cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10035641.v1
title: MOESM1 of An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation

description: Additional file 1: Tissues sampled and annotation. BRENDA tissue ontology terms are given when known, with the hyphenated number at the end of the column headings specifying level of granularity, where 1 is the lowest level of granularity and the broadest scope. Only tags mapping uniquely to the draft genome that passed our filters (Os-fgU; Figure 2b) were considered. Total Sense TPM Within NM & NR Transcripts: sum of normalized tag counts (tags per million) that mapped on the same strand and within the boundaries of NM and NR transcripts. On 3' terminus: sum of normalized tag abundance of those tags that mapped on the same strand and at the 3'-most and next to 3'-most DpnII sites on the NM or NR transcript (Figure 2a). Not on 3' terminus: sum of normalized tag abundance of those tags that did not map to the 3'-most and next to 3'-most DpnII sites on the NM or NR transcript (Figure 2a): Count Sense GeneID: total number of unique GeneIDs associated with the loci that the tags mapped to on the same strand and within the boundaries of the annotated genes. Count Sense Tags within Loci: number of unique tag sequences that mapped within the boundaries of annotated genes. Total Sense TPM within Loci: sum of normalized tag abundance of those tags that mapped on the same strand and within the boundaries of all annotated genes. The headings including the word 'AntiSense' are similarly defined, except that these tags mapped to the strand opposite to that of the annotated gene. (XLSX 41 KB)
DOI: 10.6084/m9.figshare.10035596
title: of An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation

description: of An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation
DOI: 10.6084/m9.figshare.10035590
title: of An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation

description: of An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation
DOI: 10.6084/m9.figshare.10035596.v1
title: of An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation

description: of An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation
DOI: 10.6084/m9.figshare.10035590.v1
title: of An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation

description: of An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation
DOI: 10.6084/m9.figshare.10035524
title: Additional file 1 of Adaptive selection of founder segments and epistatic control of plant height in the MAGIC winter wheat population WM-800

description: Table S1. SNP genotypes, plant height, QTL detection rate and genotype and allele frequencies for 910 MAGIC WHEAT lines and eight founders. Table S2. Plant height (cm) raw data for MAGIC WM-lines and founders for year 2015 and 2016. Table S3. Distribution of polymorphic SNPs within WM-800 according to genome positions of Wang et al.... [36]. Table S4. Mean, minimum, maximum and coefficient of variation (CV, in %) of linkage disequilibrium (r2) in WM-800, calculated per chromosome, subgenome and across the whole wheat genome. Table S5. Genetic similarity (GS) between founders and WM-800 lines based on 7849 polymorphic SNPs. Table S6. Principle Component Analysis (PCO) based on genetic similarities (GS) between founders and WM-800 lines. Table S7. Distribution of segregation distortion (SD) SNPs and segregation distortion regions (SDR) across the wheat genome and across allele frequency groups. Table S8. Selection of unique SNPs from AFG 1 and AFG 7 in WM-800. Major selection events, represented by &gt;â 10 SNPs, are indicated in bold. (ZIP 2660 kb)
DOI: 10.6084/m9.figshare.10035524.v1
title: Additional file 1 of Adaptive selection of founder segments and epistatic control of plant height in the MAGIC winter wheat population WM-800

description: Table S1. SNP genotypes, plant height, QTL detection rate and genotype and allele frequencies for 910 MAGIC WHEAT lines and eight founders. Table S2. Plant height (cm) raw data for MAGIC WM-lines and founders for year 2015 and 2016. Table S3. Distribution of polymorphic SNPs within WM-800 according to genome positions of Wang et al.... [36]. Table S4. Mean, minimum, maximum and coefficient of variation (CV, in %) of linkage disequilibrium (r2) in WM-800, calculated per chromosome, subgenome and across the whole wheat genome. Table S5. Genetic similarity (GS) between founders and WM-800 lines based on 7849 polymorphic SNPs. Table S6. Principle Component Analysis (PCO) based on genetic similarities (GS) between founders and WM-800 lines. Table S7. Distribution of segregation distortion (SD) SNPs and segregation distortion regions (SDR) across the wheat genome and across allele frequency groups. Table S8. Selection of unique SNPs from AFG 1 and AFG 7 in WM-800. Major selection events, represented by &gt;â 10 SNPs, are indicated in bold. (ZIP 2660 kb)
DOI: 10.5258/soton/d1137
title: Dataset for: X-ray Computed Tomography Imaging of Solute Movement through Ridged and Flat Plant Systems

