cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3608540_d1.v1
title: Additional file 2: Table S1. of Founder events and pre-glacial divergences shape the genetic structure of European Collembola species

description: a) Primer sequence of and b) PCR conditions for the ribosomal D3-D5 region of 28S rDNA, and the protein coding Histone 3 (H3) and COI genes. Table S2. DNA sequences available at GenBank. Table S3. Summary of additional locations and outgroup taxa included in the extended datasets (1) and (3) of the molecular clock analyses. Accession numbers from NCBI and BOLD databanks are listed. For some isotomiid species, the complete D3 fragment of 28S was not available, missing positions were filled with “?” in the alignments. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.c.3608513_d10.v1
title: Additional file 5: of Deep landscape update of dispersed and tandem repeats in the genome model of the red jungle fowl, Gallus gallus, using a series of de novo investigating tools

description: TE coverage in each galGal4 chromosomes in the ISB, REPET TE, TEannot DM and TE + DM annotations. Results are summarized within a table. (ODS 23 kb)
DOI: 10.6084/m9.figshare.c.3608513_d11.v1
title: Additional file 18: of Deep landscape update of dispersed and tandem repeats in the genome model of the red jungle fowl, Gallus gallus, using a series of de novo investigating tools

description: Graph showing thresholds calculated in permutation assays and windows calculated along chromosomes for permutation tests designed to inventory hot spots. Graphic representations about how were calculated thresholds in permutation assays and windows along chromosomes. (ODT 526 kb)
DOI: 10.6084/m9.figshare.c.3608513_d12.v1
title: Additional file 3: of Deep landscape update of dispersed and tandem repeats in the genome model of the red jungle fowl, Gallus gallus, using a series of de novo investigating tools

description: Features of SSRs in galGal4. An inventory of simples repeats, microsatellites, large tandem arrays in galGal4 is supplied. (ODT 251 kb)
DOI: 10.6084/m9.figshare.c.3608522_d7.v1
title: Additional file 1: of Polymorphisms and minihaplotypes in the VvNAC26 gene associate with berry size variation in grapevine

description: List of the 114 grapevine varieties evaluated in this study. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.c.3608513_d13.v1
title: Additional file 15: of Deep landscape update of dispersed and tandem repeats in the genome model of the red jungle fowl, Gallus gallus, using a series of de novo investigating tools

description: Graph showing the expected and observed coverages of TEs (A), genes (B), S/MAR (C) and CpG islands (D) in galGal4 chromosomes. Permutation tests were used in order to define whether TEs, genes, S/MAR and CpG islands were randomly distributed along chromosomes. (ODT 1829 kb)
DOI: 10.6084/m9.figshare.c.3608588_d1.v1
title: Additional file 1: of Whole genome annotation and comparative genomic analyses of bio-control fungus Purpureocillium lilacinum

description: Table S1. Statistics of the completeness of the genome based on 248 CEGs. Table S2. Genome size and the number of protein-coding genes in P. lilacinum and the other Hypocreales fungi. Table S3. Repeat elements in the draft genome sequence of P. lilacinum. Table S4. Total number of genes sharing homology with PHI db in the 10 Hypocreales genomes. Table S5. Fisher’s exact test for evaluation of difference in genetic make-up between P. lilacinum and P. chlamydosporia. Table S6. Gene coding for secreted proteins sharing homology with PHI db. Table S7. GPCRs sharing homology with Pth11-like GPCRs in P. lilacinum. Table S8. Genes coding for GPCRs, Histidine kinases, protein kinases, ABC transporters, MFS and CYP450 proteins in P. lilacinum. Table S9. Genes coding for proteases in the P. lilacinum genome. Table S10. Gene coding for serine proteases with homologs in the PHI db. Table S11. Carbohydrate-degrading enzymes arranged by GH family. Table S12. Carbohydrate esterases arranged by CE family. Table S13. Glycosides hydrolase and carbohydrate esterase genes sharing homology with PHI db. Table S14. Secondary metabolites genes and clusters identified by SMURF. Table S15. AntiSMASH based functional annotation of secondary metabolite clusters. Table S16. NaPDoS analysis to detect condensation (C) and ketosynthase (KS) domains. TableS 17. Primer sequences for quantitative real-time PCR analyses. Figure S1. k-mer analysis to predict assembly size of P. lilacinum. (ZIP 201 kb)
DOI: 10.6084/m9.figshare.c.3608582_d2.v1
title: Additional file 2: Figure S1. of Abiotic predictors and annual seasonal dynamics of Ixodes ricinus, the major disease vector of Central Europe

