cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3616961_d4.v1
title: Additional file 3: of Next-generation sequencing identifies altered whole blood microRNAs in neuromyelitis optica spectrum disorder which may permit discrimination from multiple sclerosis

description: ANOVA of miRNAs in whole blood.
DOI: 10.6084/m9.figshare.c.3616973_d1.v1
title: Additional file 2: of 
                     Euphorbia tirucalli modulates gene expression in larynx squamous cell carcinoma

description: Excel spreadsheet about Figure 1C – raw data on cell count. (XLS 41 kb)
DOI: 10.6084/m9.figshare.c.3616976_d1.v1
title: Additional file 2: of The global spread of Middle East respiratory syndrome: an analysis fusing traditional epidemiological tracing and molecular phylodynamics

description: Figure S1. Results of recombination analysis. Out of all 196 MERS-CoV ORF1a/b sequences, two strains were detected by Bootscan/Recscan method in RDP as recombinant strains. Figure S2. Likelihood mapping of MERS ORF1a/b (a) main dataset, (b) human subset, and (c) camel subset. Main dataset has both camel and human sequences. Each dot represents the likelihoods of the three possible unrooted trees for a set of four randomly selected sequences: dots close to the corners represent tree-like phylogenetic signal and those at the sides represent network-like signal. The central area of the likelihood map represents star-like signal of unresolved phylogenetic information. Figure S3. Temporal signal analysis using TempEst. Plots of the root-to-tip genetic distance against sampling time are shown for phylogenies estimated from three alignments: (a) main dataset with both human and camel sequences, (b) human sequences, and (c) camel sequences. Figure S4. Time-scaled phylogeographic tree of MERS-CoV ORF1a/b sequences isolated from humans and camels by country. Each color shown in legend represents country of sampled sequence (tip branches) as well as ancestral lineage (internal branches) inferred by Bayesian phylogeography. Brown camel symbols represent MERS-CoV sequences isolated from camels. * represents posterior probability for the clade &gt;0.90. ** &gt;0.95 and *** &gt;0.99. Figure S5. Time-scaled phylogeographic tree of MERS-CoV ORF1a/b sequences isolated from humans by city. Each color shown in legend represents city or region of sampled sequence (tip branches) as well as ancestral lineage (internal branches) inferred by Bayesian phylogeography. * represents posterior probability for the clade &gt;0.90. ** for &gt;0.95 and *** for &gt;0.99. Figure S6. Time-scaled phylogeographic tree of MERS-CoV ORF1a/b sequences isolated from humans by country. Each color shown in legend represents country of sampled sequence (tip branches) as well as ancestral lineage (internal branches) inferred by Bayesian phylogeography. * represents posterior probability for the clade &gt;0.90. ** for &gt;0.95 and *** for &gt;0.99. (ZIP 945 kb)
DOI: 10.6084/m9.figshare.c.3616943_d10.v1
title: MOESM1 of 50Â years of amino acid hydrophobicity scales: revisiting the capacity for peptide classification

description: Additional file 1: Table S1. Hydrophobicity scale values. Given is the index of the hydrophobicity scale (column 1), the year of publication (column 2), the authors (column 3), the name of the scale (column 4), the website for downloading the scale (column 5) and the hydrophobicity values for each amino acid (columns 6â  25).
DOI: 10.6084/m9.figshare.c.3616961_d5.v1
title: Additional file 2: of Next-generation sequencing identifies altered whole blood microRNAs in neuromyelitis optica spectrum disorder which may permit discrimination from multiple sclerosis

description: Pairwise group comparisons of miRNAs in serum.
DOI: 10.6084/m9.figshare.c.3616973_d2.v1
title: Additional file 3: of 
                     Euphorbia tirucalli modulates gene expression in larynx squamous cell carcinoma

description: Excel spreadsheet about Figure 1D – raw data on cell count. (XLS 23 kb)
DOI: 10.6084/m9.figshare.c.3617246_d1.v1
title: Additional file 4: Table S4 of Updated Rice Kinase Database RKD 2.0: enabling transcriptome and functional analysis of rice kinase genes

description: Rice kinases differentially expressed under root heavy metal treatment. (XLSX 62 kb)
DOI: 10.6084/m9.figshare.c.3617258_d1.v1
title: MOESM1 of Enabling surface dependent diffusion in spatial simulations using Smoldyn

description: Additional file 1. Smoldyn configuration files used in this manuscript.
DOI: 10.6084/m9.figshare.c.3617261_d1.v1
title: Additional file 3: of Favorable prognosis in colorectal cancer patients with co-expression of c-MYC and Ă -catenin

