cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14615321.v1
title: Additional file 1 of Gene expression and alternative splicing dynamics are perturbed in female head transcriptomes following heterospecific copulation

description: Additional file 1: Table S1. Differentially expressed genes in head transcriptomes (FDR with alpha = 0.05) of females following con- and heterospecific matings between D. mojavensis and D. arizonae. Results are showing significant DE genes for each female species (Dmoj and Dari) and postmating period (45 min and 6 h). Significant (Con- or Heterospecific) and overlapping genes (Consp. and Hetero.) are indicated. Overlapping genes showing substantial differences between con- and heterospecific crosses are indicated (Consp. and Hetero. Diferent responses). Gene IDs and Gene symbols are based on D. mojavensis genome as extracted from D. melanogaster orthologous. Gene IDs based on D. mojavensis genome, while Gene symbols are extracted from D. melanogaster orthologous. (NA: not applicable). Table S2. Alternatively spliced genes in head transcriptomes (FDR with alpha = 0.01) of females following con- and heterospecific matings between D. mojavensis and D. arizonae. Results are showing significant AS genes for each female species (Dmoj and Dari) and postmating period (45 min and 6 h). Significant (Con- or Heterospecific) and overlapping genes (Consp. and Hetero.) are indicated. Gene IDs based on D. mojavensis genome, while Gene symbols are extracted from D. melanogaster orthologous. (NA: not applicable).
DOI: 10.6084/m9.figshare.14615320
title: Additional file 2 of Lymphatic filariasis elimination endgame in an urban Indian setting: the roles of surveillance and residual microfilaremia after mass drug administration

description: Additional file 2. Infection results from routine surveys with place of birth (“state” column), year, number Mf-positive, and number tested in routine surveys.
DOI: 10.6084/m9.figshare.14615320.v1
title: Additional file 2 of Lymphatic filariasis elimination endgame in an urban Indian setting: the roles of surveillance and residual microfilaremia after mass drug administration

description: Additional file 2. Infection results from routine surveys with place of birth (“state” column), year, number Mf-positive, and number tested in routine surveys.
DOI: 10.6084/m9.figshare.14615323
title: Additional file 3 of Lymphatic filariasis elimination endgame in an urban Indian setting: the roles of surveillance and residual microfilaremia after mass drug administration

description: Additional file 3. Pre-MDA results, format as previous file.
DOI: 10.6084/m9.figshare.14615321
title: Additional file 1 of Gene expression and alternative splicing dynamics are perturbed in female head transcriptomes following heterospecific copulation

description: Additional file 1: Table S1. Differentially expressed genes in head transcriptomes (FDR with alpha = 0.05) of females following con- and heterospecific matings between D. mojavensis and D. arizonae. Results are showing significant DE genes for each female species (Dmoj and Dari) and postmating period (45 min and 6 h). Significant (Con- or Heterospecific) and overlapping genes (Consp. and Hetero.) are indicated. Overlapping genes showing substantial differences between con- and heterospecific crosses are indicated (Consp. and Hetero. Diferent responses). Gene IDs and Gene symbols are based on D. mojavensis genome as extracted from D. melanogaster orthologous. Gene IDs based on D. mojavensis genome, while Gene symbols are extracted from D. melanogaster orthologous. (NA: not applicable). Table S2. Alternatively spliced genes in head transcriptomes (FDR with alpha = 0.01) of females following con- and heterospecific matings between D. mojavensis and D. arizonae. Results are showing significant AS genes for each female species (Dmoj and Dari) and postmating period (45 min and 6 h). Significant (Con- or Heterospecific) and overlapping genes (Consp. and Hetero.) are indicated. Gene IDs based on D. mojavensis genome, while Gene symbols are extracted from D. melanogaster orthologous. (NA: not applicable).
DOI: 10.6084/m9.figshare.14615326.v1
title: Additional file 4 of Lymphatic filariasis elimination endgame in an urban Indian setting: the roles of surveillance and residual microfilaremia after mass drug administration

