cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14434030
title: Additional file 5 of A genome-wide study of PDZ-domain interactions in C. elegans reveals a high frequency of non-canonical binding

description: Additional file 5:Verification of two-hybrid interacting pairs by co-immunoprecipitation. Additional file 5 contains four tables (S10 to S13) listing interacting proteins pairs tested and results. Supplemental Table S10 lists tested pairs involving PDZ domains and their respective two-hybrid identified interacting proteins possessing a free C-terminus. Supplemental Table S11 lists tested pairs involving PDZ domains and their respective two-hybrid identified interacting proteins using a B2 tailed construct. Supplemental Table S12 lists the 59 protein fragments that did not possess a C-terminal binding motif tested by co-immunoprecipitation in a C-terminally truncated form against their respective two hybrid interacting PDZs. Sequences where there was creation of a new C-terminal consensus sites after truncation are shown. Supplemental Table S13 lists the primers pairs used to amplify and clone truncated interacting protein fragments used in the co-immunoprecipitation experiment. (XLS 78 KB)
DOI: 10.6084/m9.figshare.14434021
title: Additional file 2 of A genome-wide study of PDZ-domain interactions in C. elegans reveals a high frequency of non-canonical binding

description: Additional file 2:PDZ domains cloning and annotations. Additional file 2 contains two tables (S1 and S2) listing for each PDZ domain identified, respectively the primer sequences and the Gene Ontology annotations. Supplemental Table S1: List of primers used to clone PDZ domains. Proteins names and IDs are given according to Wormbase WS150 [44]. For multiple PDZ domains in the same protein, a ".n" extension was added to the ID of the PDZ containing protein. This extension was numbered from the ATG (eg: F54E7.3.1 is the ID for the first PDZ domain of F54E7.3). When only one PDZ was present, protein ID was kept as such. Coordinates on PDZ domain containing proteins correspond to the splice form specified in the third column (PDZ domain containing protein ID). Each primer contains the B1 and B2 Gateway recombination cloning tail. Supplemental Table S2: Gene Ontology annotation based on experimental data for PDZ domains proteins. Gene ontology annotations were retrieved from Wormbase WS190 [16]. Experimental Evidence Codes: EXP: Inferred from Experiment, IDA: Inferred from Direct Assay, IPI: Inferred from Physical Interaction, IMP: Inferred from Mutant Phenotype, IGI: Inferred from Genetic Interaction, IEP: Inferred from Expression Pattern. (XLS 68 KB)
DOI: 10.6084/m9.figshare.14434027.v1
title: Additional file 4 of A genome-wide study of PDZ-domain interactions in C. elegans reveals a high frequency of non-canonical binding

description: Additional file 4:Functional annotation of interacting proteins. Additional file 4 contains three tables (S7 to S9) listing the functional annotations of the PDZ domain interacting proteins. Supplemental Table S7: Concise description, GO terms and KOG (EuKaryotic Orthologous Groups), for each interacting protein when available, retrieved from Wormbase WS 190 [16]; note that most attributes are inferred from electronic annotation. Experimental Evidence Codes: EXP: Inferred from Experiment, IDA: Inferred from Direct Assay, IPI: Inferred from Physical Interaction, IMP: Inferred from Mutant Phenotype, IGI: Inferred from Genetic Interaction, IEP: Inferred from Expression Pattern. Computational Analysis Evidence Codes: ISS: Inferred from Sequence or Structural Similarity, ISO: Inferred from Sequence Orthology, ISA: Inferred from Sequence Alignment, ISM: Inferred from Sequence Model, IGC: Inferred from Genomic Context, RCA: inferred from Reviewed Computational Analysis. Author Statement Evidence Codes: TAS: Traceable Author Statement, NAS: Non-traceable Author Statement. Curator Statement Evidence Codes: IC: Inferred by Curator, ND: No biological Data available. Automatically-assigned Evidence Codes: IEA: Inferred from Electronic Annotation. Supplemental Table S8: Classification of interacting proteins according to Cellular Components terms: integral to membrane, nucleus and other&unknown. Supplemental Table S9: Classification of interacting proteins according to Biological Processes: manual curation of annotations retrieved from Wormbase WS190 were used to define the 11 groups of processes shown in Figure 2. (XLS 366 KB)
DOI: 10.6084/m9.figshare.14434030.v1
title: Additional file 5 of A genome-wide study of PDZ-domain interactions in C. elegans reveals a high frequency of non-canonical binding

