cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11415573.v1
title: MOESM11 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity

description: Additional file 11: Table S4. Specific loci in IFC compared to SO that contained multiple differential hypo- or hypermethylated tiles (&gt; 20% methylation difference). Enriched biological processes of hypomethylated genes in IFC compared to SO (n = 17), including the proteins involved in each GO term.
DOI: 10.6084/m9.figshare.11415564
title: MOESM10 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity

description: Additional file 10: Table S3. Differentially hypomethylated tiles (n=829) and hypermethylated tiles (n=702) with more than 20% methylation difference in IFC compared to SO. Each tile contains information about the genome location, overlapping gene, Ensembl ID, gene description and methylation percentage in each sample. Differentially methylated CGIs between IFC and SO (n=85).
DOI: 10.6084/m9.figshare.11415564.v1
title: MOESM10 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity

description: Additional file 10: Table S3. Differentially hypomethylated tiles (n=829) and hypermethylated tiles (n=702) with more than 20% methylation difference in IFC compared to SO. Each tile contains information about the genome location, overlapping gene, Ensembl ID, gene description and methylation percentage in each sample. Differentially methylated CGIs between IFC and SO (n=85).
DOI: 10.6084/m9.figshare.11415531
title: MOESM8 of A longitudinal study highlights shared aspects of the transcriptomic response to cardiogenic and septic shock

description: Additional file 8. Gene expression trends of biological processes enriched only in SS patients. Extensive information of genes shown in Figure S3 is reported in this table. Data are normalized on T1, log2FoldChanges are shown.
DOI: 10.6084/m9.figshare.11415531.v1
title: MOESM8 of A longitudinal study highlights shared aspects of the transcriptomic response to cardiogenic and septic shock

description: Additional file 8. Gene expression trends of biological processes enriched only in SS patients. Extensive information of genes shown in Figure S3 is reported in this table. Data are normalized on T1, log2FoldChanges are shown.
DOI: 10.6084/m9.figshare.11415522
title: MOESM7 of A longitudinal study highlights shared aspects of the transcriptomic response to cardiogenic and septic shock

description: Additional file 7. Clinical variables of SS and SC patients. Clinical characteristics of the patients divided by Septic Shock and Septic Controls. Data are presented as mean (SD). P-values were calculated with ANOVA and describe the significance of the difference between the variables in Septic Shock and Septic Controls over 2 timepoints.
DOI: 10.6084/m9.figshare.11415522.v1
title: MOESM7 of A longitudinal study highlights shared aspects of the transcriptomic response to cardiogenic and septic shock

description: Additional file 7. Clinical variables of SS and SC patients. Clinical characteristics of the patients divided by Septic Shock and Septic Controls. Data are presented as mean (SD). P-values were calculated with ANOVA and describe the significance of the difference between the variables in Septic Shock and Septic Controls over 2 timepoints.
DOI: 10.6084/m9.figshare.11415513
title: MOESM6 of A longitudinal study highlights shared aspects of the transcriptomic response to cardiogenic and septic shock

description: Additional file 6. Results of the GSEA of Transcription Factor Targets (TFT). Results table of the GSEA analysis of genes ranked for log2FC over one week in CS and SS. For each gene set of TFT is reported: number of DEGs and number of genes in the gene set (SIZE), Normalized Enriched Score, False Discovery Rate and type of shock.
DOI: 10.6084/m9.figshare.11415513.v1
title: MOESM6 of A longitudinal study highlights shared aspects of the transcriptomic response to cardiogenic and septic shock

description: Additional file 6. Results of the GSEA of Transcription Factor Targets (TFT). Results table of the GSEA analysis of genes ranked for log2FC over one week in CS and SS. For each gene set of TFT is reported: number of DEGs and number of genes in the gene set (SIZE), Normalized Enriched Score, False Discovery Rate and type of shock.
DOI: 10.6084/m9.figshare.11415498
title: MOESM4 of A longitudinal study highlights shared aspects of the transcriptomic response to cardiogenic and septic shock