description: Additional file 4. Disease results from routine surveys.
DOI: 10.6084/m9.figshare.14615326
title: Additional file 4 of Lymphatic filariasis elimination endgame in an urban Indian setting: the roles of surveillance and residual microfilaremia after mass drug administration

description: Additional file 4. Disease results from routine surveys.
DOI: 10.6084/m9.figshare.14615323.v1
title: Additional file 3 of Lymphatic filariasis elimination endgame in an urban Indian setting: the roles of surveillance and residual microfilaremia after mass drug administration

description: Additional file 3. Pre-MDA results, format as previous file.
DOI: 10.6084/m9.figshare.14615350
title: Additional file 4 of The prevalence of uterine fundal pressure during the second stage of labour for women giving birth in health facilities: a systematic review and meta-analysis

description: Additional file 4. Characteristics of included studies: full table presenting the characteristics of included studies, extended version of the table presented on pages 21–24 of the manuscript.
DOI: 10.6084/m9.figshare.14615350.v1
title: Additional file 4 of The prevalence of uterine fundal pressure during the second stage of labour for women giving birth in health facilities: a systematic review and meta-analysis

description: Additional file 4. Characteristics of included studies: full table presenting the characteristics of included studies, extended version of the table presented on pages 21–24 of the manuscript.
DOI: 10.6084/m9.figshare.14615395
title: Additional file 2 of Severe anemia in patients with Propionic acidemia is associated with branched-chain amino acid imbalance

description: Additional file 2. Excell data.
DOI: 10.6084/m9.figshare.14615395.v1
title: Additional file 2 of Severe anemia in patients with Propionic acidemia is associated with branched-chain amino acid imbalance

description: Additional file 2. Excell data.
DOI: 10.6084/m9.figshare.14615408
title: Additional file 1 of Signature RNAS and related regulatory roles in type 1 diabetes mellitus based on competing endogenous RNA regulatory network analysis

description: Additional file 1: Table S1. The significantly enriched gene ontology (GO) biological processes and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways for differentially expressed mRNAs.
DOI: 10.6084/m9.figshare.14615408.v1
title: Additional file 1 of Signature RNAS and related regulatory roles in type 1 diabetes mellitus based on competing endogenous RNA regulatory network analysis

description: Additional file 1: Table S1. The significantly enriched gene ontology (GO) biological processes and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways for differentially expressed mRNAs.
DOI: 10.6084/m9.figshare.14615417
title: Additional file 4 of Signature RNAS and related regulatory roles in type 1 diabetes mellitus based on competing endogenous RNA regulatory network analysis

description: Additional file 4: Table S2. The significantly enriched gene ontology (GO) biological processes and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways for mRNAs in the competing endogenous (1) regulatory network.
DOI: 10.6084/m9.figshare.14615417.v1
title: Additional file 4 of Signature RNAS and related regulatory roles in type 1 diabetes mellitus based on competing endogenous RNA regulatory network analysis

description: Additional file 4: Table S2. The significantly enriched gene ontology (GO) biological processes and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways for mRNAs in the competing endogenous (1) regulatory network.
DOI: 10.6084/m9.figshare.14615426.v1
title: Additional file 1 of Optimizing Nanopore sequencing-based detection of structural variants enables individualized circulating tumor DNA-based disease monitoring in cancer patients

description: Additional file 1: Supplementary Tables.
DOI: 10.6084/m9.figshare.14615426
title: Additional file 1 of Optimizing Nanopore sequencing-based detection of structural variants enables individualized circulating tumor DNA-based disease monitoring in cancer patients

description: Additional file 1: Supplementary Tables.
DOI: 10.6084/m9.figshare.14615450.v1
title: Additional file 15 of Prunus persica plant endogenous peptides PpPep1 and PpPep2 cause PTI-like transcriptome reprogramming in peach and enhance resistance to Xanthomonas arboricola pv. pruni