description: Data associated with and used in the production of the scientific paper "X-ray Computed Tomography Imaging of Solute Movement through Ridged and Flat Plant Systems" published in the European Journal of Soil Science.
DOI: 10.6084/m9.figshare.10035335
title: Additional file 1 of Multiplex methods provide effective integration of multi-omic data in genome-scale models

description: The improved model of Escherichia coli with underground metabolism. The model is provided as a MATLAB file compatible with the COBRA toolbox. It includes the reactions in the latest iJO1366 reconstruction, as well as underground metabolism and new gene-protein-reaction associations. The resulting model contains 1380 genes, 3027 reactions (including exchange reactions), and 2151 metabolites. (MAT 214 kb)
DOI: 10.6084/m9.figshare.10035338
title: Additional file 2 of Multiplex methods provide effective integration of multi-omic data in genome-scale models

description: Flux rates of Colombos conditions. Full list of Colombos conditions and the corresponding flux rates predicted using trilevel linear programming. (XLSX 364 kb)
DOI: 10.6084/m9.figshare.10035335.v1
title: Additional file 1 of Multiplex methods provide effective integration of multi-omic data in genome-scale models

description: The improved model of Escherichia coli with underground metabolism. The model is provided as a MATLAB file compatible with the COBRA toolbox. It includes the reactions in the latest iJO1366 reconstruction, as well as underground metabolism and new gene-protein-reaction associations. The resulting model contains 1380 genes, 3027 reactions (including exchange reactions), and 2151 metabolites. (MAT 214 kb)
DOI: 10.6084/m9.figshare.10035338.v1
title: Additional file 2 of Multiplex methods provide effective integration of multi-omic data in genome-scale models

description: Flux rates of Colombos conditions. Full list of Colombos conditions and the corresponding flux rates predicted using trilevel linear programming. (XLSX 364 kb)
DOI: 10.6084/m9.figshare.10035305
title: Additional file 1: of Oligodendrogliomas, IDH-mutant and 1p/19q-codeleted, arising during teenage years often lack TERT promoter mutation that is typical of their adult counterparts

description: Table S1. List of the 479 genes targeted for sequencing on the UCSF500 Cancer Panel. Table S2. Pathogenic mutations identified in the three oligodendrogliomas. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.10035305.v1
title: Additional file 1: of Oligodendrogliomas, IDH-mutant and 1p/19q-codeleted, arising during teenage years often lack TERT promoter mutation that is typical of their adult counterparts

description: Table S1. List of the 479 genes targeted for sequencing on the UCSF500 Cancer Panel. Table S2. Pathogenic mutations identified in the three oligodendrogliomas. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.10035281
title: MOESM4 of ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data

description: Additional file 4: Archival copy of software. (ZIP 3 MB)
DOI: 10.6084/m9.figshare.10035278
title: MOESM3 of ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data

description: Additional file 3: Data for Figure 2d. (ZIP 6 MB)
DOI: 10.6084/m9.figshare.10035275
title: MOESM2 of ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data

description: Additional file 2: Data for Figure S7 in Additional file 1. (ZIP 54 KB)
DOI: 10.6084/m9.figshare.10035278.v1
title: MOESM3 of ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data

description: Additional file 3: Data for Figure 2d. (ZIP 6 MB)
DOI: 10.6084/m9.figshare.10035281.v1
title: MOESM4 of ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data

description: Additional file 4: Archival copy of software. (ZIP 3 MB)
DOI: 10.6084/m9.figshare.10035275.v1
title: MOESM2 of ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data

description: Additional file 2: Data for Figure S7 in Additional file 1. (ZIP 54 KB)
DOI: 10.6084/m9.figshare.10035251
title: of ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data