description: Questing activity of Ixodes ricinus (nymphs and adults) recorded at different near-ground temperatures and relative air humidities during 2005 and 2006. (DOCM 104 kb)
DOI: 10.6084/m9.figshare.c.3608591_d1.v1
title: Additional file 1: Table S1 of Pre-announcement of symbiotic guests: transcriptional reprogramming by mycorrhizal lipochitooligosaccharides shows a strict co-dependency on the GRAS transcription factors NSP1 and RAM1

description: a, b, c. Compilation of gene expression responses in M. truncatula wild type A17 (WT), nfp-1 (NFP), dmi3 (DMI3), nsp1-1 (NSP1), and ram1-1 (RAM1) plantlet roots challenged with 10−8 M sMyc-LCOs (sMyc), 10−7 M nsMyc-LCOs (nsMyc), a mixture of 10−8 M sMyc- and 10−7 M nsMyc-LCOs (s/nsMyc), and 10−8 M Nod-LCOs (Nod). Treatment of M. truncatula wild type roots was performed for 6 or 24 h, respectively, whereas mutants were challenged for 6 h. Expression profiles of wild type roots towards Myc- and Nod-LCOs reported by [7] were included to facilitate comparisons to the global responses in the symbiotic mutants mentioned above. Log2 average expression values (Log AveExpr), log2 fold changes (logFC) for each LCO vs. control treatment, and associated p-values are indicated. Log2 fold changes are coloured as follows: red, log2 fold change larger than 1.0; orange, log2 fold change between 0.6 and 1.0; green, log2 fold change below −1.0. Updated annotations for all Medicago probes including correspondences to release 4.0 of the M. truncatula genome and names of known M. truncatula genes are given. The file was split in three parts for reasons of size. (ZIP 43742 kb)
DOI: 10.6084/m9.figshare.c.3608591_d2.v1
title: Additional file 4: Table S4. of Pre-announcement of symbiotic guests: transcriptional reprogramming by mycorrhizal lipochitooligosaccharides shows a strict co-dependency on the GRAS transcription factors NSP1 and RAM1

description: Ten subsets from Additional file 3: Table S3, where genes activated at least 1.5-fold (p
DOI: 10.6084/m9.figshare.c.3608591_d3.v1
title: Additional file 2: Table S2. of Pre-announcement of symbiotic guests: transcriptional reprogramming by mycorrhizal lipochitooligosaccharides shows a strict co-dependency on the GRAS transcription factors NSP1 and RAM1

description: Gene expression responses in M. truncatula wild type A17 (WT), nfp-1 (NFP), dmi3 (DMI3), nsp1-1 (NSP1), and ram1-1 (RAM1) plantlet roots challenged with 10−8 M sMyc-LCOs (sMyc), 10−7 M nsMyc-LCOs (nsMyc), a mixture of 10−8 M sMyc- and 10−7 M nsMyc-LCOs (s/nsMyc), and 10−8 M Nod-LCOs (Nod). Individual sheets contain subsets of genes, as defined in the captions. Log2 average expression values (Log AveExpr), log2 fold changes (logFC) for each LCO vs. control treatment, and associated p-values are indicated. Log2 fold changes are coloured as follows: red, log2 fold change larger than 1.0; orange, log2 fold change between 0.6 and 1.0; green, log2 fold change below -1.0. Updated annotations for all Medicago probes including correspondences to release 4.0 of the M. truncatula genome and names of known M. truncatula genes are given. (XLSX 1289 kb)
DOI: 10.6084/m9.figshare.c.3608591_d4.v1
title: Additional file 3: Table S3. of Pre-announcement of symbiotic guests: transcriptional reprogramming by mycorrhizal lipochitooligosaccharides shows a strict co-dependency on the GRAS transcription factors NSP1 and RAM1