description: Additional file 4. Results of GSEA of Gene Ontologies in CS and SS. Upregulated (Excel Sheet “GSEA_UP”) and downregulated (Excel Sheet “GSEA_DOWN”) gene sets resulting from the GSEA analysis in CS, SS and SC. For each significantly enriched GO is reported the number of DEGs, the Normalized Enriched Score (NES), the False Discovery Rate (FDR.q.val).
DOI: 10.6084/m9.figshare.11415498.v1
title: MOESM4 of A longitudinal study highlights shared aspects of the transcriptomic response to cardiogenic and septic shock

description: Additional file 4. Results of GSEA of Gene Ontologies in CS and SS. Upregulated (Excel Sheet “GSEA_UP”) and downregulated (Excel Sheet “GSEA_DOWN”) gene sets resulting from the GSEA analysis in CS, SS and SC. For each significantly enriched GO is reported the number of DEGs, the Normalized Enriched Score (NES), the False Discovery Rate (FDR.q.val).
DOI: 10.6084/m9.figshare.11415480
title: MOESM1 of A longitudinal study highlights shared aspects of the transcriptomic response to cardiogenic and septic shock

description: Additional file 1: Table S1. Description of CS, SS and SC patients included in the study. For each patient is reported the type of shock, gender and age, mortality at 28â€‰days. The cause for CS is specified for CS patients, whereas for SS and SC patients the source of infection is indicated.
DOI: 10.6084/m9.figshare.11415480.v1
title: MOESM1 of A longitudinal study highlights shared aspects of the transcriptomic response to cardiogenic and septic shock

description: Additional file 1: Table S1. Description of CS, SS and SC patients included in the study. For each patient is reported the type of shock, gender and age, mortality at 28â€‰days. The cause for CS is specified for CS patients, whereas for SS and SC patients the source of infection is indicated.
DOI: 10.6084/m9.figshare.11415297
title: MOESM4 of Identifying relevant concepts and factors for the sustainability of evidence-based practices within acute care contexts: a systematic review and theory analysis of selected sustainability frameworks

description: Additional file 4. Qualitative analysis of concepts and factors for sustainability frameworks/models/theories.
DOI: 10.6084/m9.figshare.11415297.v1
title: MOESM4 of Identifying relevant concepts and factors for the sustainability of evidence-based practices within acute care contexts: a systematic review and theory analysis of selected sustainability frameworks

description: Additional file 4. Qualitative analysis of concepts and factors for sustainability frameworks/models/theories.
DOI: 10.6084/m9.figshare.11415288
title: MOESM3 of Identifying relevant concepts and factors for the sustainability of evidence-based practices within acute care contexts: a systematic review and theory analysis of selected sustainability frameworks

description: Additional file 3. Exluded files.
DOI: 10.6084/m9.figshare.11415288.v1
title: MOESM3 of Identifying relevant concepts and factors for the sustainability of evidence-based practices within acute care contexts: a systematic review and theory analysis of selected sustainability frameworks

description: Additional file 3. Exluded files.
DOI: 10.6084/m9.figshare.11415270
title: MOESM2 of Challenges and Perspectives in Homology-Directed Gene Targeting in Monocot Plants

description: Additional file 2: Table S2. Major applications of base-editing approaches in plants.
DOI: 10.6084/m9.figshare.11415270.v1
title: MOESM2 of Challenges and Perspectives in Homology-Directed Gene Targeting in Monocot Plants

description: Additional file 2: Table S2. Major applications of base-editing approaches in plants.
DOI: 10.6084/m9.figshare.11415264
title: MOESM1 of Challenges and Perspectives in Homology-Directed Gene Targeting in Monocot Plants

description: Additional file 1: Table S1. Targeted mutagenesis-genome editing in monocots using CRISPR/Cas.
DOI: 10.6084/m9.figshare.11415264.v1
title: MOESM1 of Challenges and Perspectives in Homology-Directed Gene Targeting in Monocot Plants

description: Additional file 1: Table S1. Targeted mutagenesis-genome editing in monocots using CRISPR/Cas.
DOI: 10.6084/m9.figshare.11415258
title: MOESM3 of High cases of submicroscopic Plasmodium falciparum infections in a suburban population of Lagos, Nigeria

description: Additional file 3.Â varATS/microscopy vs varATS/RDT raw values.
DOI: 10.6084/m9.figshare.11415258.v1
title: MOESM3 of High cases of submicroscopic Plasmodium falciparum infections in a suburban population of Lagos, Nigeria

