cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17044/scilifelab.28212173.v4
title: Data for "Identification of a deep-branching lineage of algae using environmental plastid genomes"

description: Data associated with the manuscript "Identification of a deep-branching lineage of algae using environmental plastid genomes" (Jamy et al 2025). It includes the plastid MAGs (metagenome-assembled genomes), along with individual gene alignments, concatenated and trimmed alignments, and maximum-likelihood and Bayesian tree files for the phylogenomic dataset.General informationAuthor: Jamy et al, 2025<br>Contact email: mahwash.jamy@slu.se<br>DOI: https://doi.org/10.17044/scilifelab.28212173<br>License: CC BY 4.0<br>Last updated: 2025-10-27<br><br>Please cite as: Jamy et al (2025). Data for "New deep-branching environmental plastid genomes on the algal tree of life". https://doi.org/10.17044/scilifelab.28212173<br>Corresponding manuscript: Jamy M, Huber T, Antoine T, Ruscheweyh HJ, Paoli L, Pelletier E, Delmont TO, Burki F. New deep-branching environmental plastid genomes on the algal tree of life. bioRxiv. 2025:2025-01. https://doi.org/10.1101/2025.01.16.633336
DOI: 10.17044/scilifelab.21378279.v1
title: Spatially-resolved chromatin accessibility and transcriptomic profiling of human breast cancer

description: Human breast cancer OMICs data generated for the publication "Solid phase capture and profiling of open chromatin by spatial ATAC"<br>

<strong>Abstract from the publication:</strong>
Current methods for epigenomic profiling are limited in the ability to obtain genome wide information with spatial resolution. Here we introduce spatial ATAC, a method that integrates transposase-accessible chromatin profiling in tissue sections with barcoded solid-phase capture to perform spatially resolved epigenomics. We show that spatial ATAC enables the discovery of the regulatory programs underlying spatial gene expression during mouse organogenesis, lineage differentiation and in human pathology.
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<strong>Dataset description</strong>
The dataset includes spatially-resolved chromatin accessibility profiling performed on three fresh-frozen tissue sections of HER2+ breast cancer. We provide raw data in the form of fastq files, along with processed feature barcode matrices, metadata, and photomicrographs of the tissue slices. Additionally the dataset contains spatially-resolved gene expression profiling of tissue sections from the same specimen. For this too, we provide raw and processed data, along with the metadata information.
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Spatial transcriptomics data were generated using 10X Genomics' Visium platform, while spatial ATAC data were created using a method introduced in our publication, which relies on an analogous workflow. Samples were sequenced on Illumina Nextseq 550 or 2000 and raw data were processed with CellRanger Gene Expression or ATAC-seq pipelines.
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To apply for conditional access to the dataset, please contact datacentre@scilifelab.se.
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DOI: 10.17044/scilifelab.21378279.v2
title: Spatially-resolved chromatin accessibility and transcriptomic profiling of human breast cancer

description: Human breast cancer OMICs data generated for the publication "Solid phase capture and profiling of open chromatin by spatial ATAC"<br><b>Abstract from the publication:</b>Current methods for epigenomic profiling are limited in the ability to obtain genome wide information with spatial resolution. Here we introduce spatial ATAC, a method that integrates transposase-accessible chromatin profiling in tissue sections with barcoded solid-phase capture to perform spatially resolved epigenomics. We show that spatial ATAC enables the discovery of the regulatory programs underlying spatial gene expression during mouse organogenesis, lineage differentiation and in human pathology.<br><b>Dataset description</b>The dataset includes spatially-resolved chromatin accessibility profiling performed on three fresh-frozen tissue sections of HER2+ breast cancer. We provide raw data in the form of fastq files, along with processed feature barcode matrices, metadata, and photomicrographs of the tissue slices. Additionally the dataset contains spatially-resolved gene expression profiling of tissue sections from the same specimen. For this too, we provide raw and processed data, along with the metadata information.<br>Spatial transcriptomics data were generated using 10X Genomics' Visium platform, while spatial ATAC data were created using a method introduced in our publication, which relies on an analogous workflow. Samples were sequenced on Illumina Nextseq 550 or 2000 and raw data were processed with CellRanger Gene Expression or ATAC-seq pipelines.<br><br>
DOI: 10.17044/scilifelab.28212173.v3
title: Data for "New deep-branching environmental plastid genomes on the algal tree of life"