description: Gene expression responses in M. truncatula wild type A17 (WT), nfp-1 (NFP), dmi3 (DMI3), nsp1-1 (NSP1), and ram1-1 (RAM1) plantlet roots challenged with 10−8 M sMyc-LCOs (sMyc), 10−7 M nsMyc-LCOs (nsMyc), a mixture of 10−8 M sMyc- and 10−7 M nsMyc-LCOs (s/nsMyc), and 10−8 M Nod-LCOs (Nod). Individual sheets contain subsets of genes, as defined in the captions. Log2 average expression values (Log AveExpr), log2 fold changes (logFC) for each LCO vs. control treatment, and associated p-values are indicated. Log2 fold changes are coloured as follows: red, log2 fold change larger than 1.0; orange, log2 fold change between 0.6 and 1.0; green, log2 fold change below −1.0. Updated annotations for all Medicago probes including correspondences to release 4.0 of the M. truncatula genome and names of known M. truncatula genes are given. (XLSX 2932 kb)
DOI: 10.6084/m9.figshare.c.3608627_d1.v1
title: Additional file 2: of Genome comparisons provide insights into the role of secondary metabolites in the pathogenic phase of the Photorhabdus life cycle

description: All protein ortholog families. (XLSX 394Â kb)
DOI: 10.6084/m9.figshare.c.3608624_d2.v1
title: Additional file 4: Table S3. of Evolutionary loss of peroxisomes – not limited to parasites

description: Table of putative peroxisomal enzymes and the prediction of their localization. (XLS 7288 kb)
DOI: 10.6084/m9.figshare.c.3608624_d3.v1
title: Additional file 1: Table S1. of Evolutionary loss of peroxisomes – not limited to parasites

description: Table of genomes used in the analysis with the count of assigned orthologous groups (NOGs). (XLS 59 kb)
DOI: 10.6084/m9.figshare.c.3608627_d2.v1
title: Additional file 8: of Genome comparisons provide insights into the role of secondary metabolites in the pathogenic phase of the Photorhabdus life cycle

description: P. asymbiotica specific coding sequences. (XLSX 20Â kb)
DOI: 10.6084/m9.figshare.c.3608624_d4.v1
title: Additional file 2: Table S2. of Evolutionary loss of peroxisomes – not limited to parasites

description: Table of peroxins identified. (XLS 677 kb)
DOI: 10.6084/m9.figshare.c.3608627_d3.v1
title: Additional file 3: of Genome comparisons provide insights into the role of secondary metabolites in the pathogenic phase of the Photorhabdus life cycle

description: KO numbers for fully assembled genomes as assigned by the KAAS server. (XLSX 262Â kb)
DOI: 10.6084/m9.figshare.c.3608627_d4.v1
title: Additional file 4: of Genome comparisons provide insights into the role of secondary metabolites in the pathogenic phase of the Photorhabdus life cycle

description: KEGG pathway analysis. Numbers indicate number of CDS with matching KO numbers in each pathway. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.c.3608627_d8.v1
title: Additional file 7: of Genome comparisons provide insights into the role of secondary metabolites in the pathogenic phase of the Photorhabdus life cycle

description: Coding sequences mentioned in the text and their respective locus tags. (XLSX 47Â kb)
DOI: 10.6084/m9.figshare.c.3608663_d4.v1
title: Additional file 3: of Learning to use a body-powered prosthesis: changes in functionality and kinematics

description: Data Kinematics. (TXT 19 kb)
DOI: 10.6084/m9.figshare.c.3608681_d1.v1
title: MOESM2 of Spatio-temporal patterns of an anthrax outbreak in white-tailed deer, Odocoileus virginanus, and associated genetic diversity of Bacillus anthracis

description: Additional file 2: Table S1. A table of deer deaths from anthrax during the 2005 outbreak including estimated date of death, gender, and disease status.
DOI: 10.6084/m9.figshare.c.3608651_d9.v1
title: Additional file 7: Table S7. of Analysis of the FnrL regulon in Rhodobacter capsulatus reveals limited regulon overlap with orthologues from Rhodobacter sphaeroides and Escherichia coli