description: Additional file 3.Â varATS/microscopy vs varATS/RDT raw values.
DOI: 10.6084/m9.figshare.11415249
title: MOESM1 of High cases of submicroscopic Plasmodium falciparum infections in a suburban population of Lagos, Nigeria

description: Additional file 1. CalculationÂ of varATS qPCR standards.
DOI: 10.6084/m9.figshare.11415249.v1
title: MOESM1 of High cases of submicroscopic Plasmodium falciparum infections in a suburban population of Lagos, Nigeria

description: Additional file 1. CalculationÂ of varATS qPCR standards.
DOI: 10.6084/m9.figshare.11415237
title: MOESM3 of Integrated systems analysis of salivary gland transcriptomics reveals key molecular networks in Sjögren’s syndrome

description: Additional file 3. A matrix of enrichment scores by single-sample gene-set enrichment analysis Sheet #1: Data from patients with SjS (GSE7307, GSE23117, GSE40611, and GSE80805). Sheet #2: Data from SjS patients treated with rituximab (E-MEXP-1883).
DOI: 10.6084/m9.figshare.11415237.v1
title: MOESM3 of Integrated systems analysis of salivary gland transcriptomics reveals key molecular networks in Sjögren’s syndrome

description: Additional file 3. A matrix of enrichment scores by single-sample gene-set enrichment analysis Sheet #1: Data from patients with SjS (GSE7307, GSE23117, GSE40611, and GSE80805). Sheet #2: Data from SjS patients treated with rituximab (E-MEXP-1883).
DOI: 10.6084/m9.figshare.11415216
title: MOESM1 of Integrated systems analysis of salivary gland transcriptomics reveals key molecular networks in Sjögren’s syndrome

description: Additional file 1. Figure S1. Principal component analysis on the merged gene expression profiles of salivary gland before and after normalization and batch correction. Figure S2. Functional enrichment map for up-regulated DEG. Figure S3. Identification of the optimal number of clusters. Figure S4. Hierarchical clustering of pathway enrichment profiles from patients with SjS and SjS-like mouse models. Figure S5. Correlation between two key pathways enrichment score and KDGs expression values. Figure S6. Enrichment and leading-edge genes of the B cell receptor signaling pathway and B cell activation. Figure S7. Details on the KDGs and the leading edge genes from the B cell receptor signaling pathway and B cell activation.
DOI: 10.6084/m9.figshare.11415216.v1
title: MOESM1 of Integrated systems analysis of salivary gland transcriptomics reveals key molecular networks in Sjögren’s syndrome

description: Additional file 1. Figure S1. Principal component analysis on the merged gene expression profiles of salivary gland before and after normalization and batch correction. Figure S2. Functional enrichment map for up-regulated DEG. Figure S3. Identification of the optimal number of clusters. Figure S4. Hierarchical clustering of pathway enrichment profiles from patients with SjS and SjS-like mouse models. Figure S5. Correlation between two key pathways enrichment score and KDGs expression values. Figure S6. Enrichment and leading-edge genes of the B cell receptor signaling pathway and B cell activation. Figure S7. Details on the KDGs and the leading edge genes from the B cell receptor signaling pathway and B cell activation.
DOI: 10.6084/m9.figshare.11415195
title: MOESM1 of Fertility-sparing surgery and oncologic outcome among patients with early-stage ovarian cancer ~propensity score- matched analysis~

description: Additional file 1: Table S1. Cox Proportional Hazards Analyses of RFS among patients who underwent FSS (Original cohort), Table S2. Cox Proportional Hazards Analyses of OS among patients who underwent FSS (Original cohort), Table S3. Patientsâ€™ characteristics (PS-matching), Table S4. Cox Proportional Hazards Analyses of RFS among patients who underwent FSS.
DOI: 10.6084/m9.figshare.11415195.v1
title: MOESM1 of Fertility-sparing surgery and oncologic outcome among patients with early-stage ovarian cancer ~propensity score- matched analysis~

