cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13988085
title: Supplementary file 5: Estimated variance and the genomic heritability of mRNA from Genetic regulation and heritability of miRNA and mRNA expression link to phosphorus utilization and gut microbiome

description: Improved utilization of phytates and mineral phosphorus (P) in monogastric animals contributes significantly to preserving the finite resource of mineral P and mitigating environmental pollution. In order to identify pathways and to prioritize candidate genes related to P-utilization (PU), the genomic heritability of 77 and 80 trait-dependent expressed miRNAs and mRNAs in 482 Japanese quail were estimated and eQTL (expression quantitative trait loci) were detected. In total, 104 miR-eQTL (microRNA expression quantitative traits loci) were associated with SNPs markers (false discovery rate (FDR) less than 10%) including 41 eQTL of eight miRNAs. Similarly, 944 mRNA-eQTL were identified at the 5% FDR threshold with 573 being cis-eQTL of 36 mRNAs. High heritabilities of miRNA and mRNA expression coincide with highly significant eQTL. Integration of phenotypic data with transcriptome and microbiome data of the same animals revealed genetic regulated mRNA and miRNA transcripts (SMAD3, CAV1, ENNPP6, ATP2B4, miR-148a-3p, miR-146b-5p, miR-16-5p, miR-194, miR-215-5p, miR-199-3p, miR-1388a-3p) and microbes (Candidatus Arthromitus, Enterococcus) that are associated with PU. The results reveal novel insights into the role of mRNAs and miRNAs in host gut tissue functions, which are involved in PU and other related traits, in terms of the genetic regulation and inheritance of their expression and in association with microbiota components.
DOI: 10.6084/m9.figshare.13988091.v1
title: Supplementary file 1: Primer sequences for miRNA qPCR from Genetic regulation and heritability of miRNA and mRNA expression link to phosphorus utilization and gut microbiome

description: Improved utilization of phytates and mineral phosphorus (P) in monogastric animals contributes significantly to preserving the finite resource of mineral P and mitigating environmental pollution. In order to identify pathways and to prioritize candidate genes related to P-utilization (PU), the genomic heritability of 77 and 80 trait-dependent expressed miRNAs and mRNAs in 482 Japanese quail were estimated and eQTL (expression quantitative trait loci) were detected. In total, 104 miR-eQTL (microRNA expression quantitative traits loci) were associated with SNPs markers (false discovery rate (FDR) less than 10%) including 41 eQTL of eight miRNAs. Similarly, 944 mRNA-eQTL were identified at the 5% FDR threshold with 573 being cis-eQTL of 36 mRNAs. High heritabilities of miRNA and mRNA expression coincide with highly significant eQTL. Integration of phenotypic data with transcriptome and microbiome data of the same animals revealed genetic regulated mRNA and miRNA transcripts (SMAD3, CAV1, ENNPP6, ATP2B4, miR-148a-3p, miR-146b-5p, miR-16-5p, miR-194, miR-215-5p, miR-199-3p, miR-1388a-3p) and microbes (Candidatus Arthromitus, Enterococcus) that are associated with PU. The results reveal novel insights into the role of mRNAs and miRNAs in host gut tissue functions, which are involved in PU and other related traits, in terms of the genetic regulation and inheritance of their expression and in association with microbiota components.
DOI: 10.6084/m9.figshare.13988088.v1
title: Supplementary file 9 from Genetic regulation and heritability of miRNA and mRNA expression link to phosphorus utilization and gut microbiome

description: Improved utilization of phytates and mineral phosphorus (P) in monogastric animals contributes significantly to preserving the finite resource of mineral P and mitigating environmental pollution. In order to identify pathways and to prioritize candidate genes related to P-utilization (PU), the genomic heritability of 77 and 80 trait-dependent expressed miRNAs and mRNAs in 482 Japanese quail were estimated and eQTL (expression quantitative trait loci) were detected. In total, 104 miR-eQTL (microRNA expression quantitative traits loci) were associated with SNPs markers (false discovery rate (FDR) less than 10%) including 41 eQTL of eight miRNAs. Similarly, 944 mRNA-eQTL were identified at the 5% FDR threshold with 573 being cis-eQTL of 36 mRNAs. High heritabilities of miRNA and mRNA expression coincide with highly significant eQTL. Integration of phenotypic data with transcriptome and microbiome data of the same animals revealed genetic regulated mRNA and miRNA transcripts (SMAD3, CAV1, ENNPP6, ATP2B4, miR-148a-3p, miR-146b-5p, miR-16-5p, miR-194, miR-215-5p, miR-199-3p, miR-1388a-3p) and microbes (Candidatus Arthromitus, Enterococcus) that are associated with PU. The results reveal novel insights into the role of mRNAs and miRNAs in host gut tissue functions, which are involved in PU and other related traits, in terms of the genetic regulation and inheritance of their expression and in association with microbiota components.
DOI: 10.6084/m9.figshare.13988091
title: Supplementary file 1: Primer sequences for miRNA qPCR from Genetic regulation and heritability of miRNA and mRNA expression link to phosphorus utilization and gut microbiome

