional file 10:: Table S4 Endogenous gene expression stability analyzed by RefFinder software ( http://fulxie.0fees.us/ ).
DOI: 10.6084/m9.figshare.10264661.v1
title: MOESM4 of Accelerated evolution at chaperone promoters among Antarctic notothenioid fishes

description: Additional file 4. phastCons scores across chaperone promoters derived from (i) a substitution model fitted to all species and (ii) a substitution model fitted to Notothenioidei. bp numbers negatively descend in 3' - 5' order across promoters beginning at 5' end of 1st exons.
DOI: 10.6084/m9.figshare.10264655.v1
title: MOESM3 of Accelerated evolution at chaperone promoters among Antarctic notothenioid fishes

description: Additional file 3. CONACC output of base-by-base conservation/acceleration scores and p-values for each gene and clade. bp number ascends in 5' - 3' order across promoters toward 1st exons.
DOI: 10.6084/m9.figshare.10264646
title: MOESM1 of Accelerated evolution at chaperone promoters among Antarctic notothenioid fishes

description: Additional file 1:Â Links and accessions forÂ fish genome assemblies and chaperone CDS.
DOI: 10.6084/m9.figshare.10264649
title: MOESM2 of Accelerated evolution at chaperone promoters among Antarctic notothenioid fishes

description: Additional file 2. Mean HSE counts and densities per species among chaperone promoters.
DOI: 10.6084/m9.figshare.10264652.v1
title: MOESM10 of Genome-wide analysis, transcription factor network approach and gene expression profile of GH3 genes over early somatic embryogenesis in Coffea spp

description: Additional file 10:: Table S4 Endogenous gene expression stability analyzed by RefFinder software ( http://fulxie.0fees.us/ ).
DOI: 10.6084/m9.figshare.10264658.v1
title: MOESM11 of Genome-wide analysis, transcription factor network approach and gene expression profile of GH3 genes over early somatic embryogenesis in Coffea spp

description: Additional file 11: Table S4 Appendix. Primer pairs used into analysis of expression stability for endogenous genes (Freitas et al. 2017).
DOI: 10.6084/m9.figshare.10264646.v1
title: MOESM1 of Accelerated evolution at chaperone promoters among Antarctic notothenioid fishes

description: Additional file 1:Â Links and accessions forÂ fish genome assemblies and chaperone CDS.
DOI: 10.6084/m9.figshare.10264649.v1
title: MOESM2 of Accelerated evolution at chaperone promoters among Antarctic notothenioid fishes

description: Additional file 2. Mean HSE counts and densities per species among chaperone promoters.
DOI: 10.6084/m9.figshare.10264529
title: MOESM4 of Heritabilities for the puppy weight at birth in Labrador retrievers

description: Additional file 4. Datafile.
DOI: 10.6084/m9.figshare.10264529.v1
title: MOESM4 of Heritabilities for the puppy weight at birth in Labrador retrievers

description: Additional file 4. Datafile.
DOI: 10.6084/m9.figshare.10264490
title: MOESM1 of Prevalence, associated factors and consequences of substance use among health and medical science students of Haramaya University, eastern Ethiopia, 2018: a cross-sectional study

description: Additional file 1: Questionnaire A structured questionnaire used for interviewing selected health and medical science students of HU, 2018.
DOI: 10.6084/m9.figshare.10264481
title: MOESM2 of Genome survey of resistance gene analogs in sugarcane: genomic features and differential expression of the innate immune system from a smut-resistant genotype

description: Additional file 2. RGA Dataset.
DOI: 10.6084/m9.figshare.10264490.v1
title: MOESM1 of Prevalence, associated factors and consequences of substance use among health and medical science students of Haramaya University, eastern Ethiopia, 2018: a cross-sectional study

description: Additional file 1: Questionnaire A structured questionnaire used for interviewing selected health and medical science students of HU, 2018.
DOI: 10.6084/m9.figshare.10264481.v1
title: MOESM2 of Genome survey of resistance gene analogs in sugarcane: genomic features and differential expression of the innate immune system from a smut-resistant genotype