description: Additional file 5:Verification of two-hybrid interacting pairs by co-immunoprecipitation. Additional file 5 contains four tables (S10 to S13) listing interacting proteins pairs tested and results. Supplemental Table S10 lists tested pairs involving PDZ domains and their respective two-hybrid identified interacting proteins possessing a free C-terminus. Supplemental Table S11 lists tested pairs involving PDZ domains and their respective two-hybrid identified interacting proteins using a B2 tailed construct. Supplemental Table S12 lists the 59 protein fragments that did not possess a C-terminal binding motif tested by co-immunoprecipitation in a C-terminally truncated form against their respective two hybrid interacting PDZs. Sequences where there was creation of a new C-terminal consensus sites after truncation are shown. Supplemental Table S13 lists the primers pairs used to amplify and clone truncated interacting protein fragments used in the co-immunoprecipitation experiment. (XLS 78 KB)
DOI: 10.6084/m9.figshare.14178397
title: Mine-site derived particulate matter exposure exacerbates neurological and pulmonary inflammatory outcomes in an autoimmune mouse model

description: The Southwestern United States has a legacy of industrial mining due to the presence of rich mineral ore deposits. The relationship between environmental inhaled particulate matter (PM) exposures and neurological outcomes within an autoimmune context is understudied. The aim of this study was to compare two regionally-relevant dusts from high-priority abandoned mine-sites, Claim 28 PM, from Blue Gap Tachee, AZ and St. Anthony mine PM, from the Pueblo of Laguna, NM and to expose autoimmune-prone mice (NZBWF1/J). Mice were randomly assigned to one of three groups (n = 8/group): DM (dispersion media, control), Claim 28 PM, or St. Anthony PM, subjected to oropharyngeal aspiration of (100 µg/50 µl), once per week for a total of 4 consecutive doses. A battery of immunological and neurological endpoints was assessed at 24 weeks of age including: bronchoalveolar lavage cell counts, lung gene expression, brain immunohistochemistry, behavioral tasks and serum autoimmune biomarkers. Bronchoalveolar lavage results demonstrated a significant increase in number of polymorphonuclear neutrophils following Claim 28 and St. Anthony mine PM aspiration. Lung mRNA expression showed significant upregulation in CCL-2 and IL-1ß following St. Anthony mine PM aspiration. In addition, neuroinflammation was present in both Claim 28 and St. Anthony mine-site derived PM exposure groups. Behavioral tasks resulted in significant deficits as determined by Y-maze new arm frequency following Claim 28 aspiration. Neutrophil elastase was significantly upregulated in the St. Anthony mine exposure group. Interestingly, there were no significant changes in serum autoantigens suggesting systemic inflammatory effects may be mediated through other molecular mechanisms following low-dose PM exposures.
DOI: 10.6084/m9.figshare.14178397.v1
title: Mine-site derived particulate matter exposure exacerbates neurological and pulmonary inflammatory outcomes in an autoimmune mouse model

description: The Southwestern United States has a legacy of industrial mining due to the presence of rich mineral ore deposits. The relationship between environmental inhaled particulate matter (PM) exposures and neurological outcomes within an autoimmune context is understudied. The aim of this study was to compare two regionally-relevant dusts from high-priority abandoned mine-sites, Claim 28 PM, from Blue Gap Tachee, AZ and St. Anthony mine PM, from the Pueblo of Laguna, NM and to expose autoimmune-prone mice (NZBWF1/J). Mice were randomly assigned to one of three groups (n = 8/group): DM (dispersion media, control), Claim 28 PM, or St. Anthony PM, subjected to oropharyngeal aspiration of (100 µg/50 µl), once per week for a total of 4 consecutive doses. A battery of immunological and neurological endpoints was assessed at 24 weeks of age including: bronchoalveolar lavage cell counts, lung gene expression, brain immunohistochemistry, behavioral tasks and serum autoimmune biomarkers. Bronchoalveolar lavage results demonstrated a significant increase in number of polymorphonuclear neutrophils following Claim 28 and St. Anthony mine PM aspiration. Lung mRNA expression showed significant upregulation in CCL-2 and IL-1ß following St. Anthony mine PM aspiration. In addition, neuroinflammation was present in both Claim 28 and St. Anthony mine-site derived PM exposure groups. Behavioral tasks resulted in significant deficits as determined by Y-maze new arm frequency following Claim 28 aspiration. Neutrophil elastase was significantly upregulated in the St. Anthony mine exposure group. Interestingly, there were no significant changes in serum autoantigens suggesting systemic inflammatory effects may be mediated through other molecular mechanisms following low-dose PM exposures.
DOI: 10.6084/m9.figshare.14434321.v10
title: Additional file of Skeletal muscle gene expression in response to resistance exercise: sex specific regulation