description: Additional file 15. Nodes and edges input information needed for visualization of P. persica Pep DiNAR network (PEPN) on DiNAR. These databases were built using peach to A. thaliana translation based on orthologue gene information.
DOI: 10.6084/m9.figshare.14615453
title: Additional file 16 of Prunus persica plant endogenous peptides PpPep1 and PpPep2 cause PTI-like transcriptome reprogramming in peach and enhance resistance to Xanthomonas arboricola pv. pruni

description: Additional file 16. Edges input information needed for visualization of P. persica Pep DiNAR network (PEPN) on DiNAR. These databases were built using peach to A. thaliana translation based on orthologue gene information.
DOI: 10.6084/m9.figshare.14615453.v1
title: Additional file 16 of Prunus persica plant endogenous peptides PpPep1 and PpPep2 cause PTI-like transcriptome reprogramming in peach and enhance resistance to Xanthomonas arboricola pv. pruni

description: Additional file 16. Edges input information needed for visualization of P. persica Pep DiNAR network (PEPN) on DiNAR. These databases were built using peach to A. thaliana translation based on orthologue gene information.
DOI: 10.6084/m9.figshare.14615450
title: Additional file 15 of Prunus persica plant endogenous peptides PpPep1 and PpPep2 cause PTI-like transcriptome reprogramming in peach and enhance resistance to Xanthomonas arboricola pv. pruni

description: Additional file 15. Nodes and edges input information needed for visualization of P. persica Pep DiNAR network (PEPN) on DiNAR. These databases were built using peach to A. thaliana translation based on orthologue gene information.
DOI: 10.6084/m9.figshare.14615456
title: Additional file 17 of Prunus persica plant endogenous peptides PpPep1 and PpPep2 cause PTI-like transcriptome reprogramming in peach and enhance resistance to Xanthomonas arboricola pv. pruni

description: Additional file 17. Primers used in RT-qPCR assays and their properties, including those targeting 19 genes selected for RNA-Seq validation and two described P. persica reference genes (TEF2 and UBQ, [9, 71]).
DOI: 10.6084/m9.figshare.14615456.v1
title: Additional file 17 of Prunus persica plant endogenous peptides PpPep1 and PpPep2 cause PTI-like transcriptome reprogramming in peach and enhance resistance to Xanthomonas arboricola pv. pruni

description: Additional file 17. Primers used in RT-qPCR assays and their properties, including those targeting 19 genes selected for RNA-Seq validation and two described P. persica reference genes (TEF2 and UBQ, [9, 71]).
DOI: 10.6084/m9.figshare.14615459
title: Additional file 1 of Prunus persica plant endogenous peptides PpPep1 and PpPep2 cause PTI-like transcriptome reprogramming in peach and enhance resistance to Xanthomonas arboricola pv. pruni

description: Additional file 1. Quality control and mapping statistics of Prunus persica RNA-Seq analyses using Illumina.
DOI: 10.6084/m9.figshare.14615459.v1
title: Additional file 1 of Prunus persica plant endogenous peptides PpPep1 and PpPep2 cause PTI-like transcriptome reprogramming in peach and enhance resistance to Xanthomonas arboricola pv. pruni

description: Additional file 1. Quality control and mapping statistics of Prunus persica RNA-Seq analyses using Illumina.
DOI: 10.6084/m9.figshare.14615462
title: Additional file 2 of Prunus persica plant endogenous peptides PpPep1 and PpPep2 cause PTI-like transcriptome reprogramming in peach and enhance resistance to Xanthomonas arboricola pv. pruni

