cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3616574_d1.v1
title: MOESM5 of The role of antigen presenting cells in the induction of HIV-1 latency in resting CD4+ T-cells

description: Additional file 5: TableÂ S2. Comparison of gene expression between latency inducing and non-inducing antigen presenting cell subpopulations using microarray. Using the bioinformatics databases DAVID, GeneCards and GeneCodis, gene expression compartment and function was determined. Genes expressed on the antigen presenting cell (APC)-surface with the ability to signal to T-cells were shortlisted.
DOI: 10.6084/m9.figshare.c.3616556_d6.v1
title: Additional file 8: of MicroRNA and mRNA expression profiling analysis revealed the regulation of plant height in Gossypium hirsutum

description: miRNAs and their targets only identified dwarf mutant (A1) or tall-mutant (A3). (XLSX 31 kb)
DOI: 10.6084/m9.figshare.c.3616556_d7.v1
title: Additional file 4: of MicroRNA and mRNA expression profiling analysis revealed the regulation of plant height in Gossypium hirsutum

description: Novel miRNA identified in all libraries. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3617075_d7.v1
title: Additional file 1: Table S1. of A genetic framework for H2O2 induced cell death in Arabidopsis thaliana

description: Primers and restriction enzymes used for mutant genotyping. Additional information about the mutants used. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.c.3617123_d1.v1
title: Additional file 1: of Oral fosfomycin for treatment of urinary tract infection: a retrospective cohort study

description: Spreadsheet reporting 75 unique patients treated with fosfomycin for urinary tract infections. This excel file contains anonymised details of 75 unique adult patients treated with fosfomycin for urinary tract infections at Oxford University Hospitals NHS Foundation Trust from March 2013 through June 2015. Our original analysis also included patient sex, but this has been removed from the suppl. data file in order to protect anonymity. (XLSX 24Â kb)
DOI: 10.6084/m9.figshare.28049747
title: Cladrastis kentukea raw GC-MS files

description: Metabolite extraction from Cladrastis kentukea leaf tissue
DOI: 10.6084/m9.figshare.28049747.v1
title: Cladrastis kentukea raw GC-MS files

description: Metabolite extraction from Cladrastis kentukea leaf tissue
DOI: 10.6084/m9.figshare.c.3617597_d1.v1
title: Additional file 1 of A comparative study of SMILES-based compound similarity functions for drug-target interaction prediction

description: n. Excel file containing the p-values of the paired t-test comparing the AUC-ROC and AUC-PR score of each method and SIMCOMP for the methods that perform better than SIMCOMP. (XLSX 11.5 kb)
DOI: 10.6084/m9.figshare.c.3617618_d1.v1
title: MOESM1 of 
                     Plasmodium cynomolgi infections in rhesus macaques display clinical and parasitological features pertinent to modelling vivax malaria pathology and relapse infections

description: Additional file 1. Â Haematological and parasitological data of Plasmodium cynomolgi B strain infections in rhesus macaques for up to 100 days. The data used in this study are contained within this file with appropriate metadata.
DOI: 10.6084/m9.figshare.c.3618083_d2.v1
title: Additional file 1: Table S1. of Tracking crop varieties using genotyping-by-sequencing markers: a case study using cassava (Manihot esculenta Crantz)

description: Sample information associated with the 917 accessions from three regions of Ghana and the library of known varieties from CSIR-CRI. ADMIXTURE-based ancestry estimates according to predefined eleven clusters are also provided. We have also attempted to, as far as the library is concerned, classify each of the farmersâ   accessions to their matching released varieties in the CSIR-CRI library. (XLSX 151Â kb)
DOI: 10.6084/m9.figshare.c.3618074_d6.v1
title: Additional file 4: of Deep sequencing transcriptional fingerprinting of rice kernels for dissecting grain quality traits

description: Co-expression analysis results. (XLSX 1249Â kb)
DOI: 10.6084/m9.figshare.c.3618545_d2.v1
title: Additional file 3: Table S2. of Differences in procedural knowledge after a “spaced” and a “massed” version of an intensive course in emergency medicine, investigating a very short spacing interval

description: Raw data (English titles). (XLS 305 kb)
DOI: 10.6084/m9.figshare.c.3618548_d2.v1
title: Additional file 7: of The mRNA-bound proteome of the human malaria parasite Plasmodium falciparum

description: Proteins associated with polysomes during the IDC, including mass spectrometry data. (XLSX 1246 kb)
DOI: 10.6084/m9.figshare.c.3618548_d4.v1
title: Additional file 6: of The mRNA-bound proteome of the human malaria parasite Plasmodium falciparum

