cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6254435.v1
title: Additional file 4: of Functional signaling and gene regulatory networks between the oocyte and the surrounding cumulus cells

description: Annotation of the 14,011 Ensembl pairs of genes corresponding to potential ligand-receptor or receptor-receptor interactions between oocytes and cumulus cells. Table containing Ensembl identifiers, expression levels and annotation of genes corresponding to potential ligand-receptor or receptor-receptor interactions between oocytes and cumulus cells. (XLSX 1381 kb)
DOI: 10.6084/m9.figshare.6254429
title: Additional file 3: of Recently evolved human-specific methylated regionsÂ are enriched in schizophrenia signals

description: Annotation of enriched DMRs with genes, promoters, CpG islands and enhancers. This file contains detailed annotation of those human-lineage specific DMRs that are enriched for association with schizophrenia markers (except those in the MHC region). Compared to Additional file 2, these DMRs represent those that are enriched and whether they are present in any genes, promoters, enhancers or CpG islands. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.6254429.v1
title: Additional file 3: of Recently evolved human-specific methylated regionsÂ are enriched in schizophrenia signals

description: Annotation of enriched DMRs with genes, promoters, CpG islands and enhancers. This file contains detailed annotation of those human-lineage specific DMRs that are enriched for association with schizophrenia markers (except those in the MHC region). Compared to Additional file 2, these DMRs represent those that are enriched and whether they are present in any genes, promoters, enhancers or CpG islands. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.6254414
title: Additional file 3: of Functional signaling and gene regulatory networks between the oocyte and the surrounding cumulus cells

description: Tables S1-S13. Supplementary Tables to Functional signaling and gene regulatory networks between the oocyte and the surrounding cumulus cell. (XLSX 110 kb)
DOI: 10.6084/m9.figshare.6254414.v1
title: Additional file 3: of Functional signaling and gene regulatory networks between the oocyte and the surrounding cumulus cells

description: Tables S1-S13. Supplementary Tables to Functional signaling and gene regulatory networks between the oocyte and the surrounding cumulus cell. (XLSX 110 kb)
DOI: 10.6084/m9.figshare.6254402
title: Additional file 2: of Recently evolved human-specific methylated regionsÂ are enriched in schizophrenia signals

description: Annotation of all DMRs with schizophrenia-associated SNPs. This file contains annotation of all the human-lineage specific DMRs that are associated with schizophrenia markers. Details of the various markers present within each DMR is provided, along with the marker with most significant p-value. (XLSX 263 kb)
DOI: 10.6084/m9.figshare.6254402.v1
title: Additional file 2: of Recently evolved human-specific methylated regionsÂ are enriched in schizophrenia signals

description: Annotation of all DMRs with schizophrenia-associated SNPs. This file contains annotation of all the human-lineage specific DMRs that are associated with schizophrenia markers. Details of the various markers present within each DMR is provided, along with the marker with most significant p-value. (XLSX 263 kb)
DOI: 10.6084/m9.figshare.6254393
title: Additional file 2: of Functional signaling and gene regulatory networks between the oocyte and the surrounding cumulus cells

description: List of genes specifically expressed in oocytes and cumulus cells. Four spreadsheets containing genes specifically expressed in oocytes, inner CCs, outerCC and CCs, average FPKM, and Ensembl annotation. (XLSX 314 kb)
DOI: 10.6084/m9.figshare.6254393.v1
title: Additional file 2: of Functional signaling and gene regulatory networks between the oocyte and the surrounding cumulus cells

description: List of genes specifically expressed in oocytes and cumulus cells. Four spreadsheets containing genes specifically expressed in oocytes, inner CCs, outerCC and CCs, average FPKM, and Ensembl annotation. (XLSX 314 kb)
DOI: 10.6084/m9.figshare.6254333
title: MOESM4 of A Pseudomonas putida efflux pump acts on short-chain alcohols