description: Additional file 2. RGA Dataset.
DOI: 10.6084/m9.figshare.10264472
title: MOESM1 of Genome survey of resistance gene analogs in sugarcane: genomic features and differential expression of the innate immune system from a smut-resistant genotype

description: Additional file 1. PRGdb Dataset.
DOI: 10.6084/m9.figshare.10264472.v1
title: MOESM1 of Genome survey of resistance gene analogs in sugarcane: genomic features and differential expression of the innate immune system from a smut-resistant genotype

description: Additional file 1. PRGdb Dataset.
DOI: 10.6084/m9.figshare.10264457
title: MOESM1 of Low prevalence of p16-positive HPV-related head-neck cancers in Thailand: tertiary referral center experience

description: Additional file 1. Microsoft Office Excel with all the raw data relevant to the present study, including anonymized baseline, histological, and clinical variables.
DOI: 10.6084/m9.figshare.10264433
title: MOESM4 of Genome-wide expression profiling in colorectal cancer focusing on lncRNAs in the adenoma-carcinoma transition

description: Additional file 4 : Table S3. lncRNA-mRNA co-expression network data, GO analysis.
DOI: 10.6084/m9.figshare.10264427
title: MOESM3 of Genome-wide expression profiling in colorectal cancer focusing on lncRNAs in the adenoma-carcinoma transition

description: Additional file 3: Table S2. In silico validation on independent datasets.
DOI: 10.6084/m9.figshare.10264433.v1
title: MOESM4 of Genome-wide expression profiling in colorectal cancer focusing on lncRNAs in the adenoma-carcinoma transition

description: Additional file 4 : Table S3. lncRNA-mRNA co-expression network data, GO analysis.
DOI: 10.6084/m9.figshare.10264415
title: MOESM2 of Genome-wide expression profiling in colorectal cancer focusing on lncRNAs in the adenoma-carcinoma transition

description: Additional file 2: Table S1. Differentially expressed lncRNAs in the adenoma-carcinoma sequence.
DOI: 10.6084/m9.figshare.10264415.v1
title: MOESM2 of Genome-wide expression profiling in colorectal cancer focusing on lncRNAs in the adenoma-carcinoma transition

description: Additional file 2: Table S1. Differentially expressed lncRNAs in the adenoma-carcinoma sequence.
DOI: 10.6084/m9.figshare.10264328
title: MOESM2 of Phenotypic and genotypic characterization of clinical Staphylococcus aureus isolates from Kenya

description: Additional file 2. List of reference genomes used in this study.
DOI: 10.6084/m9.figshare.10264328.v1
title: MOESM2 of Phenotypic and genotypic characterization of clinical Staphylococcus aureus isolates from Kenya

description: Additional file 2. List of reference genomes used in this study.
DOI: 10.6084/m9.figshare.10264319
title: MOESM1 of Phenotypic and genotypic characterization of clinical Staphylococcus aureus isolates from Kenya

description: Additional file 1. Table of susceptibility testing results obtained from the Vitek 2 platform and genotypes detected using ARIBA. MICs were interpreted using the CLSI guidelines and expert deductions on the Vitek Advanced Expert System (AES). * indicates forced resistance by the AES. **denotes presence of only the ubiquitous resistance genes in the isolates (S. aureus 23S, arlR, arlS, mgrA and tet38). Isolates in bold are confirmed MRSA validated as MecA positive by PCR testing. Fusidic acid is not shown as results were missing for some isolates.
DOI: 10.6084/m9.figshare.10264319.v1
title: MOESM1 of Phenotypic and genotypic characterization of clinical Staphylococcus aureus isolates from Kenya