description: Improved utilization of phytates and mineral phosphorus (P) in monogastric animals contributes significantly to preserving the finite resource of mineral P and mitigating environmental pollution. In order to identify pathways and to prioritize candidate genes related to P-utilization (PU), the genomic heritability of 77 and 80 trait-dependent expressed miRNAs and mRNAs in 482 Japanese quail were estimated and eQTL (expression quantitative trait loci) were detected. In total, 104 miR-eQTL (microRNA expression quantitative traits loci) were associated with SNPs markers (false discovery rate (FDR) less than 10%) including 41 eQTL of eight miRNAs. Similarly, 944 mRNA-eQTL were identified at the 5% FDR threshold with 573 being cis-eQTL of 36 mRNAs. High heritabilities of miRNA and mRNA expression coincide with highly significant eQTL. Integration of phenotypic data with transcriptome and microbiome data of the same animals revealed genetic regulated mRNA and miRNA transcripts (SMAD3, CAV1, ENNPP6, ATP2B4, miR-148a-3p, miR-146b-5p, miR-16-5p, miR-194, miR-215-5p, miR-199-3p, miR-1388a-3p) and microbes (Candidatus Arthromitus, Enterococcus) that are associated with PU. The results reveal novel insights into the role of mRNAs and miRNAs in host gut tissue functions, which are involved in PU and other related traits, in terms of the genetic regulation and inheritance of their expression and in association with microbiota components.
DOI: 10.6084/m9.figshare.13988094.v1
title: Supplementary file 10 from Genetic regulation and heritability of miRNA and mRNA expression link to phosphorus utilization and gut microbiome

description: Improved utilization of phytates and mineral phosphorus (P) in monogastric animals contributes significantly to preserving the finite resource of mineral P and mitigating environmental pollution. In order to identify pathways and to prioritize candidate genes related to P-utilization (PU), the genomic heritability of 77 and 80 trait-dependent expressed miRNAs and mRNAs in 482 Japanese quail were estimated and eQTL (expression quantitative trait loci) were detected. In total, 104 miR-eQTL (microRNA expression quantitative traits loci) were associated with SNPs markers (false discovery rate (FDR) less than 10%) including 41 eQTL of eight miRNAs. Similarly, 944 mRNA-eQTL were identified at the 5% FDR threshold with 573 being cis-eQTL of 36 mRNAs. High heritabilities of miRNA and mRNA expression coincide with highly significant eQTL. Integration of phenotypic data with transcriptome and microbiome data of the same animals revealed genetic regulated mRNA and miRNA transcripts (SMAD3, CAV1, ENNPP6, ATP2B4, miR-148a-3p, miR-146b-5p, miR-16-5p, miR-194, miR-215-5p, miR-199-3p, miR-1388a-3p) and microbes (Candidatus Arthromitus, Enterococcus) that are associated with PU. The results reveal novel insights into the role of mRNAs and miRNAs in host gut tissue functions, which are involved in PU and other related traits, in terms of the genetic regulation and inheritance of their expression and in association with microbiota components.
DOI: 10.6084/m9.figshare.13988088
title: Supplementary file 9 from Genetic regulation and heritability of miRNA and mRNA expression link to phosphorus utilization and gut microbiome