description: Orthologues of Rba. capsulatus in Rba. sphaeroides and presence of FnrL ChIP signals. (XLSX 67Â kb)
DOI: 10.6084/m9.figshare.c.3608678_d2.v1
title: Additional file 5: Figure S2. of Mice lacking the conserved transcription factor Grainyhead-like 3 (Grhl3) display increased apposition of the frontal and parietal bones during embryonic development

description: 3D rotating movies of representative adult skulls. Representative movies allowing better visualisation of the skull bones and coronal sutures in both WT (A) and Grhl3 +/â   (B) adult skulls. (ZIP 2 mb)
DOI: 10.6084/m9.figshare.c.3608651_d10.v1
title: Additional file 8: Table S8. of Analysis of the FnrL regulon in Rhodobacter capsulatus reveals limited regulon overlap with orthologues from Rhodobacter sphaeroides and Escherichia coli

description: Orthologues of Rba. capsulatus in E. coli and their differential expression. (XLSX 85Â kb)
DOI: 10.6084/m9.figshare.c.3608678_d3.v1
title: Additional file 3: Figure S4. of Mice lacking the conserved transcription factor Grainyhead-like 3 (Grhl3) display increased apposition of the frontal and parietal bones during embryonic development

description: Analysis of gene expression in the developing coronal sutures of WT and Grhl3â  /â   embryos at E16.5 (A-B) The expression of Î˛-galactosidase (corresponding to the LacZ transgene inserted within the Grhl3 locus, simultaneously disrupting gene function, as well as acting as a reporter to confirm presence of the deleted allele [7]) was used to confirm loss of Grhl3. The expression of total FGFR1 (C-D), pFGFR1 (E-F), FGFR2 (G-H), Twist (I-J), Runx2 (K-L) and Noggin (M-N) was examined by immunohistochemical analysis. no significant differences in the expression of any of these genes was detected, at E16.5 within the calvaria, dura or suture regions. (ZIP 353 kb)
DOI: 10.6084/m9.figshare.c.3608711_d3.v1
title: Additional file 3: of Heritable gene expression differences between apomictic clone members in Taraxacum officinale: Insights into early stages of evolutionary divergence in asexual plants

description: Differentially expressed genes identified using DESeq, heritability index and annotations from SwissProt and Arabidopsis thaliana coding sequence databases for the semi-natural field experiment. (XLSX 9161Â kb)
DOI: 10.6084/m9.figshare.c.3608723_d2.v1
title: MOESM3 of A proteomic evaluation of urinary changes associated with cardiopulmonary bypass

description: Additional file 3: Table S3. (A) An overview of the peptide and protein identifications and resulting differential quantitation for the 2D-LC DDA/IDA and SWATH run datasets. (B) The impact of the application of a DDA/IDA and SWATH intensity correlation filtering to the differential analysis.
DOI: 10.6084/m9.figshare.c.3608723_d3.v1
title: MOESM1 of A proteomic evaluation of urinary changes associated with cardiopulmonary bypass

description: Additional file 1: Table S1. The use of custom retention alignment peptides to map peptide retention times from 2D DDA/IDA runs into the SWATH extraction library, and their corresponding SWATH extracted retention times.
DOI: 10.6084/m9.figshare.c.3608732_d1.v1
title: MOESM6 of DAMe: a toolkit for the initial processing of datasets with PCR replicates of double-tagged amplicons for DNA metabarcoding analyses

description: Additional file 6. Taxonomic identification. This file contains the number of unique sequences from each identified taxon from sample pA1 from dataset 2.
DOI: 10.6084/m9.figshare.c.3608711_d4.v1
title: Additional file 9: of Heritable gene expression differences between apomictic clone members in Taraxacum officinale: Insights into early stages of evolutionary divergence in asexual plants

description: Read mapping statistics of the SNP analysis on the reference de novo transcriptome assembly per accession. (RTF 59Â kb)
DOI: 10.6084/m9.figshare.c.3608723_d4.v1
title: MOESM4 of A proteomic evaluation of urinary changes associated with cardiopulmonary bypass