description: Additional file 4. Quantification of extracellular n-butanol using GC-FID. The spreadsheet contains the estimated fraction of viable cells after incubation in PBS containing 0.2 and 1% n-butanol, and the measurement values of quantified extracellular n-butanol in induced (ttgABC + ) and non-induced strains (ttgABC - ). The original readings for n-butanol and the internal standard isoprenol are shown, as well as the n-butanol measurements normalized by the standard, and the derived concentrations as volume per volume and milligrams per milliliter. The inlay shows the n-butanol standard curve, indicating that concentrations are in a linear measurement range.
DOI: 10.6084/m9.figshare.6254333.v1
title: MOESM4 of A Pseudomonas putida efflux pump acts on short-chain alcohols

description: Additional file 4. Quantification of extracellular n-butanol using GC-FID. The spreadsheet contains the estimated fraction of viable cells after incubation in PBS containing 0.2 and 1% n-butanol, and the measurement values of quantified extracellular n-butanol in induced (ttgABC + ) and non-induced strains (ttgABC - ). The original readings for n-butanol and the internal standard isoprenol are shown, as well as the n-butanol measurements normalized by the standard, and the derived concentrations as volume per volume and milligrams per milliliter. The inlay shows the n-butanol standard curve, indicating that concentrations are in a linear measurement range.
DOI: 10.6084/m9.figshare.6254291
title: Additional file 9: of Analysis of the canid Y-chromosome phylogeny using short-read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs

description: Table S4. Diagnostic mutations for each major branch. (XLS 132 kb)
DOI: 10.6084/m9.figshare.6254291.v1
title: Additional file 9: of Analysis of the canid Y-chromosome phylogeny using short-read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs

description: Table S4. Diagnostic mutations for each major branch. (XLS 132 kb)
DOI: 10.6084/m9.figshare.6254285
title: Additional file 5 of Additional oxidative stress reroutes the global response of Aspergillus fumigatus to iron depletion

description: Results of RT-qPCR measurements. Relative transcription levels were quantified with ΔΔCP = ΔCPtreated – ΔCPcontrol. ΔCPtreated = CPreference gene - CPtested gene measured from treated cultures. ΔCPcontrol = CPreference gene - CPtested gene measured from control cultures or from the iron depleted cultures. CP values stand for the qRT-PCR cycle numbers of crossing points. The fks1 gene was used as reference gene. qRT-PCR data are presented as the mean and S.D. data calculated from three measurements. Significantly higher or lower than 0 ΔΔCP values (up- or down-regulated gene) are marked with red and blue colors, respectively (Student’s t-test, p
DOI: 10.6084/m9.figshare.6254285.v1
title: Additional file 5 of Additional oxidative stress reroutes the global response of Aspergillus fumigatus to iron depletion

description: Results of RT-qPCR measurements. Relative transcription levels were quantified with ΔΔCP = ΔCPtreated – ΔCPcontrol. ΔCPtreated = CPreference gene - CPtested gene measured from treated cultures. ΔCPcontrol = CPreference gene - CPtested gene measured from control cultures or from the iron depleted cultures. CP values stand for the qRT-PCR cycle numbers of crossing points. The fks1 gene was used as reference gene. qRT-PCR data are presented as the mean and S.D. data calculated from three measurements. Significantly higher or lower than 0 ΔΔCP values (up- or down-regulated gene) are marked with red and blue colors, respectively (Student’s t-test, p
DOI: 10.6084/m9.figshare.6254273
title: Additional file 4: of Additional oxidative stress reroutes the global response of Aspergillus fumigatus to iron depletion

description: Regulation of secondary metabolite cluster genes and proteins. Up- and down-regulated genes and proteins were defined in the Materials and methods section and were marked with red and blue colors, respectively. Figures represent log2FC values, whereby FC is short for “fold-change”. The FC ratios were calculated for the transcriptome data based on FPKM values and for the proteome data based on iTRAQ reporter ion intensities. Results of gene/protein enrichment analysis (Fisher’s exact test) are also enclosed. (XLS 116 kb)
DOI: 10.6084/m9.figshare.6254273.v1
title: Additional file 4: of Additional oxidative stress reroutes the global response of Aspergillus fumigatus to iron depletion