description: Improved utilization of phytates and mineral phosphorus (P) in monogastric animals contributes significantly to preserving the finite resource of mineral P and mitigating environmental pollution. In order to identify pathways and to prioritize candidate genes related to P-utilization (PU), the genomic heritability of 77 and 80 trait-dependent expressed miRNAs and mRNAs in 482 Japanese quail were estimated and eQTL (expression quantitative trait loci) were detected. In total, 104 miR-eQTL (microRNA expression quantitative traits loci) were associated with SNPs markers (false discovery rate (FDR) less than 10%) including 41 eQTL of eight miRNAs. Similarly, 944 mRNA-eQTL were identified at the 5% FDR threshold with 573 being cis-eQTL of 36 mRNAs. High heritabilities of miRNA and mRNA expression coincide with highly significant eQTL. Integration of phenotypic data with transcriptome and microbiome data of the same animals revealed genetic regulated mRNA and miRNA transcripts (SMAD3, CAV1, ENNPP6, ATP2B4, miR-148a-3p, miR-146b-5p, miR-16-5p, miR-194, miR-215-5p, miR-199-3p, miR-1388a-3p) and microbes (Candidatus Arthromitus, Enterococcus) that are associated with PU. The results reveal novel insights into the role of mRNAs and miRNAs in host gut tissue functions, which are involved in PU and other related traits, in terms of the genetic regulation and inheritance of their expression and in association with microbiota components.
DOI: 10.6084/m9.figshare.13988097
title: Supplementary file 7 from Genetic regulation and heritability of miRNA and mRNA expression link to phosphorus utilization and gut microbiome

description: Improved utilization of phytates and mineral phosphorus (P) in monogastric animals contributes significantly to preserving the finite resource of mineral P and mitigating environmental pollution. In order to identify pathways and to prioritize candidate genes related to P-utilization (PU), the genomic heritability of 77 and 80 trait-dependent expressed miRNAs and mRNAs in 482 Japanese quail were estimated and eQTL (expression quantitative trait loci) were detected. In total, 104 miR-eQTL (microRNA expression quantitative traits loci) were associated with SNPs markers (false discovery rate (FDR) less than 10%) including 41 eQTL of eight miRNAs. Similarly, 944 mRNA-eQTL were identified at the 5% FDR threshold with 573 being cis-eQTL of 36 mRNAs. High heritabilities of miRNA and mRNA expression coincide with highly significant eQTL. Integration of phenotypic data with transcriptome and microbiome data of the same animals revealed genetic regulated mRNA and miRNA transcripts (SMAD3, CAV1, ENNPP6, ATP2B4, miR-148a-3p, miR-146b-5p, miR-16-5p, miR-194, miR-215-5p, miR-199-3p, miR-1388a-3p) and microbes (Candidatus Arthromitus, Enterococcus) that are associated with PU. The results reveal novel insights into the role of mRNAs and miRNAs in host gut tissue functions, which are involved in PU and other related traits, in terms of the genetic regulation and inheritance of their expression and in association with microbiota components.
DOI: 10.6084/m9.figshare.13988094
title: Supplementary file 10 from Genetic regulation and heritability of miRNA and mRNA expression link to phosphorus utilization and gut microbiome

description: Improved utilization of phytates and mineral phosphorus (P) in monogastric animals contributes significantly to preserving the finite resource of mineral P and mitigating environmental pollution. In order to identify pathways and to prioritize candidate genes related to P-utilization (PU), the genomic heritability of 77 and 80 trait-dependent expressed miRNAs and mRNAs in 482 Japanese quail were estimated and eQTL (expression quantitative trait loci) were detected. In total, 104 miR-eQTL (microRNA expression quantitative traits loci) were associated with SNPs markers (false discovery rate (FDR) less than 10%) including 41 eQTL of eight miRNAs. Similarly, 944 mRNA-eQTL were identified at the 5% FDR threshold with 573 being cis-eQTL of 36 mRNAs. High heritabilities of miRNA and mRNA expression coincide with highly significant eQTL. Integration of phenotypic data with transcriptome and microbiome data of the same animals revealed genetic regulated mRNA and miRNA transcripts (SMAD3, CAV1, ENNPP6, ATP2B4, miR-148a-3p, miR-146b-5p, miR-16-5p, miR-194, miR-215-5p, miR-199-3p, miR-1388a-3p) and microbes (Candidatus Arthromitus, Enterococcus) that are associated with PU. The results reveal novel insights into the role of mRNAs and miRNAs in host gut tissue functions, which are involved in PU and other related traits, in terms of the genetic regulation and inheritance of their expression and in association with microbiota components.
DOI: 10.6084/m9.figshare.13988097.v1
title: Supplementary file 7 from Genetic regulation and heritability of miRNA and mRNA expression link to phosphorus utilization and gut microbiome