description: Additional file 4: Table S4. Correlation filtered 2D DDA/IDA and SWATH protein difference values.
DOI: 10.6084/m9.figshare.c.3608711_d5.v1
title: Additional file 7: of Heritable gene expression differences between apomictic clone members in Taraxacum officinale: Insights into early stages of evolutionary divergence in asexual plants

description: Genes highly connected from overall differentially expressed greenhouse genes (67 genes); in grey, DEGs unique to greenhouse conditions (in white common in both experiments). Annotations and functions were retrieved from the TAIR website ( www.arabidopsis.org ). (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.c.3608741_d1.v1
title: Additional file 3: of Sudden death due to paralysis and synaptic and behavioral deficits when Hip14/Zdhhc17 is deleted in adult mice

description: One-way and two-way ANOVA values and replicates. (XLSX 40Â kb)
DOI: 10.6084/m9.figshare.c.3608744_d1.v1
title: MOESM2 of The effect of DNA extraction methodology on gut microbiota research applications

description: Additional file 2: Table S1. Sample raw data of read qualities and read lengths after each step of the pipeline and before OTUs construction.
DOI: 10.6084/m9.figshare.c.3608747_d1.v1
title: Additional file 1: Table S1. of A method for automated pathogenic content estimation with application to rheumatoid arthritis

description: Human bacteria pathogens in a Genus-Species table collected from six public database and manual searching, this table is integral to the eudysbiome package, reported here for convenience. (XLSX 73 kb)
DOI: 10.6084/m9.figshare.c.3608732_d3.v1
title: MOESM4 of DAMe: a toolkit for the initial processing of datasets with PCR replicates of double-tagged amplicons for DNA metabarcoding analyses

description: Additional file 4. RSI values. This file contains the RSI values from datasets 1 and 2.
DOI: 10.6084/m9.figshare.c.3608711_d6.v1
title: Additional file 2: of Heritable gene expression differences between apomictic clone members in Taraxacum officinale: Insights into early stages of evolutionary divergence in asexual plants

description: Mapping results of ERCC spike-in control and correlations with theoretical concentrations. (XLSX 62Â kb)
DOI: 10.6084/m9.figshare.c.3608741_d2.v1
title: Additional file 4 of Sudden death due to paralysis and synaptic and behavioral deficits when Hip14/Zdhhc17 is deleted in adult mice

description: Individual data values for experiments where N
DOI: 10.6084/m9.figshare.c.3608732_d4.v1
title: MOESM3 of DAMe: a toolkit for the initial processing of datasets with PCR replicates of double-tagged amplicons for DNA metabarcoding analyses

description: Additional file 3. Tag combinations. This file contains the copy number information of sequences carrying used and unused tag combinations from datasets 1 and 2.
DOI: 10.6084/m9.figshare.c.3608747_d2.v1
title: Additional file 3: Table S3. of A method for automated pathogenic content estimation with application to rheumatoid arthritis

description: Differential genera by comparison of NORA, UCRA, MTX, Prednisone with HLT arms. (XLSX 43 kb)
DOI: 10.6084/m9.figshare.c.3608711_d7.v1
title: Additional file 4: of Heritable gene expression differences between apomictic clone members in Taraxacum officinale: Insights into early stages of evolutionary divergence in asexual plants

description: Differentially expressed genes identified using DESeq, heritability index and annotations from SwissProt and Arabidopsis thaliana coding sequence databases for the greenhouse experiment. (XLSX 61Â kb)
DOI: 10.6084/m9.figshare.c.3608795_d1.v1
title: Additional file 1: Table S1. of Association between human leukocyte antigen class II and pulmonary tuberculosis due to mycobacterium tuberculosis in Uganda

description: Observed numbers and percentages of human leukocyte antigen Class II HLA-DRB and -DQB antigens in pulmonary TB patients compared to healthy controls. Description of data: Table comparing the observed numbers and the percentages of HLA Class II HLA-DRB and -DQB antigens in pulmonary TB patients and healthy controls. (XLS 32 kb)
DOI: 10.6084/m9.figshare.c.3608813_d1.v1
title: Additional file 2: of Cost analysis of tuberculin skin test and the QuantiFERON-TB Gold In-tube test for tuberculosis screening in a correctional setting in Dallas, Texas, USA