description: Regulation of secondary metabolite cluster genes and proteins. Up- and down-regulated genes and proteins were defined in the Materials and methods section and were marked with red and blue colors, respectively. Figures represent log2FC values, whereby FC is short for “fold-change”. The FC ratios were calculated for the transcriptome data based on FPKM values and for the proteome data based on iTRAQ reporter ion intensities. Results of gene/protein enrichment analysis (Fisher’s exact test) are also enclosed. (XLS 116 kb)
DOI: 10.6084/m9.figshare.6254267
title: Additional file 8: of Analysis of the canid Y-chromosome phylogeny using short-read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs

description: Y-chromosome SNV genotypes. (GZ 35059 kb)
DOI: 10.6084/m9.figshare.6254267.v1
title: Additional file 8: of Analysis of the canid Y-chromosome phylogeny using short-read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs

description: Y-chromosome SNV genotypes. (GZ 35059 kb)
DOI: 10.6084/m9.figshare.6254264
title: Additional file 3: of Low-abundant bacteria drive compositional changes in the gut microbiota after dietary alteration

description: Complete taxonomy table. Rarified (18,000 sequences) taxonomy table used in this study. (XLSX 219Â kb)
DOI: 10.6084/m9.figshare.6254264.v1
title: Additional file 3: of Low-abundant bacteria drive compositional changes in the gut microbiota after dietary alteration

description: Complete taxonomy table. Rarified (18,000 sequences) taxonomy table used in this study. (XLSX 219Â kb)
DOI: 10.6084/m9.figshare.6254261
title: Additional file 3: of Additional oxidative stress reroutes the global response of Aspergillus fumigatus to iron depletion

description: Regulation of certain gene/protein groups. Up- and down-regulated genes and proteins were defined in the Materials and methods section and were marked with red and blue colors, respectively. Figures represent log2FC values, whereby FC is short for “fold-change”. The FC ratios were calculated for the transcriptome data based on FPKM values and for the proteome data based on iTRAQ reporter ion intensities. Results of gene/protein enrichment analysis (Fisher’s exact test) are also enclosed. (XLS 210 kb)
DOI: 10.6084/m9.figshare.6254261.v1
title: Additional file 3: of Additional oxidative stress reroutes the global response of Aspergillus fumigatus to iron depletion

description: Regulation of certain gene/protein groups. Up- and down-regulated genes and proteins were defined in the Materials and methods section and were marked with red and blue colors, respectively. Figures represent log2FC values, whereby FC is short for “fold-change”. The FC ratios were calculated for the transcriptome data based on FPKM values and for the proteome data based on iTRAQ reporter ion intensities. Results of gene/protein enrichment analysis (Fisher’s exact test) are also enclosed. (XLS 210 kb)
DOI: 10.6084/m9.figshare.6254246
title: Additional file 2: of Low-abundant bacteria drive compositional changes in the gut microbiota after dietary alteration

description: 16S rRNA gene sequencing OTU table. The Qiime generated OTU table for the samples used in this study. (XLSX 663Â kb)
DOI: 10.6084/m9.figshare.6254246.v1
title: Additional file 2: of Low-abundant bacteria drive compositional changes in the gut microbiota after dietary alteration

description: 16S rRNA gene sequencing OTU table. The Qiime generated OTU table for the samples used in this study. (XLSX 663Â kb)
DOI: 10.6084/m9.figshare.6254243
title: Additional file 2: of Additional oxidative stress reroutes the global response of Aspergillus fumigatus to iron depletion

description: Gene/protein enrichment analysis. Significant shared GO, FunCat or KEGG pathway terms were determined with AspGD Gene Ontology Term Finder ( http://www.aspergillusgenome.org/cgi-bin/GO/goTermFinder ) or FungiFun2 ( https://elbe.hki-jena.de/fungifun/fungifun.php ). Terms highlighted with yellow are presented in Tables 2 and 3. (XLS 790 kb)
DOI: 10.6084/m9.figshare.6254243.v1
title: Additional file 2: of Additional oxidative stress reroutes the global response of Aspergillus fumigatus to iron depletion

description: Gene/protein enrichment analysis. Significant shared GO, FunCat or KEGG pathway terms were determined with AspGD Gene Ontology Term Finder ( http://www.aspergillusgenome.org/cgi-bin/GO/goTermFinder ) or FungiFun2 ( https://elbe.hki-jena.de/fungifun/fungifun.php ). Terms highlighted with yellow are presented in Tables 2 and 3. (XLS 790 kb)
DOI: 10.6084/m9.figshare.6254231
title: Additional file 1: of Low-abundant bacteria drive compositional changes in the gut microbiota after dietary alteration