description: Enriched GO terms and enrichment of mRNA-binding domains among experimentally captured RNA-binding proteins. (XLSX 45 kb)
DOI: 10.6084/m9.figshare.c.3618548_d5.v1
title: Additional file 1: of The mRNA-bound proteome of the human malaria parasite Plasmodium falciparum

description: List of RNA-binding domains used for HMM searches. (XLSX 67 kb)
DOI: 10.6084/m9.figshare.c.3618548_d6.v1
title: Additional file 4: of The mRNA-bound proteome of the human malaria parasite Plasmodium falciparum

description: Comparative analysis of the abundance of RNA-binding domains in various organisms. (XLSX 191 kb)
DOI: 10.6084/m9.figshare.c.3618548_d7.v1
title: Additional file 2: of The mRNA-bound proteome of the human malaria parasite Plasmodium falciparum

description: List of predicted RNA-binding proteins in P. falciparum. (XLSX 112 kb)
DOI: 10.6084/m9.figshare.c.3618581_d1.v1
title: Additional file 2: Table S2. of Transcriptome analysis in calorie-restricted rats implicates epigenetic and post-translational mechanisms in neuroprotection and aging

description: All genes DE with age. (XLSX 44 kb)
DOI: 10.6084/m9.figshare.c.3618566_d4.v1
title: Additional file 3: Table S2. of Insights from the draft genome of the subsection V (Stigonematales) cyanobacterium Hapalosiphon sp. Strain MRB220 associated with 2-MIB production

description: BLAST comparison between Open reading frames of MRB 220 and those in query genomes. Table S3. Open reading frames present in the genome of MRB220 but not detected in the three most closely related Stigonematales. (XLSX 2467Â kb)
DOI: 10.6084/m9.figshare.c.3618581_d2.v1
title: Additional file 8: Table S6. of Transcriptome analysis in calorie-restricted rats implicates epigenetic and post-translational mechanisms in neuroprotection and aging

description: The 137 longevity genes and the DAVID enrichments. (XLSX 48 kb)
DOI: 10.6084/m9.figshare.c.3618581_d3.v1
title: Additional file 6: Table S5. of Transcriptome analysis in calorie-restricted rats implicates epigenetic and post-translational mechanisms in neuroprotection and aging

description: All genes altered in three comparisons. First, the extended longevity effect of CR switching to AL with lipoic acid. Next, the inhibitory effect lipoic acid had on extended longevity when switching from AL to CR feeding. Finally, the genes specific to CR feeding when switched to AL feeding with lipoic acid supplementation in comparison with the opposite switch which does not induce increased longevity. The DAVID enrichments are also included. (XLSX 157 kb)
DOI: 10.6084/m9.figshare.c.3618587_d1.v1
title: MOESM1 of RNA-Seq and microarray analysis of the Xenopus inner ear transcriptome discloses orthologous OMIM® genes for hereditary disorders of hearing and balance

description: Additional file 1. Master table for Xenopus OMIM auditory and vestibular genes. This spreadsheet contains the list of OMIM® deafness and vestibular disorder genes, mappings to the JGI predicted proteins and Xl-PSID’S (E-value for alignment, E-value for expression, scaffold number and coordinates), RNA-Seq reads associated with each OMIM® gene and microarray GCRMA value for each OMIM® gene. The original data discussed in this publication have been deposited in NCBI’s Gene Expression Omnibus and can be accessed under GEO Series accession numbers GSE69701 (RNA-Seq) and GSE73829 (microarray).
DOI: 10.6084/m9.figshare.c.3618581_d4.v1
title: Additional file 9: Table S7. of Transcriptome analysis in calorie-restricted rats implicates epigenetic and post-translational mechanisms in neuroprotection and aging

description: The 28 longevity genes that have been identified as longevity-associated genes (LAGs) or partners of LAGs. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.28049753
title: Claytonia virginica raw GC-MS files

description: Metabolite extraction from Claytonia virginica leaf tissue
DOI: 10.6084/m9.figshare.28049753.v1
title: Claytonia virginica raw GC-MS files

description: Metabolite extraction from Claytonia virginica leaf tissue
DOI: 10.6084/m9.figshare.c.3619049_d6.v1
title: MOESM11 of Histone modifications rather than the novel regional centromeres of Zymoseptoria tritici distinguish core and accessory chromosomes