description: Raw data of c-MYC and Ă -catenin status obtained from cohort1. (XLSX 51 kb)
DOI: 10.6084/m9.figshare.c.3617246_d4.v1
title: Additional file 2: Table S2. of Updated Rice Kinase Database RKD 2.0: enabling transcriptome and functional analysis of rice kinase genes

description: Rice kinases with abiotic stress responses. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.c.3617264_d1.v1
title: MOESM1 of Genotypic differences in intruder-evoked immediate early gene activation in male, but not female, vasopressin 1b receptor knockout mice

description: Additional file 1. Witchey et al. Data.xlsx contains the raw data for all of the experiments described in this manuscript.
DOI: 10.6084/m9.figshare.c.3617261_d2.v1
title: Additional file 4: of Favorable prognosis in colorectal cancer patients with co-expression of c-MYC and Ă -catenin

description: Raw data of c-MYC and Ă -catenin status obtained from cohort2. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.c.3617426_d6.v1
title: Additional file 10: Table S4. of Identification of Nicotiana benthamiana microRNAs and their targets using high throughput sequencing and degradome analysis

description: Oligonucleotide sequences used for probes in Northern blot analysis and RT-PCR validation. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3617444_d2.v1
title: Additional file 2: of Countdown to 2015 country case studies: systematic tools to address the â  black boxâ   of health systems and policy assessment

description: Policy and Programme Timeline Tool. (XLS 39Â kb)
DOI: 10.6084/m9.figshare.c.3617450_d1.v1
title: MOESM1 of Genetic and epigenetic variation among inbred mouse littermates: identification of inter-individual differentially methylated regions

description: Additional file 1: Table S1. Variant calls from whole genome sequencing of two Avy mice, one yellow and one pseudoagouti. The variant calls and associated genomic coordinates are relative to the NCBI37/mm9 genome assembly. Table S2. Validation of variant calls. A set of 105 SNP variants were selected at random from those that differed between the two mice or were heterozygous in both mice. Of the 96 that could be PCR amplified and sequenced, those that did or did not validate are shown. Table S3. Variably methylated regions designated iiDMRs. A list of 356 regions that display differential methylation between inbred individuals, generated from 6 adjacent CpGs that support differential methylation and a difference of at least 20Â % between the highest and lowest value. Values from the Yellow excluded from calling regions. Table S4. Variably methylated regions that overlap ERV elements, designated ERV iiDMRs. A list of 55 regions that display differential methylation between inbred individuals and overlap with ERV elements from the UCSC mm9 repeatmasker database. Differentially methylated regions were generated from 6 adjacent CpGs that support differential methylation and a difference of at least 20Â % between the highest and lowest value. Values from the Yellow mouse were excluded from calling regions. Table S5. Primers used in the study.
DOI: 10.6084/m9.figshare.c.3617444_d4.v1
title: Additional file 3: of Countdown to 2015 country case studies: systematic tools to address the â  black boxâ   of health systems and policy assessment

description: Health Policy Tracer Indicators Dashboard. (XLS 23Â kb)
DOI: 10.6084/m9.figshare.c.3617456_d2.v1
title: Additional file 5: Table S3. of Deciphering common and specific transcriptional immune responses in pea towards the oomycete pathogens Aphanomyces euteiches and Phytophthora pisi

description: List of differentially expressed pea genes during interaction with A. euteiches and P. pisi. Microsoft Excel spreadsheet containing M. truncatula gene IDs (column A), annotation (column B), minimum E-value (the lowest E-value of the ten best hits, column C), mean similarity (the average similarity value of the ten best hits, column E) and enzyme code (column E) provided by Blast2GO. Ratio of the log2 expression between each treatment and the corresponded control samples is presented in column F to I. Genes are clustered based on their expression patterns as shown in Fig.Â 2. Sheets 2 and 3 represent the genes in sub-clusters 1b and 2a, respectively, which are mainly induced in response to both pathogens at 6 hpi. Sheets 1 and 4 represent the genes in sub-clusters 1a and 2b that are specifically induced in response to P. pisi and A. euteiches at 6 hpi, respectively. Sheets 6 and 7 represent the genes in sub-clusters 3b and 4a, respectively, which are induced in response to both pathogens at 20 hpi. Sheets 5 and 8 represent the genes in sub-clusters 3a and 4b that are specifically induced at 20 hpi in response to A. euteiches and P. pisi, respectively. (XLSX 280 kb)
DOI: 10.6084/m9.figshare.c.3617426_d9.v1
title: Additional file 1: Table S1. of Identification of Nicotiana benthamiana microRNAs and their targets using high throughput sequencing and degradome analysis