description: Improved utilization of phytates and mineral phosphorus (P) in monogastric animals contributes significantly to preserving the finite resource of mineral P and mitigating environmental pollution. In order to identify pathways and to prioritize candidate genes related to P-utilization (PU), the genomic heritability of 77 and 80 trait-dependent expressed miRNAs and mRNAs in 482 Japanese quail were estimated and eQTL (expression quantitative trait loci) were detected. In total, 104 miR-eQTL (microRNA expression quantitative traits loci) were associated with SNPs markers (false discovery rate (FDR) less than 10%) including 41 eQTL of eight miRNAs. Similarly, 944 mRNA-eQTL were identified at the 5% FDR threshold with 573 being cis-eQTL of 36 mRNAs. High heritabilities of miRNA and mRNA expression coincide with highly significant eQTL. Integration of phenotypic data with transcriptome and microbiome data of the same animals revealed genetic regulated mRNA and miRNA transcripts (SMAD3, CAV1, ENNPP6, ATP2B4, miR-148a-3p, miR-146b-5p, miR-16-5p, miR-194, miR-215-5p, miR-199-3p, miR-1388a-3p) and microbes (Candidatus Arthromitus, Enterococcus) that are associated with PU. The results reveal novel insights into the role of mRNAs and miRNAs in host gut tissue functions, which are involved in PU and other related traits, in terms of the genetic regulation and inheritance of their expression and in association with microbiota components.
DOI: 10.6084/m9.figshare.13988100
title: Supplementary file 3: Estimated variance and the genomic heritability of miRNA from Genetic regulation and heritability of miRNA and mRNA expression link to phosphorus utilization and gut microbiome

description: Improved utilization of phytates and mineral phosphorus (P) in monogastric animals contributes significantly to preserving the finite resource of mineral P and mitigating environmental pollution. In order to identify pathways and to prioritize candidate genes related to P-utilization (PU), the genomic heritability of 77 and 80 trait-dependent expressed miRNAs and mRNAs in 482 Japanese quail were estimated and eQTL (expression quantitative trait loci) were detected. In total, 104 miR-eQTL (microRNA expression quantitative traits loci) were associated with SNPs markers (false discovery rate (FDR) less than 10%) including 41 eQTL of eight miRNAs. Similarly, 944 mRNA-eQTL were identified at the 5% FDR threshold with 573 being cis-eQTL of 36 mRNAs. High heritabilities of miRNA and mRNA expression coincide with highly significant eQTL. Integration of phenotypic data with transcriptome and microbiome data of the same animals revealed genetic regulated mRNA and miRNA transcripts (SMAD3, CAV1, ENNPP6, ATP2B4, miR-148a-3p, miR-146b-5p, miR-16-5p, miR-194, miR-215-5p, miR-199-3p, miR-1388a-3p) and microbes (Candidatus Arthromitus, Enterococcus) that are associated with PU. The results reveal novel insights into the role of mRNAs and miRNAs in host gut tissue functions, which are involved in PU and other related traits, in terms of the genetic regulation and inheritance of their expression and in association with microbiota components.
DOI: 10.5281/zenodo.4534660
title: Datasets for "Recreating the Horizontal Magnetic Field at Colaba During the Carrington Event with Geospace Simulations", Blake et al. (2021), Space Weather

description: Sample datasets that appear in the 2021 paper "<strong><em>Recreating the Horizontal Magnetic Field at Colaba During the Carrington Event with Geospace Simulations</em></strong>", Blake et al. (2021), submitted to the AGU Space Weather Journal, DOI: TBD The complete SWMF simulation folders (including parameter and log files etc.) can be requested from NASA's Community Coordinated Modeling Center. ################################# <strong>Solar_Wind_Drivers/</strong> Both SWMF solar wind input files for Scenarios 1 and 2 referenced in the paper. These have the following columns: Year, Month, Day, Hour, Minute, Second, Milisecond, Bx(nT), By(nT), Bz(nT), Vx(km/s), Vy(km/s), Vz(km/s), n(cm^-3), T(K) <strong>#-----------------------------------------------------</strong> <strong>Digitised_Historical_Bfields/</strong> Contains digitised BH data minus baseline for: - Barnaul and St. Petersburg (taken from <em>Nevanlinna et al.</em> 2008, 10.5194/angeo-28-917-2010) - Rome (taken from <em>Blake et al.</em> 2020, 10.1029/2019JA027336) - Colaba (taken from Tsurutani et al. 2003, 10.1029/2002JA009504). These data were digitised using WebPlotDigitiser. <strong>#-----------------------------------------------------</strong> <strong>ScenarioX_Bdata.zip</strong> -Each zipped folder contains all of the SWMF calculated B-fields for the three Scenarios in the paper. Also included are log files (log* and geo*) containing calculated indices such as Dst. The times referenced are for 2019, but as described in the paper, conditions were changed to emulate 1859. <strong>#-----------------------------------------------------</strong> <strong>Scenario1_Magnetosphere3D_0630.out</strong> -Single SWMF 3D magnetosphere output file for 0630 GMT during Scenario 1. This data can be read and plotted using the pybats Python library. <strong>Scenario1_Ionosphere2D.tec</strong> -Single SWMF 2D ionosphere output for 0630 GMT during Scenario 1. <strong>#-----------------------------------------------------</strong>
DOI: 10.5281/zenodo.4534659
title: Datasets for "Recreating the Horizontal Magnetic Field at Colaba During the Carrington Event with Geospace Simulations", Blake et al. (2021), Space Weather