description: Additional file 1: Table S1. Cox Proportional Hazards Analyses of RFS among patients who underwent FSS (Original cohort), Table S2. Cox Proportional Hazards Analyses of OS among patients who underwent FSS (Original cohort), Table S3. Patientsâ€™ characteristics (PS-matching), Table S4. Cox Proportional Hazards Analyses of RFS among patients who underwent FSS.
DOI: 10.6084/m9.figshare.11415168
title: MOESM5 of RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics

description: Additional file 5: Table S4. BLAST search output summaries for transcript candidates involved in the phenylpropanoid pathway for 13 berry fruit species: Enzymes of the core pathway and its decorating, modifying and regulatory proteins.
DOI: 10.6084/m9.figshare.11415171
title: MOESM6 of RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics

description: Additional file 6: Table S5. Peptide annotation for the transcriptomes of R. genevieri and R. idaeus cv. Prestige.
DOI: 10.6084/m9.figshare.11415168.v1
title: MOESM5 of RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics

description: Additional file 5: Table S4. BLAST search output summaries for transcript candidates involved in the phenylpropanoid pathway for 13 berry fruit species: Enzymes of the core pathway and its decorating, modifying and regulatory proteins.
DOI: 10.6084/m9.figshare.11415171.v1
title: MOESM6 of RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics

description: Additional file 6: Table S5. Peptide annotation for the transcriptomes of R. genevieri and R. idaeus cv. Prestige.
DOI: 10.6084/m9.figshare.11415159
title: MOESM4 of RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics

description: Additional file 4: Table S3. RNA-seq descriptors for two Rubus species at three fruit ripening stages: green, immature and ripe.
DOI: 10.6084/m9.figshare.11415159.v1
title: MOESM4 of RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics

description: Additional file 4: Table S3. RNA-seq descriptors for two Rubus species at three fruit ripening stages: green, immature and ripe.
DOI: 10.6084/m9.figshare.11415147
title: MOESM3 of RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics

description: Additional file 3: Table S2. RNA-seq descriptors for 13 berry fruit species.
DOI: 10.6084/m9.figshare.11415147.v1
title: MOESM3 of RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics

description: Additional file 3: Table S2. RNA-seq descriptors for 13 berry fruit species.
DOI: 10.6084/m9.figshare.11415135
title: MOESM1 of RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics

description: Additional file 1: Table S1. Classification and description of berry fruit species.
DOI: 10.6084/m9.figshare.11415135.v1
title: MOESM1 of RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics

description: Additional file 1: Table S1. Classification and description of berry fruit species.
DOI: 10.6084/m9.figshare.11415114
title: MOESM15 of RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics

description: Additional file 15: Table S9. Differential expression of candidate transcripts homologous to enzymes involved in the phenylpropanoid pathway of R. genevieri and R. idaeus cv. Prestige during three fruit ripening stages: Examples of candidate enzymes of the general phenylpropanoid pathway, flavonoid regulatory enzymes, transporters, decorating and modifying enzymes.
DOI: 10.6084/m9.figshare.11415114.v1
title: MOESM15 of RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics

description: Additional file 15: Table S9. Differential expression of candidate transcripts homologous to enzymes involved in the phenylpropanoid pathway of R. genevieri and R. idaeus cv. Prestige during three fruit ripening stages: Examples of candidate enzymes of the general phenylpropanoid pathway, flavonoid regulatory enzymes, transporters, decorating and modifying enzymes.
DOI: 10.6084/m9.figshare.11415090
title: MOESM12 of RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics

description: Additional file 12: Table S8. Homologues of the regulatory genes cloned in this study in the collection of the 13 berry fruit species.
DOI: 10.6084/m9.figshare.11415090.v1
title: MOESM12 of RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics

description: Additional file 12: Table S8. Homologues of the regulatory genes cloned in this study in the collection of the 13 berry fruit species.
DOI: 10.6084/m9.figshare.11415063
title: MOESM9 of Network analysis uncovers putative genes affecting resistance to tick infestation in Braford cattle skin

description: Additional file 9: Table S9. Estimates of statistic parameters used to select genetically divergent hosts. Statistic estimates of the mean (mCount), mean standard deviation (mSD), minimum (minCount) and maximum (maxCount) tick counts, and estimated breeding value (EBV) are shown individually for resistant (R) and susceptible (S) hosts. (XLS 32 kb)
DOI: 10.6084/m9.figshare.11415063.v1
title: MOESM9 of Network analysis uncovers putative genes affecting resistance to tick infestation in Braford cattle skin