description: MFEI values of conserved and other known miRNAs in Nicotiana benthamiana. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.c.3617456_d3.v1
title: Additional file 2: Table S1. of Deciphering common and specific transcriptional immune responses in pea towards the oomycete pathogens Aphanomyces euteiches and Phytophthora pisi

description: List of all pea responsive genes to infection with A. euteiches. Microsoft Excel spreadsheet containing complete list of pea responsive genes to A. euteiches infection at 6 hpi (A6UP, A6DOWN) and 20 hpi (A20UP, A20DOWN). All genes have P ≤ 0.05 on log2 of fold change (FC) expression levels compared to the control samples. Each gene is presented by the M. truncatula gene ID (column A), annotation (column B), minimum E-value (the lowest E-value of the ten best hits) (column C), mean similarity (the average similarity value of the ten best hits) (column D) and enzyme code (column E) provided by Blast2GO. Ratios of log2 on the FC between each treatment and the corresponding control samples are presented in column F. Differentially expressed genes (P ≤ 0.05, ≥ 1.5 fold induction or ≤ 0.67 fold repression) are marked with light blue colour. (XLSX 465 kb)
DOI: 10.6084/m9.figshare.c.3617723_d1.v1
title: MOESM9 of A comparison of the protein-coding genomes of two green sulphur bacteria, Chlorobium tepidum TLS and Pelodictyon phaeoclathratiforme BU-1

description: Additional file 9. ensembl_1_copy_both_spp.pl. The Perl script used to identify the protein families with one copy in both species from Ensembl Genomes.
DOI: 10.6084/m9.figshare.c.3617723_d3.v1
title: MOESM1 of A comparison of the protein-coding genomes of two green sulphur bacteria, Chlorobium tepidum TLS and Pelodictyon phaeoclathratiforme BU-1

description: Additional file 1. groups.txt. Predicted protein families (groups) output by OrthoMCL for C. tepidum and P. phaeoclathratiforme UniProt protein sets.
DOI: 10.6084/m9.figshare.c.3617657_d16.v1
title: Additional file 12: of Identification of the BRD1 interaction network and its impact on mental disorder risk

description: Metadata and statistics of integrative ChIP-seq and expression analysis. This file contains three Excel spreadsheets. Spreadsheet 1 contains information on the number of genes common to both the exon expression array and ChIPseq analyses. Spreadsheets 2 and 3 include statistical and permutation tests concerning enrichment of DEGs among BRD1 PTGs. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3617723_d4.v1
title: MOESM17 of A comparison of the protein-coding genomes of two green sulphur bacteria, Chlorobium tepidum TLS and Pelodictyon phaeoclathratiforme BU-1

description: Additional file 17. 1_cp_cct_x_cp_ppb.pl. Perl script used to identify the protein families containing one copy in C. tepidum and multiple copies in P. phaeoclathratiforme from UniProt.
DOI: 10.6084/m9.figshare.c.3617723_d5.v1
title: MOESM18 of A comparison of the protein-coding genomes of two green sulphur bacteria, Chlorobium tepidum TLS and Pelodictyon phaeoclathratiforme BU-1

description: Additional file 18. 1_cp_ppb_x_cp_cct.pl. Perl script used to identify the protein families containing one copy in P. phaeoclathratiforme and multiple copies in C. tepidum from UniProt.
DOI: 10.6084/m9.figshare.c.3617723_d6.v1
title: MOESM16 of A comparison of the protein-coding genomes of two green sulphur bacteria, Chlorobium tepidum TLS and Pelodictyon phaeoclathratiforme BU-1

description: Additional file 16. multi_cp_both_spp.pl. Perl script used to identify the protein families with more than one copy for both species from UniProt.
DOI: 10.15468/dl.cs62cp
title: Occurrence Download

description: A dataset containing 337 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Inventario Nacional de Candelilla (Euphorbia antisyphilitica) Fase I.",
 "Geometry POLYGON((-131.52786 12.89340,-78.47214 12.89340,-78.47214 34.10660,-131.52786 34.10660,-131.52786 12.89340))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 337 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037943-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3617723_d7.v1
title: MOESM4 of A comparison of the protein-coding genomes of two green sulphur bacteria, Chlorobium tepidum TLS and Pelodictyon phaeoclathratiforme BU-1