description: Control samples for 16S rRNA gene sequencing. A Qiime generated OTU table for the positive and negative controls used in the 16S rRNA gene sequencing portion of the manuscript. (XLSX 98Â kb)
DOI: 10.6084/m9.figshare.6254231.v1
title: Additional file 1: of Low-abundant bacteria drive compositional changes in the gut microbiota after dietary alteration

description: Control samples for 16S rRNA gene sequencing. A Qiime generated OTU table for the positive and negative controls used in the 16S rRNA gene sequencing portion of the manuscript. (XLSX 98Â kb)
DOI: 10.6084/m9.figshare.6254210
title: Additional file 4: of Analysis of the canid Y-chromosome phylogeny using short-read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs

description: Table S3. Amplicon coordinates. (XLS 32 kb)
DOI: 10.6084/m9.figshare.6254210.v1
title: Additional file 4: of Analysis of the canid Y-chromosome phylogeny using short-read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs

description: Table S3. Amplicon coordinates. (XLS 32 kb)
DOI: 10.7284/109540
title: GNSS (Global Navigation Satellite System) data collected during research cruise MV1213 using a Ashtech ADU2 instrument system onboard the platform RV Melville

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.6254138
title: Additional file 1: of Analysis of the canid Y-chromosome phylogeny using short-read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs

description: Table S1. SRA Sample IDs. (XLS 77 kb)
DOI: 10.6084/m9.figshare.6254138.v1
title: Additional file 1: of Analysis of the canid Y-chromosome phylogeny using short-read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs

description: Table S1. SRA Sample IDs. (XLS 77 kb)
DOI: 10.6084/m9.figshare.6253979
title: Mapping the yearly extent of surface coal mining in Central Appalachia using Landsat and Google Earth Engine — Yearly Mining Areas (KML)

description: These data accompany the 2018 manuscript published in <i>PLOS One</i> titled "Mapping the yearly extent of surface coal mining in Central Appalachia using Landsat and Google Earth Engine". In this manuscript, researchers used the Google Earth Engine platform and freely-accessible Landsat imagery to create a yearly dataset (1985 through 2015) of surface coal mining in the Appalachian region of the United States of America. <br>This specific dataset is a collection of KML files of the mining areas as determined by this study for each year from 1985 through 2015. Individual file names within the dataset indicate the specific year. These files show the mining “footprint” in Appalachia for that given year, indicating that mining was occurring in a given location during that year. These files do not, however, indicate the year at which mining began or ceased in any given location.
DOI: 10.6084/m9.figshare.6253979.v1
title: Mapping the yearly extent of surface coal mining in Central Appalachia using Landsat and Google Earth Engine — Yearly Mining Areas (KML)

description: These data accompany the 2018 manuscript published in <i>PLOS One</i> titled "Mapping the yearly extent of surface coal mining in Central Appalachia using Landsat and Google Earth Engine". In this manuscript, researchers used the Google Earth Engine platform and freely-accessible Landsat imagery to create a yearly dataset (1985 through 2015) of surface coal mining in the Appalachian region of the United States of America. <br>This specific dataset is a collection of KML files of the mining areas as determined by this study for each year from 1985 through 2015. Individual file names within the dataset indicate the specific year. These files show the mining “footprint” in Appalachia for that given year, indicating that mining was occurring in a given location during that year. These files do not, however, indicate the year at which mining began or ceased in any given location.
DOI: 10.6084/m9.figshare.6253976
title: Mapping the yearly extent of surface coal mining in Central Appalachia using Landsat and Google Earth Engine — Yearly Mining Areas (shapefile)