description: Additional file 9: Table S9. Estimates of statistic parameters used to select genetically divergent hosts. Statistic estimates of the mean (mCount), mean standard deviation (mSD), minimum (minCount) and maximum (maxCount) tick counts, and estimated breeding value (EBV) are shown individually for resistant (R) and susceptible (S) hosts. (XLS 32 kb)
DOI: 10.6084/m9.figshare.11415057
title: MOESM8 of Network analysis uncovers putative genes affecting resistance to tick infestation in Braford cattle skin

description: Additional file 8: Table S8. Transcription factors (TFs) prediction for susceptible hosts. Network analysis predicted potential TFs underlying the regulation of gene expression, based on the variation of TopDEGs. The output file was manually-curated, and only the TFs found in cattle were classified according to their z-score. TopDEGs TFs were also indicated with their respective modulation and statistical significance. Network object name: network object name in MetaBase®; Actual: number of network objects in the activated dataset(s) which interact with the chosen object; n: number of network objects in the activated dataset(s); R: number of network objects in the complete database or background list which interact with the chosen object; N: total number of gene-based objects in the complete database or background list; Expected: mean value for hypergeometric distribution (n*R/N); Ratio: connectivity ratio (Actual/Expected); z-score: ((Actual-Expected)/sqrt(variance)); p-value: probability to have the given value of Actual or higher (or lower for negative z-score); Input IDs: original probe/gene IDs in the activated dataset(s); Signal: variation of gene expression in log2 FC; p-value2: statistical significance in the differential expression analysis. (XLS 48 kb)
DOI: 10.6084/m9.figshare.11415057.v1
title: MOESM8 of Network analysis uncovers putative genes affecting resistance to tick infestation in Braford cattle skin

description: Additional file 8: Table S8. Transcription factors (TFs) prediction for susceptible hosts. Network analysis predicted potential TFs underlying the regulation of gene expression, based on the variation of TopDEGs. The output file was manually-curated, and only the TFs found in cattle were classified according to their z-score. TopDEGs TFs were also indicated with their respective modulation and statistical significance. Network object name: network object name in MetaBase®; Actual: number of network objects in the activated dataset(s) which interact with the chosen object; n: number of network objects in the activated dataset(s); R: number of network objects in the complete database or background list which interact with the chosen object; N: total number of gene-based objects in the complete database or background list; Expected: mean value for hypergeometric distribution (n*R/N); Ratio: connectivity ratio (Actual/Expected); z-score: ((Actual-Expected)/sqrt(variance)); p-value: probability to have the given value of Actual or higher (or lower for negative z-score); Input IDs: original probe/gene IDs in the activated dataset(s); Signal: variation of gene expression in log2 FC; p-value2: statistical significance in the differential expression analysis. (XLS 48 kb)
DOI: 10.6084/m9.figshare.11415051
title: MOESM7 of Network analysis uncovers putative genes affecting resistance to tick infestation in Braford cattle skin

description: Additional file 7: Table S7. Transcription factors (TFs) prediction for resistant hosts. Network analysis predicted potential TFs underlying the regulation of gene expression, based on the variation of TopDEGs. The output file was manually-curated, and only TFs found in cattle were classified according to their z-score. TopDEGs TFs were also indicated with their respective modulation and statistical significance. Network object name: network object name in MetaBase®; Actual: number of network objects in the activated dataset(s) which interact with the chosen object; n: number of network objects in the activated dataset(s); R: number of network objects in the complete database or background list which interact with the chosen object; N: total number of gene-based objects in the complete database or background list; Expected: mean value for hypergeometric distribution (n*R/N); Ratio: connectivity ratio (Actual/Expected); z-score: ((Actual-Expected)/sqrt(variance)); p-value: probability to have the given value of Actual or higher (or lower for negative z-score); Input IDs: original probe/gene IDs in the activated dataset(s); Signal: variation of gene expression in log2 FC; p-value2: statistical significance in the differential expression analysis. (XLS 52 kb)