description: Additional file 2. RNA-Seq results were validated by RT-qPCR. Identification and GO classification of the 19 selected genes and log2FC values obtained for the same samples through both techniques. Cell colors distinguish statistically significant regulated genes (blue, down-regulated; red, up-regulated) from non-significant, shown in white (adj. p &lt; 0.01, |log2FC| &gt; 1.0 for RNA-Seq; adj. p &lt; 0.05 for RT-qPCR). Graph on the right shows simple linear regression between log2FC values using the two techniques with correlation coefficient of 0.92.
DOI: 10.6084/m9.figshare.14615462.v1
title: Additional file 2 of Prunus persica plant endogenous peptides PpPep1 and PpPep2 cause PTI-like transcriptome reprogramming in peach and enhance resistance to Xanthomonas arboricola pv. pruni

description: Additional file 2. RNA-Seq results were validated by RT-qPCR. Identification and GO classification of the 19 selected genes and log2FC values obtained for the same samples through both techniques. Cell colors distinguish statistically significant regulated genes (blue, down-regulated; red, up-regulated) from non-significant, shown in white (adj. p &lt; 0.01, |log2FC| &gt; 1.0 for RNA-Seq; adj. p &lt; 0.05 for RT-qPCR). Graph on the right shows simple linear regression between log2FC values using the two techniques with correlation coefficient of 0.92.
DOI: 10.6084/m9.figshare.14615465
title: Additional file 3 of Prunus persica plant endogenous peptides PpPep1 and PpPep2 cause PTI-like transcriptome reprogramming in peach and enhance resistance to Xanthomonas arboricola pv. pruni

description: Additional file 3. Interactive principal component analysis (PCA) of regularized–logarithm normalized expression data from the 500 genes showing the highest variance (DESeq2 1.20.0 package [60]) conducted in R [63] using scatter plot 3d library [73]. Three principal components, PC1, PC2 and PC3, with Eigenvalues above 1 explained 83.84%, 7.04% and 2.81% of the overall variability, respectively. The peptide treatments are shown in different colors: tan, time zero (t0); turquoise, 1 h PpPep1 (P1t1); light green, 1 h PpPep2 (P2t1); blue, 24 h PpPep1 (P1t24); pink, 24 h PpPep2 (P2t24); orange, 48 h PpPep1 (P1t48); yellow, 48 h PpPep2 (P2t48). Three biological replicates per sample are shown.
DOI: 10.6084/m9.figshare.14615471
title: Additional file 5 of Prunus persica plant endogenous peptides PpPep1 and PpPep2 cause PTI-like transcriptome reprogramming in peach and enhance resistance to Xanthomonas arboricola pv. pruni

description: Additional file 5. Table of number and percentages of differentially expressed genes (DEG) in response to PpPep1 and PpPep2 at 1, 24 and 48 h after peptide application, with adjusted p-value cut-off 0.01. Contrasts are defined in the first column, where t stands for time, P for Pep, ‘_’ separates the conditions and ∩ for intersecting data between comparisons. DEG percentages are calculated according to the total number of genes in the P. persica genome.
DOI: 10.6084/m9.figshare.14615468.v1
title: Additional file 4 of Prunus persica plant endogenous peptides PpPep1 and PpPep2 cause PTI-like transcriptome reprogramming in peach and enhance resistance to Xanthomonas arboricola pv. pruni

description: Additional file 4. RT-qPCR analysis of the same 19 genes used to validate RNA-Seq results (where the expression is regulated by application of PpPeps, Additional file 2), in mock samples taken at the 0, 1, 24 and 48 h time-points (p &gt; 0.01, IBM SPSS statistics 25).
DOI: 10.6084/m9.figshare.14615465.v1
title: Additional file 3 of Prunus persica plant endogenous peptides PpPep1 and PpPep2 cause PTI-like transcriptome reprogramming in peach and enhance resistance to Xanthomonas arboricola pv. pruni