description: Additional file 11: Table S7. Repetitive DNA at the subtelomeric regions. Percentage of TE-families and repetitive elements is shown for each subtelomeric region. The length of the subtelomeric region, TE-families/repeats with a coverage &gt; 10 % and the total amount of TE/repeats (%) are shown. Categorized TE-families are labeled according to nomenclature proposed recently [34]. “NoCat” means that repetitive DNA does not match TE sequences.
DOI: 10.6084/m9.figshare.c.3619049_d7.v1
title: MOESM2 of Histone modifications rather than the novel regional centromeres of Zymoseptoria tritici distinguish core and accessory chromosomes

description: Additional file 2: Table S1. Statistics of ChIP-seq experiments. Number of total reads after filtering and mapping is shown. Percentage of reads mapping uniquely, in more than one position or that remained unmapped is based on the total amount of reads. Data were submitted to SRA under accession number SRP059394.
DOI: 10.6084/m9.figshare.c.3619049_d8.v1
title: MOESM15 of Histone modifications rather than the novel regional centromeres of Zymoseptoria tritici distinguish core and accessory chromosomes

description: Additional file 15: Table S10. Primers used for construction of plasmids in this study. Primer ID and primer sequence used for construction of the GFPâ  CenH3 plasmid are shown.
DOI: 10.6084/m9.figshare.c.3619049_d9.v1
title: MOESM5 of Histone modifications rather than the novel regional centromeres of Zymoseptoria tritici distinguish core and accessory chromosomes

description: Additional file 5: Table S2. Primers and length of the amplification products to verify the length of the centromeres. For each centromere, three PCR reactions were performed. PCR reactionÂ 1 amplifies the whole centromeric region, and PCR reactionsÂ 2 and 3 amplify two parts of the centromeric region. Primer IDs, primers sequences and the expected product are shown for all PCR amplifications.
DOI: 10.6084/m9.figshare.c.3619067_d4.v1
title: Additional file 1:Supplementary Tables. of Prognostic relevance of molecular subtypes and master regulators in pancreatic ductal adenocarcinoma

description: Table S1. Differential expression analysis performed by limma R package. Table S2. HNF1Î˛ expression in different human pancreatic cancer cell lines. Table S3. Master regulatory Results of gene set up-regulated in PDAC versus Control. The results are based on the enrichment score of the motifs (column 1), scores are the Area Under the Curve (AUC) and the Normalized Enrichment Score (NES). Motifs clusters are shown in Cluster code column. Predicted associated Transcription factors and predicted targets are shown in the two last columns. The TF view display by iRegulon integrates the results per clusterCode and prioritize the putative TF associated to a given cluster of motifs. Table S4. Master regulatory Results of gene set down-regulated in PDAC versus Control. See legend in Table S3. (XLSX 205Â kb)
DOI: 10.6084/m9.figshare.c.3619049_d11.v1
title: MOESM10 of Histone modifications rather than the novel regional centromeres of Zymoseptoria tritici distinguish core and accessory chromosomes

description: Additional file 10: Table S6. Length of telomeric repeat sequences on core and accessory chromosomes. The length of the telomere repeat tracts (TTAGGG)n was determined from the available genome sequence. As sequencing into chromosome ends leaves some uncertainty about the true length of telomeres in Z. tritici, these data are included to show that there are no significant differences between the currently available sequence from core and accessory chromosomes. Near TTAGGG repeat sequences abutting the telomere tracts are also shown. Overall, core chromosomes have slightly longer telomeres than accessory chromosomes (133Â bp vs. 118Â bp) with 2.5 additional repeats (22.3 vs. 19.8 repeats/telomere).
DOI: 10.6084/m9.figshare.c.3619484_d11.v1
title: Additional file 12: of Transcript profiling for early stages during embryo development in Scots pine

description: Differentially expressed transcripts (FC &gt; 2; RPKM &gt; 10) between consecutive megagametophyte developmental stages. Only DETs with positive matches against TAIR database are included. Transcript name (Transcript ID), fold-change (FC), expression values at each megagametophyte developmental stage (RPKM) and the best match against TAIR database (At locus ID, At name, At annotation) are shown. Transcripts GO annotated for developmental biological process are coloured in red or green, in the up- or down-regulated lists, respectively. All transcripts GO annotated for response to stimulus and stress are highlighted in bold. (PDF 12.2 kb)
DOI: 10.6084/m9.figshare.c.3619511_d3.v1
title: Additional file 5: of Transcriptome analysis revealed that a quorum sensing system regulates the transfer of the pAt megaplasmid in Agrobacterium tumefaciens

description: Differentially expressed genes. Xlsx. Four repeats are show for the mutant strain P4cinI (col. B to E) with repetition numbers (e.g. rep1_cinI) and three repeats for the wild type strain P4 (col. F to H), also with repetition numbers (e.g. rep1_P4). Average values are given for the mutant strain P4cinI (col. I) and the wild type strain P4 (col. J). Fold change and Log2 fold change are also shown (col. K and L) along with the raw p values and adjusted p values (col. M and N). (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.c.3619484_d12.v1
title: Additional file 5: of Transcript profiling for early stages during embryo development in Scots pine