description: Additional file 1. Table of susceptibility testing results obtained from the Vitek 2 platform and genotypes detected using ARIBA. MICs were interpreted using the CLSI guidelines and expert deductions on the Vitek Advanced Expert System (AES). * indicates forced resistance by the AES. **denotes presence of only the ubiquitous resistance genes in the isolates (S. aureus 23S, arlR, arlS, mgrA and tet38). Isolates in bold are confirmed MRSA validated as MecA positive by PCR testing. Fusidic acid is not shown as results were missing for some isolates.
DOI: 10.6084/m9.figshare.10264211
title: MOESM3 of Unraveling genomic associations with feed efficiency and body weight traits in chickens through an integrative approach

description: Additional file 3. List with the Ensembl Gene ID and their respective gene names of the 386 genes annotated within the QTL detected.
DOI: 10.6084/m9.figshare.10264211.v1
title: MOESM3 of Unraveling genomic associations with feed efficiency and body weight traits in chickens through an integrative approach

description: Additional file 3. List with the Ensembl Gene ID and their respective gene names of the 386 genes annotated within the QTL detected.
DOI: 10.6084/m9.figshare.10264196
title: MOESM1 of Unraveling genomic associations with feed efficiency and body weight traits in chickens through an integrative approach

description: Additional file 1. The characterization of all the 943 1-Mb SNP windows analyzed including the percentage of the genetic variance explained by each one.
DOI: 10.6084/m9.figshare.10264196.v1
title: MOESM1 of Unraveling genomic associations with feed efficiency and body weight traits in chickens through an integrative approach

description: Additional file 1. The characterization of all the 943 1-Mb SNP windows analyzed including the percentage of the genetic variance explained by each one.
DOI: 10.6084/m9.figshare.10264151
title: MOESM3 of From cytogenetics to cytogenomics: whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability

description: Additional file 3: Table S2. Number of detected CNVs using array and WGS.
DOI: 10.6084/m9.figshare.10264151.v1
title: MOESM3 of From cytogenetics to cytogenomics: whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability

description: Additional file 3: Table S2. Number of detected CNVs using array and WGS.
DOI: 10.6084/m9.figshare.10264145
title: MOESM1 of Optimized sequencing depth and de novo assembler for deeply reconstructing the transcriptome of the tea plant, an economically important plant species

description: Additional file 1: Figure S1. Venn diagram shows the transcripts intersected in different assemblers. Figure S2. Transcripts mapped to coding sequences and genome sequences with different coverage and identity thresholds. Figure S3. Assembly quality of transcripts at different expression levels. Figure S4. Completeness of the assembled transcripts at different expression levels. Figure S5. Comparison of the assembly performances between two replications of datasets randomly selected from eight representative tissues of tea plant. Figure S6. Statistic of the transcriptome assemblies using Bridger with different amount of sequencing data from replicate 2. Table S1. Summary of transcriptome assemblies of tea plant in previous studies. Table S2. Summary of the data used in this study. Table S3. Coverage of transcripts mapped to the reference genome. Table S4. Statistic of the Bridger assembly using different k-mer values. (a) Assembly characteristics; (b) completeness assessment using BUSCO; (c) length distribution. Table S5. Statistics of assembly. (a) Apical bud; (b) flower; (c) fruit; (d) second young leaf; (e) mature leaf in summer; (f) first young leaf; (g) root; (h) stem. Table S6. Length distribution of assembly. (a) Apical bud; (b) flower; (c) fruit, (d) second young leaf; (e) mature leaf in summer; (f) first young leaf; (g) root; (h) stem. Table S7. BUSCO evaluation of assembly. (a) Apical bud; (b) flower; (c) fruit; (d) second young leaf; (e) mature leaf in summer; (f) first young leaf; (g) root; (h) stem. Table S8. Statistic of assembly. (a) Apical bud and first young leaf; (b) apical bud and root. Table S9. Statistic of pooledÂ assembly. (a) Assembly characteristics; (b) length distribution; (c) BUSCO evaluation. Table S10. Runtime (hours) performance for each assembler with different amount of input data. (a) 0.5 Gb; (b) 1 Gb; (c) 3 Gb. Table S11. Completeness of transcriptomes generated in tea plant using PacBio technology.