description: Final Cost Analysis Tree. This file contains the structure of the cost analysis tree used for this study, which assumes that repeat testing for LTBI screening is performed annually for individuals who are incarcerated more than once. (XLSX 53Â kb)
DOI: 10.6084/m9.figshare.c.3608807_d2.v1
title: Additional file 3: Table S3. of An advanced bioinformatics approach for analyzing RNA-seq data reveals sigma H-dependent regulation of competence genes in Listeria monocytogenes

description: Significant fragments found with the sliding window approach. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.c.3608807_d3.v1
title: Additional file 2: Table S2. of An advanced bioinformatics approach for analyzing RNA-seq data reveals sigma H-dependent regulation of competence genes in Listeria monocytogenes

description: Listeria genomes used for comparative analysis of SigmaH-dependent promoters. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3608873_d2.v1
title: Additional file 8: Table S6. of Preliminary analysis of Psoroptes ovis transcriptome in different developmental stages

description: DEGseq analysis results for DEGs. (XLSX 110Â kb)
DOI: 10.6084/m9.figshare.c.3608870_d3.v1
title: Additional file 5: of Wheat germ-based protein libraries for the functional characterisation of the Arabidopsis E2 ubiquitin conjugating enzymes and the RING-type E3 ubiquitin ligase enzymes

description: List of primers employed for RING domain mutagenesis. (XLSX 34 kb)
DOI: 10.6084/m9.figshare.c.3608870_d5.v1
title: Additional file 4: of Wheat germ-based protein libraries for the functional characterisation of the Arabidopsis E2 ubiquitin conjugating enzymes and the RING-type E3 ubiquitin ligase enzymes

description: List of primers employed for the construction of transcription templates for Arabidopsis E2s and RING protein. (XLSX 42 kb)
DOI: 10.6084/m9.figshare.c.3608873_d4.v1
title: Additional file 3: Table S3. of Preliminary analysis of Psoroptes ovis transcriptome in different developmental stages

description: The frequency distribution of splice length. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.c.3608888_d1.v1
title: Additional file 1: of Womenâ  s experience with home-based self-sampling for human papillomavirus testing

description: HPV Self-Sampling Survey. (ZIP 115 kb)
DOI: 10.6084/m9.figshare.c.3608873_d5.v1
title: Additional file 2: Table S2. of Preliminary analysis of Psoroptes ovis transcriptome in different developmental stages

description: The quality of transcriptome data. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.c.3608873_d6.v1
title: Additional file 13: Table S10. of Preliminary analysis of Psoroptes ovis transcriptome in different developmental stages

description: Allergen genes among the unigenes in the two developmental stages. (XLSX 83Â kb)
DOI: 10.6084/m9.figshare.c.3608900_d1.v1
title: Additional file 1 of A deformable template method for describing and averaging the anatomical variation of the human nasal cavity

description: Cross-sections for final UoA-UC geometry. File is a HDF5 data set containing cross-sectional slices for computed mean geometry. (H5 347kb)
DOI: 10.6084/m9.figshare.c.3608903_d1.v1
title: Additional file 2: of Pubertal development and prostate cancer risk: Mendelian randomization study in a population-based cohort

description: Summary data of the association of each SNP in the pubertal development genetic risk score with exposure and outcomes in the PRACTICAL consortium. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3608873_d13.v1
title: Additional file 17: Table S14. of Preliminary analysis of Psoroptes ovis transcriptome in different developmental stages

description: Allergen genes which did not result in Blast hits with genes from other mites or ticks among the upregulated DEGs. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.c.3608933_d1.v1
title: Additional file 2: of Complete genome sequence of and proposal of Thermofilum uzonense sp. nov. a novel hyperthermophilic crenarchaeon and emended description of the genus Thermofilum

description: Biosynthetic COGs. List of biosynthetic COGs among Thermofilum representatives with sequenced genomes. (XLSX 16 kb)