description: Differentially expressed transcripts in embryos and megagametophytes at different stages of seed development. DETs with the highest fold-changes in embryos and megagametophytes at different developmental stages are included. Transcript name (Transcript ID), fold-change (log2 E/M), expression values (RPKM Embryos and RPKM Megagametophytes) and the best match against TAIR database (At locus ID, At name, At annotation) are shown. (XLSX 6.02 kb)
DOI: 10.6084/m9.figshare.c.3619529_d1.v1
title: Additional file 1: Table S1. of Identification and validation of multiple cell surface markers of clinical-grade adipose-derived mesenchymal stromal cells as novel release criteria for good manufacturing practice-compliant production

description: Oligonucleotide primer sequences used in qPCR reactions for the detection of CD marker gene transcript abundance. (XLSX 17.6 kb)
DOI: 10.6084/m9.figshare.c.3619532_d3.v1
title: Additional file 3 of Evolution of transcriptional networks in yeast: alternative teams of transcriptional factors for different species

description: Supplementary material: database of the computed transcription factor binding probabilities. We report the database of the computed binding probabilities of 126 transcription factors to 2557 genes shared by 23 species. (TXT 415 kb)
DOI: 10.6084/m9.figshare.c.3619958_d4.v1
title: Additional file 3: of 
                     Capparis Spinosa L. promotes anti-inflammatory response in vitro through the control of cytokine gene expression in human peripheral blood mononuclear cells

description: Raw data Figure 3. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3619958_d5.v1
title: Additional file 1: of 
                     Capparis Spinosa L. promotes anti-inflammatory response in vitro through the control of cytokine gene expression in human peripheral blood mononuclear cells

description: Raw data Figure 1. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.c.3620309_d8.v1
title: Additional file 7: of SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis

description: Comparison of workflow management systems. (XLS 35Â kb)
DOI: 10.6084/m9.figshare.c.3620303_d9.v1
title: Additional file 1: Table S1. of Genes associated with polymorphic variants predicting lung function are differentially expressed during human lung development

description: SNPs within/near 54 previously identified genes associated with lung function measures FEV1, FVC and FEV1/FVC. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.c.3620342_d2.v1
title: Additional file 2: of Integrating mean and variance heterogeneities to identify differentially expressed genes

description: The null independence between tests statistics on mean and variance heterogeneities. This file is composed of three appendixes. Appendix A: The null independence under normality setting. Appendix B: The null independence under generic spherically symmetric setting. Appendix C: Additional empirical results on the null joint distributions of mean and variance test statistics. (ZIP 311Â kb)
DOI: 10.6084/m9.figshare.c.3620345_d2.v1
title: MOESM1 of Profiling placental and fetal DNA methylation in human neural tube defects

description: Additional file 1: Table S1 is a table listing the clinical and technical variables for the tissue samples used in the 450k microarray analysis. Table S2 is a table listing the samples used in follow-up pyrosequencing in chorionic villi. Table S3 is a table listing conditions used for each pyrosequencing assay. Table S4 is a table listing probes used in the candidate gene 450k analysis. Table S5 is a table listing the additional control kidney samples downloaded from GEO. Table S6 is a table summarizing the results of the candidate gene differential methylation analysis. Table S7 is a table summarizing the results of the array-wide differential methylation analysis.
DOI: 10.6084/m9.figshare.c.3620303_d10.v1
title: Additional file 9: Table S5. of Genes associated with polymorphic variants predicting lung function are differentially expressed during human lung development

description: Evidence of regulated expression (by LD and Lung eQTL) in 5 top differentially expressed genes associated with lung function. (XLSX 33 kb)
DOI: 10.6084/m9.figshare.c.3620360_d1.v1
title: Additional file 3: of Three-dimensional structure model and predicted ATP interaction rewiring of a deviant RNA ligase 2

description: ITasser threading of DpRNL on 3QWU. Atomic coordinates of DpRNL and 3QWU model. (PDB 11 kb)
DOI: 10.6084/m9.figshare.c.3620303_d12.v1
title: Additional file 8: Table S4. of Genes associated with polymorphic variants predicting lung function are differentially expressed during human lung development