description: Additional file of Skeletal muscle gene expression in response to resistance exercise: sex specific regulation
DOI: 10.6084/m9.figshare.14434312
title: Additional file 7 of Skeletal muscle gene expression in response to resistance exercise: sex specific regulation

description: Additional file 7: Table S7: Key genes involved in RE-induced transcriptional regulation in male and female biceps branchii. (XLSX 57 KB)
DOI: 10.6084/m9.figshare.14434312.v1
title: Additional file 7 of Skeletal muscle gene expression in response to resistance exercise: sex specific regulation

description: Additional file 7: Table S7: Key genes involved in RE-induced transcriptional regulation in male and female biceps branchii. (XLSX 57 KB)
DOI: 10.6084/m9.figshare.14434339.v1
title: Additional file of Comparative analyses of vertebrate posterior HoxD clusters reveal atypical cluster architecture in the caecilian Typhlonectes natans

description: Additional file of Comparative analyses of vertebrate posterior HoxD clusters reveal atypical cluster architecture in the caecilian Typhlonectes natans
DOI: 10.6084/m9.figshare.14434324.v1
title: Additional file 1 of Comparative analyses of vertebrate posterior HoxD clusters reveal atypical cluster architecture in the caecilian Typhlonectes natans

description: Additional file 1: Summary of the conserved sequences in vertebrate Hox clusters. This table gives an overview of the positions of the coding regions in the vertebrate sequences as well as all footprint positions identified by the tracker software. The footprints are named fp1 to fp33, and footprints that are expressed in at least two species are indicated in bold. (XLS 26 KB)
DOI: 10.6084/m9.figshare.14434327
title: Additional file 2 of Comparative analyses of vertebrate posterior HoxD clusters reveal atypical cluster architecture in the caecilian Typhlonectes natans

description: Additional file 2: EST blast hits of expressed footprints. All ESTs that correspond to the expressed footprints are given with Genbank accession number, species name and tissue source. (XLS 22 KB)
DOI: 10.6084/m9.figshare.14434327.v1
title: Additional file 2 of Comparative analyses of vertebrate posterior HoxD clusters reveal atypical cluster architecture in the caecilian Typhlonectes natans

description: Additional file 2: EST blast hits of expressed footprints. All ESTs that correspond to the expressed footprints are given with Genbank accession number, species name and tissue source. (XLS 22 KB)
DOI: 10.6084/m9.figshare.14434339.v2
title: Additional file of Comparative analyses of vertebrate posterior HoxD clusters reveal atypical cluster architecture in the caecilian Typhlonectes natans

description: Additional file of Comparative analyses of vertebrate posterior HoxD clusters reveal atypical cluster architecture in the caecilian Typhlonectes natans
DOI: 10.6084/m9.figshare.14434324
title: Additional file 1 of Comparative analyses of vertebrate posterior HoxD clusters reveal atypical cluster architecture in the caecilian Typhlonectes natans

description: Additional file 1: Summary of the conserved sequences in vertebrate Hox clusters. This table gives an overview of the positions of the coding regions in the vertebrate sequences as well as all footprint positions identified by the tracker software. The footprints are named fp1 to fp33, and footprints that are expressed in at least two species are indicated in bold. (XLS 26 KB)
DOI: 10.6084/m9.figshare.14434408.v4
title: Additional file of Bovine proteins containing poly-glutamine repeats are often polymorphic and enriched for components of transcriptional regulatory complexes

description: Additional file of Bovine proteins containing poly-glutamine repeats are often polymorphic and enriched for components of transcriptional regulatory complexes
DOI: 10.6084/m9.figshare.14434408.v7
title: Additional file of Bovine proteins containing poly-glutamine repeats are often polymorphic and enriched for components of transcriptional regulatory complexes

description: Additional file of Bovine proteins containing poly-glutamine repeats are often polymorphic and enriched for components of transcriptional regulatory complexes
DOI: 10.6084/m9.figshare.14434381.v1
title: Additional file 1 of Bovine proteins containing poly-glutamine repeats are often polymorphic and enriched for components of transcriptional regulatory complexes