description: Sample datasets that appear in the 2021 paper "<strong><em>Recreating the Horizontal Magnetic Field at Colaba During the Carrington Event with Geospace Simulations</em></strong>", Blake et al. (2021), submitted to the AGU Space Weather Journal, DOI: TBD The complete SWMF simulation folders (including parameter and log files etc.) can be requested from NASA's Community Coordinated Modeling Center. ################################# <strong>Solar_Wind_Drivers/</strong> Both SWMF solar wind input files for Scenarios 1 and 2 referenced in the paper. These have the following columns: Year, Month, Day, Hour, Minute, Second, Milisecond, Bx(nT), By(nT), Bz(nT), Vx(km/s), Vy(km/s), Vz(km/s), n(cm^-3), T(K) <strong>#-----------------------------------------------------</strong> <strong>Digitised_Historical_Bfields/</strong> Contains digitised BH data minus baseline for: - Barnaul and St. Petersburg (taken from <em>Nevanlinna et al.</em> 2008, 10.5194/angeo-28-917-2010) - Rome (taken from <em>Blake et al.</em> 2020, 10.1029/2019JA027336) - Colaba (taken from Tsurutani et al. 2003, 10.1029/2002JA009504). These data were digitised using WebPlotDigitiser. <strong>#-----------------------------------------------------</strong> <strong>ScenarioX_Bdata.zip</strong> -Each zipped folder contains all of the SWMF calculated B-fields for the three Scenarios in the paper. Also included are log files (log* and geo*) containing calculated indices such as Dst. The times referenced are for 2019, but as described in the paper, conditions were changed to emulate 1859. <strong>#-----------------------------------------------------</strong> <strong>Scenario1_Magnetosphere3D_0630.out</strong> -Single SWMF 3D magnetosphere output file for 0630 GMT during Scenario 1. This data can be read and plotted using the pybats Python library. <strong>Scenario1_Ionosphere2D.tec</strong> -Single SWMF 2D ionosphere output for 0630 GMT during Scenario 1. <strong>#-----------------------------------------------------</strong>
DOI: 10.6084/m9.figshare.13988085.v1
title: Supplementary file 5: Estimated variance and the genomic heritability of mRNA from Genetic regulation and heritability of miRNA and mRNA expression link to phosphorus utilization and gut microbiome

description: Improved utilization of phytates and mineral phosphorus (P) in monogastric animals contributes significantly to preserving the finite resource of mineral P and mitigating environmental pollution. In order to identify pathways and to prioritize candidate genes related to P-utilization (PU), the genomic heritability of 77 and 80 trait-dependent expressed miRNAs and mRNAs in 482 Japanese quail were estimated and eQTL (expression quantitative trait loci) were detected. In total, 104 miR-eQTL (microRNA expression quantitative traits loci) were associated with SNPs markers (false discovery rate (FDR) less than 10%) including 41 eQTL of eight miRNAs. Similarly, 944 mRNA-eQTL were identified at the 5% FDR threshold with 573 being cis-eQTL of 36 mRNAs. High heritabilities of miRNA and mRNA expression coincide with highly significant eQTL. Integration of phenotypic data with transcriptome and microbiome data of the same animals revealed genetic regulated mRNA and miRNA transcripts (SMAD3, CAV1, ENNPP6, ATP2B4, miR-148a-3p, miR-146b-5p, miR-16-5p, miR-194, miR-215-5p, miR-199-3p, miR-1388a-3p) and microbes (Candidatus Arthromitus, Enterococcus) that are associated with PU. The results reveal novel insights into the role of mRNAs and miRNAs in host gut tissue functions, which are involved in PU and other related traits, in terms of the genetic regulation and inheritance of their expression and in association with microbiota components.