description: of ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data
DOI: 10.6084/m9.figshare.10035248
title: of ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data

description: of ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data
DOI: 10.6084/m9.figshare.10035251.v1
title: of ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data

description: of ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data
DOI: 10.6084/m9.figshare.10035245
title: of ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data

description: of ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data
DOI: 10.6084/m9.figshare.10035245.v1
title: of ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data

description: of ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data
DOI: 10.6084/m9.figshare.10035248.v1
title: of ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data

description: of ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data
DOI: 10.6084/m9.figshare.10035047
title: codeclones_testcode.zip

description: The dataset of our work "Clone Detection in Test Code: an Empirical Evaluation". It contains the source code of the test suites, the classified code clones from the test suites, and all python scripts used during the postprocessing step of our evaluation.
DOI: 10.6084/m9.figshare.10035047.v2
title: codeclones_testcode.zip

description: The dataset of our work "Clone Detection in Test Code: an Empirical Evaluation". It contains the source code of the test suites, the classified code clones from the test suites, and all python scripts used during the postprocessing step of our evaluation.
DOI: 10.6084/m9.figshare.10035047.v1
title: codeclones_testcode.zip

description: The dataset of our work "Clone Detection in Test Code: an Empirical Evaluation". It contains the source code of the test suites, the classified code clones from the test suites, and all python scripts used during the postprocessing step of our evaluation.
DOI: 10.6084/m9.figshare.10034939
title: Additional file 1: Table S1. of Erratum to: Pathway reporter genes define molecular phenotypes of human cells

description: List of reporter genes and pathways. (XLSX 398 kb)
DOI: 10.6084/m9.figshare.10034942
title: Additional file 2: Table S2. of Erratum to: Pathway reporter genes define molecular phenotypes of human cells

description: AmpliSeq identifiers and primer pairs of reporter genes. (XLSX 84 kb)
DOI: 10.6084/m9.figshare.10034942.v1
title: Additional file 2: Table S2. of Erratum to: Pathway reporter genes define molecular phenotypes of human cells

description: AmpliSeq identifiers and primer pairs of reporter genes. (XLSX 84 kb)
DOI: 10.6084/m9.figshare.10034939.v1
title: Additional file 1: Table S1. of Erratum to: Pathway reporter genes define molecular phenotypes of human cells

description: List of reporter genes and pathways. (XLSX 398 kb)
DOI: 10.6084/m9.figshare.10034906
title: MOESM13 of Droplet-based microfluidic high-throughput screening of heterologous enzymes secreted by the yeast Yarrowia lipolytica

description: Additional file 13: Table S3. List of primers used to check cassette integration at the specific Zeta locus.
DOI: 10.6084/m9.figshare.10034903
title: MOESM12 of Droplet-based microfluidic high-throughput screening of heterologous enzymes secreted by the yeast Yarrowia lipolytica

description: Additional file 12: Table S2. Y. lipolytica and E. coli strains used in this study.
DOI: 10.6084/m9.figshare.10034906.v1
title: MOESM13 of Droplet-based microfluidic high-throughput screening of heterologous enzymes secreted by the yeast Yarrowia lipolytica

description: Additional file 13: Table S3. List of primers used to check cassette integration at the specific Zeta locus.
DOI: 10.6084/m9.figshare.10034897
title: MOESM10 of Droplet-based microfluidic high-throughput screening of heterologous enzymes secreted by the yeast Yarrowia lipolytica

description: Additional file 10: Table S1. Thermostable variants of endo-β-1,4-xylanase C. Xylanase activity (RFU average) before and after heat treatment (90 °C) and residual activity of the 6 thermoresistant clones.
DOI: 10.6084/m9.figshare.10034903.v1
title: MOESM12 of Droplet-based microfluidic high-throughput screening of heterologous enzymes secreted by the yeast Yarrowia lipolytica

description: Additional file 12: Table S2. Y. lipolytica and E. coli strains used in this study.
DOI: 10.6084/m9.figshare.10034897.v1
title: MOESM10 of Droplet-based microfluidic high-throughput screening of heterologous enzymes secreted by the yeast Yarrowia lipolytica