description: Additional file 1:Bovine poly-Q encoding genes. This file contains details of the bovine poly-Q encoding genes including gene symbols, gene and protein accessions, GLEAN5 accessions [19], the number, sizes and purities of poly-Q tracts encoded in each gene and corresponding annotation information for human orthologs. The reciprocal mapping highlighted human orthologs that map to more than one GLEAN5 model which may represent local assembly issues in the bovine genome assembly, incomplete gene models or inability to discriminate between paralogs. Also included are multiple accessions for some bovine genes which are used to discriminate between splice variants. Bovine genes containing poly-Q tracts that were not present in their human or murine orthologs are bolded. The purity of each tract was defined by a combination of G (for CAG) or A (for CAA) symbols followed by numbers. Genes that were assessed for polymorphic variation in the large cattle diversity panel are also listed with the number of identified alleles. (XLS 70 KB)
DOI: 10.6084/m9.figshare.14434381
title: Additional file 1 of Bovine proteins containing poly-glutamine repeats are often polymorphic and enriched for components of transcriptional regulatory complexes

description: Additional file 1:Bovine poly-Q encoding genes. This file contains details of the bovine poly-Q encoding genes including gene symbols, gene and protein accessions, GLEAN5 accessions [19], the number, sizes and purities of poly-Q tracts encoded in each gene and corresponding annotation information for human orthologs. The reciprocal mapping highlighted human orthologs that map to more than one GLEAN5 model which may represent local assembly issues in the bovine genome assembly, incomplete gene models or inability to discriminate between paralogs. Also included are multiple accessions for some bovine genes which are used to discriminate between splice variants. Bovine genes containing poly-Q tracts that were not present in their human or murine orthologs are bolded. The purity of each tract was defined by a combination of G (for CAG) or A (for CAA) symbols followed by numbers. Genes that were assessed for polymorphic variation in the large cattle diversity panel are also listed with the number of identified alleles. (XLS 70 KB)
DOI: 10.6084/m9.figshare.14434390
title: Additional file 4 of Bovine proteins containing poly-glutamine repeats are often polymorphic and enriched for components of transcriptional regulatory complexes

description: Additional file 4:Functional clustering of bovine poly-Q encoding genes. Summary table listing enriched Functional Annotation Clusters and functional terms significantly associated with the bovine poly-Q encoding genes. The analysis was performed using DAVID analysis tools [26]. The conservative high stringency option was elected. P-values were corrected for multiple testing using the Benjamini correction. The enrichment score for a Functional Annotation Cluster is the -log (geometric mean of the term P-values within the cluster). An enrichment score ≥1.3 was considered significant. (XLS 72 KB)
DOI: 10.6084/m9.figshare.14434390.v1
title: Additional file 4 of Bovine proteins containing poly-glutamine repeats are often polymorphic and enriched for components of transcriptional regulatory complexes

description: Additional file 4:Functional clustering of bovine poly-Q encoding genes. Summary table listing enriched Functional Annotation Clusters and functional terms significantly associated with the bovine poly-Q encoding genes. The analysis was performed using DAVID analysis tools [26]. The conservative high stringency option was elected. P-values were corrected for multiple testing using the Benjamini correction. The enrichment score for a Functional Annotation Cluster is the -log (geometric mean of the term P-values within the cluster). An enrichment score ≥1.3 was considered significant. (XLS 72 KB)
DOI: 10.6084/m9.figshare.14434426.v1
title: Additional file of Transcriptome analysis of a barley breeding program examines gene expression diversity and reveals target genes for malting quality improvement

description: Additional file of Transcriptome analysis of a barley breeding program examines gene expression diversity and reveals target genes for malting quality improvement
DOI: 10.6084/m9.figshare.14434411
title: Additional file 1 of Transcriptome analysis of a barley breeding program examines gene expression diversity and reveals target genes for malting quality improvement

description: Additional file 1:Prior malting quality data for the fifteen barley genotypes. Data were collected from five field trials conducted in Minnesota in 2002 and 2003 (data previously published in [13]). (XLS 27 KB)
DOI: 10.6084/m9.figshare.14434426.v3
title: Additional file of Transcriptome analysis of a barley breeding program examines gene expression diversity and reveals target genes for malting quality improvement

description: Additional file of Transcriptome analysis of a barley breeding program examines gene expression diversity and reveals target genes for malting quality improvement
DOI: 10.6084/m9.figshare.14434417.v1
title: Additional file 3 of Transcriptome analysis of a barley breeding program examines gene expression diversity and reveals target genes for malting quality improvement