description: These data accompany the 2018 manuscript published in <i>PLOS One</i> titled "Mapping the yearly extent of surface coal mining in Central Appalachia using Landsat and Google Earth Engine". In this manuscript, researchers used the Google Earth Engine platform and freely-accessible Landsat imagery to create a yearly dataset (1985 through 2015) of surface coal mining in the Appalachian region of the United States of America. <br>This specific dataset is a collection of Esri shapefiles of the mining areas as determined by this study for each year from 1985 through 2015. Individual file names within the dataset indicate the specific year. These files show the mining “footprint” in Appalachia for that given year, indicating that mining was occurring in a given location during that year. These files do not, however, indicate the year at which mining began or ceased in any given location.
DOI: 10.6084/m9.figshare.6253976.v1
title: Mapping the yearly extent of surface coal mining in Central Appalachia using Landsat and Google Earth Engine — Yearly Mining Areas (shapefile)

description: These data accompany the 2018 manuscript published in <i>PLOS One</i> titled "Mapping the yearly extent of surface coal mining in Central Appalachia using Landsat and Google Earth Engine". In this manuscript, researchers used the Google Earth Engine platform and freely-accessible Landsat imagery to create a yearly dataset (1985 through 2015) of surface coal mining in the Appalachian region of the United States of America. <br>This specific dataset is a collection of Esri shapefiles of the mining areas as determined by this study for each year from 1985 through 2015. Individual file names within the dataset indicate the specific year. These files show the mining “footprint” in Appalachia for that given year, indicating that mining was occurring in a given location during that year. These files do not, however, indicate the year at which mining began or ceased in any given location.
DOI: 10.6084/m9.figshare.6253970
title: Mapping the yearly extent of surface coal mining in Central Appalachia using Landsat and Google Earth Engine — Yearly Mining Areas (GeoJSON)

description: These data accompany the 2018 manuscript published in <i>PLOS One</i> titled "Mapping the yearly extent of surface coal mining in Central Appalachia using Landsat and Google Earth Engine". In this manuscript, researchers used the Google Earth Engine platform and freely-accessible Landsat imagery to create a yearly dataset (1985 through 2015) of surface coal mining in the Appalachian region of the United States of America. <br>This specific dataset is a collection of GeoJSON files of the mining areas as determined by this study for each year from 1985 through 2015. Individual file names within the dataset indicate the specific year. These files show the mining “footprint” in Appalachia for that given year, indicating that mining was occurring in a given location during that year. These files do not, however, indicate the year at which mining began or ceased in any given location.
DOI: 10.6084/m9.figshare.6253970.v1
title: Mapping the yearly extent of surface coal mining in Central Appalachia using Landsat and Google Earth Engine — Yearly Mining Areas (GeoJSON)

description: These data accompany the 2018 manuscript published in <i>PLOS One</i> titled "Mapping the yearly extent of surface coal mining in Central Appalachia using Landsat and Google Earth Engine". In this manuscript, researchers used the Google Earth Engine platform and freely-accessible Landsat imagery to create a yearly dataset (1985 through 2015) of surface coal mining in the Appalachian region of the United States of America. <br>This specific dataset is a collection of GeoJSON files of the mining areas as determined by this study for each year from 1985 through 2015. Individual file names within the dataset indicate the specific year. These files show the mining “footprint” in Appalachia for that given year, indicating that mining was occurring in a given location during that year. These files do not, however, indicate the year at which mining began or ceased in any given location.
DOI: 10.6084/m9.figshare.6253946
title: Mapping the yearly extent of surface coal mining in Central Appalachia using Landsat and Google Earth Engine — Cumulative Mining Area (KML)

description: p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; line-height: 15.0px; font: 13.0px Arial; -webkit-text-stroke: #000000} p.p2 {margin: 0.0px 0.0px 0.0px 0.0px; line-height: 15.0px; font: 13.0px Arial; -webkit-text-stroke: #000000; min-height: 15.0px} span.s1 {font-kerning: none} These data accompany the 2018 manuscript published in <i>PLOS One</i> titled "Mapping the yearly extent of surface coal mining in Central Appalachia using Landsat and Google Earth Engine". In this manuscript, researchers used the Google Earth Engine platform and freely-accessible Landsat imagery to create a yearly dataset (1985 through 2015) of surface coal mining in the Appalachian region of the United States of America. <br> This specific dataset is a KML file of the cumulative mining area as determined by this study from the period 1985 through 2015. This dataset is the overall mining “footprint” in Appalachia, indicating any location where mining has occurred during this period. This dataset does not indicate, however, which year(s) mining was occurring in any given location.