description: Additional file 10: Table S1. Thermostable variants of endo-β-1,4-xylanase C. Xylanase activity (RFU average) before and after heat treatment (90 °C) and residual activity of the 6 thermoresistant clones.
DOI: 10.6084/m9.figshare.10034651
title: of Transcriptome-wide based identification of miRs in congenital anomalies of the kidney and urinary tract (CAKUT) in children: the significant upregulation of tissue miR-144 expression

description: of Transcriptome-wide based identification of miRs in congenital anomalies of the kidney and urinary tract (CAKUT) in children: the significant upregulation of tissue miR-144 expression
DOI: 10.6084/m9.figshare.10034657
title: MOESM3 of Transcriptome-wide based identification of miRs in congenital anomalies of the kidney and urinary tract (CAKUT) in children: the significant upregulation of tissue miR-144 expression

description: Additional file 3. Statistically significant GO terms from Gene Ontology analysis performed on a cluster of 511 hsa-miR-144 target genes.
DOI: 10.6084/m9.figshare.10034651.v1
title: of Transcriptome-wide based identification of miRs in congenital anomalies of the kidney and urinary tract (CAKUT) in children: the significant upregulation of tissue miR-144 expression

description: of Transcriptome-wide based identification of miRs in congenital anomalies of the kidney and urinary tract (CAKUT) in children: the significant upregulation of tissue miR-144 expression
DOI: 10.6084/m9.figshare.10034657.v1
title: MOESM3 of Transcriptome-wide based identification of miRs in congenital anomalies of the kidney and urinary tract (CAKUT) in children: the significant upregulation of tissue miR-144 expression

description: Additional file 3. Statistically significant GO terms from Gene Ontology analysis performed on a cluster of 511 hsa-miR-144 target genes.
DOI: 10.6084/m9.figshare.10034570
title: Additional file 3: of RIP-Chip analysis supports different roles for AGO2 and GW182 proteins in recruiting and processing microRNA targets

description: Summary of enriched and underrepresented genes. Summary of enriched and underrepresented genes in AGO2 and GW182-IP vs FT comparisons performed by SAMR (column 2–3). The enrichment results obtained with the REA algorithm are reported in columns 4–5. Columns 6 and 7 report the 3’UTR and Coding region (CR) lengths respectively. In columns 8–21 we report the number of binding sites predicted by Targetscan in the 3’UTR and the Coding region of seven highly expressed miRNAs. (XLS 294 kb)
DOI: 10.6084/m9.figshare.10034567
title: Additional file 2: of RIP-Chip analysis supports different roles for AGO2 and GW182 proteins in recruiting and processing microRNA targets

description: Gene set enrichment analysis results with seven top expressed miRNA predicted targets sets. Predicted targets of miRNAs (column 1) were predicted with three different target prediction tools (column 2). The total number of predicted targets is indicated in column 3. Five lists of genes were analyzed. For each list of genes the number of genes in common with the predicted targets and the associated hypergeometric test pvalue are provided. The total number of genes considered in the analysis is 16,392. The five considered lists are: a list of genes enriched in AGO2 IP sample from [13]; lists of genes enriched in AGO2 IP vs IN and IP vs FT samples; lists of genes enriched in GW182 IP vs IN and IP vs FT samples. (XLS 64 kb)
DOI: 10.6084/m9.figshare.10034567.v1
title: Additional file 2: of RIP-Chip analysis supports different roles for AGO2 and GW182 proteins in recruiting and processing microRNA targets

description: Gene set enrichment analysis results with seven top expressed miRNA predicted targets sets. Predicted targets of miRNAs (column 1) were predicted with three different target prediction tools (column 2). The total number of predicted targets is indicated in column 3. Five lists of genes were analyzed. For each list of genes the number of genes in common with the predicted targets and the associated hypergeometric test pvalue are provided. The total number of genes considered in the analysis is 16,392. The five considered lists are: a list of genes enriched in AGO2 IP sample from [13]; lists of genes enriched in AGO2 IP vs IN and IP vs FT samples; lists of genes enriched in GW182 IP vs IN and IP vs FT samples. (XLS 64 kb)
DOI: 10.6084/m9.figshare.10034570.v1
title: Additional file 3: of RIP-Chip analysis supports different roles for AGO2 and GW182 proteins in recruiting and processing microRNA targets