description: Additional file 3:Quality-related genes whose expression was fixed through the breeding process. Differentially expressed genes only between the "older" lines that are correlated with any of the six malting quality traits. Significant correlations for each of the six quality-assurance parameters are shown (*: p &lt; 0.05, **: p &lt; 0.01 and ***: p &lt; 0.001), together with the sign of the correlation (+: positive correlation, -: negative correlation). Bold type indicates common genes to both time points. (XLS 394 KB)
DOI: 10.6084/m9.figshare.14434411.v1
title: Additional file 1 of Transcriptome analysis of a barley breeding program examines gene expression diversity and reveals target genes for malting quality improvement

description: Additional file 1:Prior malting quality data for the fifteen barley genotypes. Data were collected from five field trials conducted in Minnesota in 2002 and 2003 (data previously published in [13]). (XLS 27 KB)
DOI: 10.6084/m9.figshare.14434417
title: Additional file 3 of Transcriptome analysis of a barley breeding program examines gene expression diversity and reveals target genes for malting quality improvement

description: Additional file 3:Quality-related genes whose expression was fixed through the breeding process. Differentially expressed genes only between the "older" lines that are correlated with any of the six malting quality traits. Significant correlations for each of the six quality-assurance parameters are shown (*: p &lt; 0.05, **: p &lt; 0.01 and ***: p &lt; 0.001), together with the sign of the correlation (+: positive correlation, -: negative correlation). Bold type indicates common genes to both time points. (XLS 394 KB)
DOI: 10.6084/m9.figshare.14434468.v5
title: Additional file of Independent evolution of the core and accessory gene sets in the genus Neisseria: insights gained from the genome of Neisseria lactamica isolate 020-06

description: Additional file of Independent evolution of the core and accessory gene sets in the genus Neisseria: insights gained from the genome of Neisseria lactamica isolate 020-06
DOI: 10.6084/m9.figshare.14434498.v2
title: Additional file of LAB-Secretome: a genome-scale comparative analysis of the predicted extracellular and surface-associated proteins of Lactic Acid Bacteria

description: Additional file of LAB-Secretome: a genome-scale comparative analysis of the predicted extracellular and surface-associated proteins of Lactic Acid Bacteria
DOI: 10.6084/m9.figshare.14434498.v4
title: Additional file of LAB-Secretome: a genome-scale comparative analysis of the predicted extracellular and surface-associated proteins of Lactic Acid Bacteria

description: Additional file of LAB-Secretome: a genome-scale comparative analysis of the predicted extracellular and surface-associated proteins of Lactic Acid Bacteria
DOI: 10.6084/m9.figshare.14434498.v3
title: Additional file of LAB-Secretome: a genome-scale comparative analysis of the predicted extracellular and surface-associated proteins of Lactic Acid Bacteria

description: Additional file of LAB-Secretome: a genome-scale comparative analysis of the predicted extracellular and surface-associated proteins of Lactic Acid Bacteria
DOI: 10.6084/m9.figshare.14434471
title: Additional file 1 of LAB-Secretome: a genome-scale comparative analysis of the predicted extracellular and surface-associated proteins of Lactic Acid Bacteria

description: Additional file 1:The overview of LAB-Secretome. Sheet S1: an overview of secretomes included in this research; sheet S2: the presence and absence patterns of the LaCOGs in 26 LAB genomes; sheet S3: the ubiquitous LaCOGs; sheet S4: the niche-specific LaCOGs; sheet S5: the species-specific LaCOGs; sheet S6: the ORFans; S7: the proteins with only distant homologs. (XLS 343 KB)
DOI: 10.6084/m9.figshare.14434498.v1
title: Additional file of LAB-Secretome: a genome-scale comparative analysis of the predicted extracellular and surface-associated proteins of Lactic Acid Bacteria

description: Additional file of LAB-Secretome: a genome-scale comparative analysis of the predicted extracellular and surface-associated proteins of Lactic Acid Bacteria
DOI: 10.6084/m9.figshare.14434471.v1
title: Additional file 1 of LAB-Secretome: a genome-scale comparative analysis of the predicted extracellular and surface-associated proteins of Lactic Acid Bacteria

description: Additional file 1:The overview of LAB-Secretome. Sheet S1: an overview of secretomes included in this research; sheet S2: the presence and absence patterns of the LaCOGs in 26 LAB genomes; sheet S3: the ubiquitous LaCOGs; sheet S4: the niche-specific LaCOGs; sheet S5: the species-specific LaCOGs; sheet S6: the ORFans; S7: the proteins with only distant homologs. (XLS 343 KB)