description: Additional file 4. ensembl_cct.fa. The Fasta file containing the genome-wide protein set of Chlorobium tepidum TLS from Ensembl Genomes.
DOI: 10.6084/m9.figshare.c.3617744_d1.v1
title: Additional file 2: Figures S1 and S2. of No evidence of prenatal diversifying selection at locus or supertype levels in the dog MHC class II loci

description: Merging cost showing the amount of variance within clusters in Ward’s method. This information was used in deciding the number of supertype clusters in DLA-DRB1 (Figure S1) and DLA-DQB1 (Figure S2) loci. (ZIP 3 kb)
DOI: 10.6084/m9.figshare.c.3617939_d4.v1
title: Additional file 3: Table S3. of Differential variability and correlation of gene expression identifies key genes involved in neuronal differentiation

description: 671 DVC genes from mouse ES cells. (XLSX 86 kb)
DOI: 10.6084/m9.figshare.c.3617939_d7.v1
title: Additional file 7: Table S5. of Differential variability and correlation of gene expression identifies key genes involved in neuronal differentiation

description: 284 DVC genes from human iPS cells. (XLSX 62 kb)
DOI: 10.6084/m9.figshare.c.3617963_d1.v1
title: Additional file 2: of Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs

description: Curated list of "well-characterized lncRNAs". (XLSX 52 kb)
DOI: 10.6084/m9.figshare.c.3617903_d14.v1
title: Additional file 1: of Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction

description: Supplementary Table. Supplementary tables with legends in the first sheet called "Supplementary Table Legends". (XLSX 985 kb)
DOI: 10.6084/m9.figshare.c.3617966_d1.v1
title: Additional file 1: of Comparative epidemiology of influenza A and B viral infection in a subtropical region: a 7-year surveillance in Okinawa, Japan

description: Dataset 1. Positivity rate. Dataset 2. Patiantâ  s age (XLSX 161Â kb)
DOI: 10.6084/m9.figshare.c.3617963_d2.v1
title: Additional file 4: of Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs

description: Excel file of evolutionary metrics of all lncRNAs found to be conserved to the human/chimp/rat/mouse ancestor. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.c.3617963_d3.v1
title: Additional file 3: of Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs

description: Bed file of lncRNAs discovered from mouse (mm9), human (hg19), chimp/bonobo (panTro4), and rat (rn5). (XLSX 229 kb)
DOI: 10.6084/m9.figshare.c.3618428_d6.v1
title: Additional file 3: of Genetic variants in the upstream region of activin receptor IIA are associated with female fertility in Japanese Black cattle

description: Genes on BTA2 in the ANAI 4 -associated region. The positions are based on the UMD3.1 assembly of the bovine genome. (XLSX 36Â kb)
DOI: 10.6084/m9.figshare.c.3618431_d6.v1
title: Additional file 21 of Comparison of statistical models for nested association mapping in rapeseed (Brassica napus L.) through computer simulations

description: Table S113. Phenotypes for the 50 BC-NAM subpopulations in a scenario where QTLs = 50, h 2=0.8, 0.25 of explained ratio by QTL Ă  genetic background interactions to the total genetic variance with 25 replications. (TXT 2088 kb)
DOI: 10.6084/m9.figshare.c.3618431_d7.v1
title: Additional file 13 of Comparison of statistical models for nested association mapping in rapeseed (Brassica napus L.) through computer simulations

description: Table S14. Phenotypes for the 50 DH-NAM subpopulations in a scenario where QTLs = 50, h 2=0.8 with 25 replications. (TXT 2088 kb)
DOI: 10.6084/m9.figshare.c.3618464_d1.v1
title: Additional file 4: Table S9. of Performance comparison of two commercial human whole-exome capture systems on formalin-fixed paraffin-embedded lung adenocarcinoma samples

description: Coverage distribution across all the coding exons of the 623 cancer related genes in each library. For each gene, the table reports the number of coding RefSeq exons downloaded from UCSC, their presence within 21 commercial re-sequencing cancer panels and further four cancer genes databases. The coverage distribution across all coding exons was performed using the GATK DiagnoseTarget tool. For each WES capture platform we reported: the number of ‘critical’ exons (average depth of coverage
DOI: 10.6084/m9.figshare.c.3618431_d8.v1
title: Additional file 19 of Comparison of statistical models for nested association mapping in rapeseed (Brassica napus L.) through computer simulations

description: Table S11. Phenotypes for the 50 BC-NAM subpopulations in a scenario where QTLs = 50, h 2=0.8, 0.05 of explained ratio by QTL Ă  genetic background interactions to the total genetic variance with 25 replications. (TXT 2078 kb)
DOI: 10.15468/dl.4f57f9
title: Occurrence Download

description: A dataset listing the 1 species recorded in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "TaxonKey is Suillus tomentosus Singer, Snell & E.A.Dick"
 ]
}