description: Summary of enriched and underrepresented genes. Summary of enriched and underrepresented genes in AGO2 and GW182-IP vs FT comparisons performed by SAMR (column 2–3). The enrichment results obtained with the REA algorithm are reported in columns 4–5. Columns 6 and 7 report the 3’UTR and Coding region (CR) lengths respectively. In columns 8–21 we report the number of binding sites predicted by Targetscan in the 3’UTR and the Coding region of seven highly expressed miRNAs. (XLS 294 kb)
DOI: 10.6084/m9.figshare.10034438
title: Additional file 1: of Glucose screening within six months postpartum among Chinese mothers with a history of gestational diabetes mellitus: a prospective cohort study

description: The socio-demographic data sheet of the participants. This data sheet includes the socio-demographic information of all the participants. (SAV 3 kb)
DOI: 10.6084/m9.figshare.10034438.v1
title: Additional file 1: of Glucose screening within six months postpartum among Chinese mothers with a history of gestational diabetes mellitus: a prospective cohort study

description: The socio-demographic data sheet of the participants. This data sheet includes the socio-demographic information of all the participants. (SAV 3 kb)
DOI: 10.6084/m9.figshare.10034411
title: Additional file 5: of Differential proteomic comparison of breast cancer secretome using a quantitative paired analysis workflow

description: Table S5. Summary result of the proteins monitored by SRM (NAF samples from breast cancer patients). a) Protein Report: List of the 9 proteins monitored by SRM and statistically evaluated after paired comparisons of NAF samples from breast cancer patients; b) Peptide Report: List of the 9 proteins and the respective peptides monitored by SRM and statistically evaluated according to the paired comparisons of NAF samples from breast cancer patients. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.10034399
title: Additional file 2: of Differential proteomic comparison of breast cancer secretome using a quantitative paired analysis workflow

description: Table S2. Result summary of protein and peptide identifications (NAF samples from control women). a) Protein Report: Complete list of 578 proteins statistically evaluated after paired comparisons of non diseased breast NAF samples from control women; b) Peptide Report: Complete list of 578 proteins and the respective peptides statistically evaluated after paired comparisons of non diseased breast NAF samples from control women. (XLSX 364 kb)
DOI: 10.6084/m9.figshare.10034402
title: Additional file 3: of Differential proteomic comparison of breast cancer secretome using a quantitative paired analysis workflow

description: Table S3. Functional analysis of differentially abundant proteins (NAF samples from breast cancer patients). a) Cancer_vs_Nondiseased: Reactome pathways categorization of the proteins found as differentially abundant after paired comparison of NAF samples from breast cancer patients; b) ERpos_vs_Nondiseased: Reactome pathways categorization for differentially abundant proteins according to the paired comparison of NAF samples from ERpos breast cancer patients. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.10034405
title: Additional file 4: of Differential proteomic comparison of breast cancer secretome using a quantitative paired analysis workflow

description: Table S4. Summary result of protein and peptide identifications (NAF samples from ERpos breast cancer patients). a) Protein Report: List of all 873 proteins statistically evaluated after paired comparisons of NAF samples from ERpos breast cancer patients; b) Peptide Report: List of all 873 proteins and the respective peptides statistically evaluated according to the paired comparisons of NAF samples from ERpos breast cancer patients. (XLSX 639 kb)
DOI: 10.6084/m9.figshare.10034396
title: Additional file 1: of Differential proteomic comparison of breast cancer secretome using a quantitative paired analysis workflow

description: Table S1. Result summary of the protein and peptide identifications from the NAF samples from breast cancer patients. a) Protein Report: List of all 1227 proteins statistically evaluated after paired comparisons of NAF samples from breast cancer patients; b) Peptide Report: List of all 1227 proteins and the respective peptides statistically evaluated after paired comparisons of NAF samples from breast cancer patients. (XLSX 1245 kb)