description: Additional file 3. Interactive principal component analysis (PCA) of regularized–logarithm normalized expression data from the 500 genes showing the highest variance (DESeq2 1.20.0 package [60]) conducted in R [63] using scatter plot 3d library [73]. Three principal components, PC1, PC2 and PC3, with Eigenvalues above 1 explained 83.84%, 7.04% and 2.81% of the overall variability, respectively. The peptide treatments are shown in different colors: tan, time zero (t0); turquoise, 1 h PpPep1 (P1t1); light green, 1 h PpPep2 (P2t1); blue, 24 h PpPep1 (P1t24); pink, 24 h PpPep2 (P2t24); orange, 48 h PpPep1 (P1t48); yellow, 48 h PpPep2 (P2t48). Three biological replicates per sample are shown.
DOI: 10.6084/m9.figshare.14615468
title: Additional file 4 of Prunus persica plant endogenous peptides PpPep1 and PpPep2 cause PTI-like transcriptome reprogramming in peach and enhance resistance to Xanthomonas arboricola pv. pruni

description: Additional file 4. RT-qPCR analysis of the same 19 genes used to validate RNA-Seq results (where the expression is regulated by application of PpPeps, Additional file 2), in mock samples taken at the 0, 1, 24 and 48 h time-points (p &gt; 0.01, IBM SPSS statistics 25).
DOI: 10.6084/m9.figshare.14615471.v1
title: Additional file 5 of Prunus persica plant endogenous peptides PpPep1 and PpPep2 cause PTI-like transcriptome reprogramming in peach and enhance resistance to Xanthomonas arboricola pv. pruni

description: Additional file 5. Table of number and percentages of differentially expressed genes (DEG) in response to PpPep1 and PpPep2 at 1, 24 and 48 h after peptide application, with adjusted p-value cut-off 0.01. Contrasts are defined in the first column, where t stands for time, P for Pep, ‘_’ separates the conditions and ∩ for intersecting data between comparisons. DEG percentages are calculated according to the total number of genes in the P. persica genome.
DOI: 10.6084/m9.figshare.14615480
title: Additional file 8 of Prunus persica plant endogenous peptides PpPep1 and PpPep2 cause PTI-like transcriptome reprogramming in peach and enhance resistance to Xanthomonas arboricola pv. pruni

description: Additional file 8. Interpretation of the transcriptomic response of P. persica leaves to treatment with PpPeps. Gene set enrichment analysis using GSEA and p &lt; 0.01 in time and peptide comparisons (left and right, respectively). In time comparison, red indicates upregulation and blue downregulation of the genes contributing to each BIN in the first vs. the second time condition in the upper row. In peptide comparison, orange and green indicate overexpression in PpPep1 and PpPep2, respectively, of the genes contributing to each bin. Bright red, blue, orange or green indicate statistically significant enrichment. Light colors indicate the absence of statistically significant enrichment. Size indicates the number of genes in the gene set after filtering out those not in the expression dataset.
DOI: 10.6084/m9.figshare.14615477
title: Additional file 7 of Prunus persica plant endogenous peptides PpPep1 and PpPep2 cause PTI-like transcriptome reprogramming in peach and enhance resistance to Xanthomonas arboricola pv. pruni

description: Additional file 7. Interactive heat map showing relative expression levels of genes that are regulated in at least one comparison (adj. p &lt; 0.01, |log2FC| &gt;1.0): P1t1 vs. t0, P2t1 vs. t0, P1t24 vs. t1, P2t24 vs. t1, P1t48 vs. t24, and P2t48 vs. t24. P1: treatment with PpPep1; P2: treatment with PpPep2; t stands for time and is given in hours; and the dash corresponds to vs.. The rainbow color scale represents highly positive to highly negative log2FC (7 to -7), white corresponding to 0. Gene codes are displayed on the left. Top right menu helps surfing the plot, zooming interesting areas or identifying gene codes for each expression value.
DOI: 10.6084/m9.figshare.14615477.v1
title: Additional file 7 of Prunus persica plant endogenous peptides PpPep1 and PpPep2 cause PTI-like transcriptome reprogramming in peach and enhance resistance to Xanthomonas arboricola pv. pruni