 The dataset's 1 records were derived from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037938-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3618431_d9.v1
title: Additional file 14 of Comparison of statistical models for nested association mapping in rapeseed (Brassica napus L.) through computer simulations

description: Table S15. Phenotypes for the 50 RIL-NAM subpopulations in a scenario where QTLs = 50, h 2=0.8 with 25 replications. (TXT 2078 kb)
DOI: 10.6084/m9.figshare.c.3618431_d10.v1
title: Additional file 12 of Comparison of statistical models for nested association mapping in rapeseed (Brassica napus L.) through computer simulations

description: Table S7. Genotypes for the 50 RIL-NAM subpopulations, where 0 and 2 denote the homozygous gentoype of parents, respectively, while 1 denotes the heterozygous genotype. (TXT 88,883 kb)
DOI: 10.6084/m9.figshare.c.3618464_d4.v1
title: Additional file 5: Table S10. of Performance comparison of two commercial human whole-exome capture systems on formalin-fixed paraffin-embedded lung adenocarcinoma samples

description: Clinically actionable mutations within low coverage exons of database-prioritized cancer related genes. For each selected genomic interval the table reports the mean coverage and SD values in both Agilent SureSelect and Roche NimbleGen libraries, and the list of clinically actionable mutations belonging to that interval, retrieved from Gene-Drug Knowledge Database v9.0 [43]. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3618659_d6.v1
title: Additional file 1: Table S1. of Skin fungal community and its correlation with bacterial community of urban Chinese individuals

description: OTU counts and taxonomic information of all samples included in this study. (XLSX 579Â kb)
DOI: 10.6084/m9.figshare.c.3618659_d8.v1
title: Additional file 2: Table S2. of Skin fungal community and its correlation with bacterial community of urban Chinese individuals

description: Taxonomic coverage of UNITE and curated databases for skin mycobiomes of HK and American cohorts, and accuracy comparison for HK cohort. (XLSX 99Â kb)
DOI: 10.6084/m9.figshare.c.3618659_d9.v1
title: Additional file 3: Table S3. of Skin fungal community and its correlation with bacterial community of urban Chinese individuals

description: Relative abundances of genera and Malassezia species across samples, households, and individuals. (XLSX 80Â kb)
DOI: 10.6084/m9.figshare.c.3618884_d4.v1
title: Additional file 3: Table S3. of Hypomethylation of miR-142 promoter and upregulation of microRNAs that target the oxytocin receptor gene in the autism prefrontal cortex

description: Primers used in our analysis. (XLSX 9.48 KB)
DOI: 10.6084/m9.figshare.c.3618941_d3.v1
title: Additional file 3: Table S6. of Illness progression in chronic fatigue syndrome: a shifting immune baseline

description: Supplemental table containing the full data set used in this work including subject age, body mass index (BMI), diagnostic class (i.e. ME/CFS or control), cohort reference and illness duration as well as the normalized and coded values for each cytokine species measured in each subject. Table S7. Supplemental table containing symptom severity based on the Multidimensional Fatigue Inventory (MFI) for all ME/CFS subjects aged 18Â years and older. (XLS 86 kb)
DOI: 10.6084/m9.figshare.c.3618941_d4.v1
title: Additional file 1: Tables S1, S2, S3. of Illness progression in chronic fatigue syndrome: a shifting immune baseline

description: Supplemental tables containing summary statistics of the data collected in each cohort segment, group-wise comparative statistics and normalization constants for each cytokine species. Table S4. contains Spearman correlation and corresponding null probability values for pair-wise correlation of the Multidimensional Fatigue Inventory (MFI) with IL-1Îą, IL-6 and IL-8 levels in subjects older than 18Â years of age. Table S5 contains the performance of classification based on IL-1Îą, IL-6 and IL-8 levels where the relative contribution of each cytokine is adjusted on the basis of duration of illness only as described in Additional file 4: Figure S2. (XLS 51 kb)
DOI: 10.15468/dl.sdvsx8
title: Occurrence Download

description: A dataset containing 72021 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Machine Observation, Human Observation, Occurrence evidence)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Pelecanus thagus Molina, 1782"
 ]
}

 The dataset includes 72021 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037947-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.