description: Evidence of regulated expression (by LD and Blood eQTL) in 5 top differentially expressed genes associated with lung function. SNP = single nucleotide polymorphism, LD = linkage disequilibrium, Chr = chromosome, FDR = false discovery rate, eQTL = expression quantitative loci. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.c.3620879_d1.v1
title: Additional file 4: of Uncovering the pathways underlying whole body regeneration in a chordate model, Botrylloides leachi using de novo transcriptome analysis

description: De novo assembled B. leachi transcripts with significant match to the UniProt protein database (E-value cut off atâ
DOI: 10.6084/m9.figshare.c.3620879_d4.v1
title: Additional file 7: of Uncovering the pathways underlying whole body regeneration in a chordate model, Botrylloides leachi using de novo transcriptome analysis

description: KEGG Pathway analysis with DEG during early and late WBR, in comparison to Stage 0. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3620879_d5.v1
title: Additional file 3: of Uncovering the pathways underlying whole body regeneration in a chordate model, Botrylloides leachi using de novo transcriptome analysis

description: De novo assembled B. leachi transcripts with significant match to the C. intestinalis protein database (E-value cut off atâ
DOI: 10.6084/m9.figshare.c.3620879_d6.v1
title: Additional file 6: of Uncovering the pathways underlying whole body regeneration in a chordate model, Botrylloides leachi using de novo transcriptome analysis

description: PANTHER overrepresentation test showing the GO-Slim Biological Process that were overrepresented among the DE contigs in both early and later stages of WBR. (XLSX 48 kb)
DOI: 10.6084/m9.figshare.c.3621422_d1.v1
title: Additional file 2: of Complete genome sequence of Leuconostoc gelidum subsp. gasicomitatum KG16-1, isolated from vacuum-packaged vegetable sausages

description: Pangenome matrix for Leuconostoc genus, core and softcore genes. (XLSX 1692 kb)
DOI: 10.6084/m9.figshare.c.3621428_d1.v1
title: Additional file 1: Table S1. of Recurrent Merkel cell carcinoma of the testis with unknown primary site: a case report

description: Clinical details of all known cases of testicular Merkel cell carcinoma. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3621443_d1.v1
title: Additional file 1: Table S1. of Computational prediction and experimental validation of novel Hedgehog-responsive enhancers linked to genes of the Hedgehog pathway

description: GLI binding motif 12-mers. Library of 12-mers enriched in GLIFLAG datasets. Motifs were considered high confidence (HC) if the 12-mer occurred in all four GLIFLAG datasets, medium confidence (MC) if it occurred in 2 or 3, or low confidence (LC) if it only occurred in one dataset. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.c.3621443_d2.v1
title: Additional file 6: Table S4. of Computational prediction and experimental validation of novel Hedgehog-responsive enhancers linked to genes of the Hedgehog pathway

description: Overlap of predicted high confidence positive and negative regions with embryonic open chromatin. Tabulation of the number of genomic regions predicted by both LDwGBM and NPwGBM that are classified with high confidence as Hh enhancer regions or as nonregulatory regions that overlap with mesoderm DNaseI (E 11.5) or enhancer markers (E14.5). (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3622019_d1.v1
title: MOESM2 of Using a constraint-based regression method for relative quantification of somatic mutations in pyrosequencing signals: a case for NRAS analysis

description: Additional file 2. Dataset NRAS-61.txt. A dataset to illustrate the use of the Shiny web interactive application. The dataset includes the pyro-signals (i.e.the raw peak heights) corresponding to four samples (A1, A2, A3, and A4).
DOI: 10.6084/m9.figshare.c.3622019_d2.v1
title: MOESM1 of Using a constraint-based regression method for relative quantification of somatic mutations in pyrosequencing signals: a case for NRAS analysis

description: Additional file 1. Source code of AdvISER-PYRO-SMQ. The source code for the new R package which implements the AdvISER-PYRO-SMQ algorithm.
DOI: 10.6084/m9.figshare.c.3622001_d4.v1
title: Additional file 3: of HiFive: a tool suite for easy and efficient HiC and 5C data analysis

description: A tar archive containing all scripts using to generate the data, analyses, and figures presented in this paper. (BZ2 20009 kb)
DOI: 10.6084/m9.figshare.c.3622037_d2.v1
title: Additional file 2: of Draft genome of a commonly misdiagnosed multidrug resistant pathogen Candida auris

description: Table S1. Number of reports regarding various Candida infections. Table S2: 95 Conserved Proteins in Candida and Saccharomyces used for phylogenetic analysis. Table S3: Related Protein Families as categorized based on orthologues to C. albicans. Table S4: Upstream and Downstream Neighbours of MAT alpha loci. Table S5: NCBI accession numbers used for Phylogenetic analysis. (XLSX 26 kb)