description: Additional file 7. Interactive heat map showing relative expression levels of genes that are regulated in at least one comparison (adj. p &lt; 0.01, |log2FC| &gt;1.0): P1t1 vs. t0, P2t1 vs. t0, P1t24 vs. t1, P2t24 vs. t1, P1t48 vs. t24, and P2t48 vs. t24. P1: treatment with PpPep1; P2: treatment with PpPep2; t stands for time and is given in hours; and the dash corresponds to vs.. The rainbow color scale represents highly positive to highly negative log2FC (7 to -7), white corresponding to 0. Gene codes are displayed on the left. Top right menu helps surfing the plot, zooming interesting areas or identifying gene codes for each expression value.
DOI: 10.6084/m9.figshare.14615480.v1
title: Additional file 8 of Prunus persica plant endogenous peptides PpPep1 and PpPep2 cause PTI-like transcriptome reprogramming in peach and enhance resistance to Xanthomonas arboricola pv. pruni

description: Additional file 8. Interpretation of the transcriptomic response of P. persica leaves to treatment with PpPeps. Gene set enrichment analysis using GSEA and p &lt; 0.01 in time and peptide comparisons (left and right, respectively). In time comparison, red indicates upregulation and blue downregulation of the genes contributing to each BIN in the first vs. the second time condition in the upper row. In peptide comparison, orange and green indicate overexpression in PpPep1 and PpPep2, respectively, of the genes contributing to each bin. Bright red, blue, orange or green indicate statistically significant enrichment. Light colors indicate the absence of statistically significant enrichment. Size indicates the number of genes in the gene set after filtering out those not in the expression dataset.
DOI: 10.6084/m9.figshare.14615483
title: Additional file 9 of Prunus persica plant endogenous peptides PpPep1 and PpPep2 cause PTI-like transcriptome reprogramming in peach and enhance resistance to Xanthomonas arboricola pv. pruni

description: Additional file 9. Detailed data of gene set enrichment analysis using GSEA and adjusted p &lt; 0.01 in time comparisons. For every statistically enriched bin, all genes contributing to the enrichment are listed, as well as expression, description traits and additional GSEA ranking information.
DOI: 10.6084/m9.figshare.14615483.v1
title: Additional file 9 of Prunus persica plant endogenous peptides PpPep1 and PpPep2 cause PTI-like transcriptome reprogramming in peach and enhance resistance to Xanthomonas arboricola pv. pruni

description: Additional file 9. Detailed data of gene set enrichment analysis using GSEA and adjusted p &lt; 0.01 in time comparisons. For every statistically enriched bin, all genes contributing to the enrichment are listed, as well as expression, description traits and additional GSEA ranking information.
DOI: 10.6084/m9.figshare.14615297
title: Additional file 1 of VISTA regulates microglia homeostasis and myelin phagocytosis, and is associated with MS lesion pathology

description: Additional file 1. Extended data containing Tables S1-S5. Table S1. Information on MS patients. Table S2. Morphometric features of individual cells. Table S3. Genes in published microglia gene sets. Table S4. Normcounts and differential gene expression in LPS experiment. Table S5. Normcounts and differential gene expression in EAEexperiment
DOI: 10.6084/m9.figshare.14615297.v1
title: Additional file 1 of VISTA regulates microglia homeostasis and myelin phagocytosis, and is associated with MS lesion pathology

description: Additional file 1. Extended data containing Tables S1-S5. Table S1. Information on MS patients. Table S2. Morphometric features of individual cells. Table S3. Genes in published microglia gene sets. Table S4. Normcounts and differential gene expression in LPS experiment. Table S5. Normcounts and differential gene expression in EAEexperiment
DOI: 10.5281/zenodo.4771282
title: FM-index of ~400k SARS-CoV-2 genomes

description: SARS-CoV-2 genome sequences were downloaded from EBI's COVID-19 Data Portal on May 16, 2021. File "sars-cov-2.fmd" was generated by "ropebwt2 -do sars-cov-2.fmd sequences_fasta_2021-05-15.fa.gz".