description: Data associated with the manuscript "New deep-branching environmental plastid genomes on the algal tree of life" (Jamy et al 2025). It includes the plastid MAGs (metagenome-assembled genomes), along with individual gene alignments, concatenated and trimmed alignments, and maximum-likelihood and Bayesian tree files for the phylogenomic dataset.General informationAuthor: Jamy et al, 2025<br>Contact email: mahwash.jamy@slu.se<br>DOI: https://doi.org/10.17044/scilifelab.28212173<br>License: CC BY 4.0<br>Last updated: 2025-10-27<br><br>Please cite as: Jamy et al (2025). Data for "New deep-branching environmental plastid genomes on the algal tree of life". https://doi.org/10.17044/scilifelab.28212173<br>Corresponding manuscript: Jamy M, Huber T, Antoine T, Ruscheweyh HJ, Paoli L, Pelletier E, Delmont TO, Burki F. New deep-branching environmental plastid genomes on the algal tree of life. bioRxiv. 2025:2025-01. https://doi.org/10.1101/2025.01.16.633336
DOI: 10.15468/dl.8f6np6
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"within","geometry":"POLYGON ((116.357 -1.770821, 116.286703 -1.776386, 116.218136 -1.792946, 116.152986 -1.820092, 116.092856 -1.857157, 116.039225 -1.903229, 115.993414 -1.957173, 115.956552 -2.017662, 115.929545 -2.083208, 115.913061 -2.152197, 115.907506 -2.222931, 115.913019 -2.293668, 115.929465 -2.362667, 115.956441 -2.428228, 115.993284 -2.488736, 116.039088 -2.542701, 116.092726 -2.588794, 116.152875 -2.625877, 116.218056 -2.653038, 116.286661 -2.669608, 116.357 -2.675176, 116.427339 -2.669608, 116.495944 -2.653038, 116.561125 -2.625877, 116.621274 -2.588794, 116.674912 -2.542701, 116.720716 -2.488736, 116.757559 -2.428228, 116.784535 -2.362667, 116.800981 -2.293668, 116.806494 -2.222931, 116.800939 -2.152197, 116.784455 -2.083208, 116.757448 -2.017662, 116.720586 -1.957173, 116.674775 -1.903229, 116.621144 -1.857157, 116.561014 -1.820092, 116.495864 -1.792946, 116.427297 -1.776386, 116.357 -1.770821))"},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046848-251120083545085/datasets/export for details.
DOI: 10.25666/dataubfc-2020-11-12-02
title: Monitoring of the vegetation of extensive mountain hay meadows in eastern France (Jura and Vosges)
title: Suivi de la végétation des prairies de fauche extensives dans l'est de la France (Jura et Vosges)

description: Diachronic observations of the plant communities of extensive hay meadows in the Jura and the Vosges mountains. The data include 66 old floristic relevés (realized between 2005 and 2009), 66 recent floristic relevés (realized in 2019) and plant community descriptors.
description: Observations diachroniques des communautés végétales des prairies de fauche extensives dans les massifs du Jura et des Vosges. Les données comprennent 66 relevés de végétation anciens (réalisés entre 2005 et 2009), 66 relevés de végétation récents (réalisés en 2019) ainsi que les descripteurs des communautés végétales.
description: Audience: University: master, Research
description: UpdatePeriodicity: as needed
description: Project: Thèse de doctorat de Corentin Nicod, Contrat doctoral Ministère de l'Enseignement Supérieur, de la Recherche et de l'Innovation (MESRI) (Ministry)
description: Label: ZAAJ (Zone Atelier Arc Jurassien)
description: Observational data: floristic relevés realized using the seven degrees of the Braun-Blanquet scale (r, +, 1, 2, 3, 4, 5).
description: Données d'observation: relevés phytosociologiques réalisés en utilisant l'échelle de Braun-Blanquet (r, +, 1, 2, 3, 4, 5)
DOI: 10.6084/m9.figshare.30858434
title: <b>Assessing the Role of lncRNA GAS5 in Thyroid Function Regulation and Their Potential Use as Biomarkers for Hyperthyroidism Management</b>

description: This dataset contains all raw and processed data used in the article<br>“Assessing the Role of lncRNA GAS5 in Thyroid Function Regulation and Its Potential Use as a Biomarker for Hyperthyroidism Management.”The dataset includes:Raw Ct values for GAS5 and GAPDHΔCt and ΔΔCt calculationsFold-change expression valuesClinical parameters for all participants (TSH, T3, T4, BMI, age)All values used to generate figures and statistical analysesAll data are anonymized and do not include personally identifiable information.<br>The dataset is provided under a CC-BY 4.0 license.
DOI: 10.6084/m9.figshare.30858434.v1
title: <b>Assessing the Role of lncRNA GAS5 in Thyroid Function Regulation and Their Potential Use as Biomarkers for Hyperthyroidism Management</b>

description: This dataset contains all raw and processed data used in the article<br>“Assessing the Role of lncRNA GAS5 in Thyroid Function Regulation and Its Potential Use as a Biomarker for Hyperthyroidism Management.”The dataset includes:Raw Ct values for GAS5 and GAPDHΔCt and ΔΔCt calculationsFold-change expression valuesClinical parameters for all participants (TSH, T3, T4, BMI, age)All values used to generate figures and statistical analysesAll data are anonymized and do not include personally identifiable information.<br>The dataset is provided under a CC-BY 4.0 license.
DOI: 10.5281/zenodo.17883227
title: FTIR Degradation Repository
DOI: 10.5281/zenodo.17883226
title: FTIR Degradation Repository
DOI: 10.3886/e241081v2
title: Price Discovery and Long-Distance Market Integration

description: Market integration is vital for economic development; its determinants have been extensively documented in the literature. However, relatively little attention has been paid to the role of economic organizations. This paper seeks to fill this gap by investigating the role of futures exchanges in Republican China. Using manually collected primary data, we employ a continuous difference-in-differences approach to analyze the impact of the Chinese Cotton Goods Exchange on long-distance market integration. We find that, following the exchange's establishment in 1921, geographically distant cities experienced a stronger increase in market integration with Shanghai than nearby cities. Regarding the underlying mechanism, we show that the price-discovery function of the futures exchange promoted long-distance market integration by centralizing markets and reducing price uncertainty.
DOI: 10.15468/dl.pajfvz
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"within","geometry":"POLYGON ((111.459 -1.768821, 111.388703 -1.774386, 111.320137 -1.790946, 111.254986 -1.818092, 111.194856 -1.855157, 111.141225 -1.901229, 111.095415 -1.955173, 111.058552 -2.015662, 111.031546 -2.081208, 111.015062 -2.150197, 111.009507 -2.220931, 111.01502 -2.291668, 111.031466 -2.360667, 111.058442 -2.426228, 111.095285 -2.486736, 111.141089 -2.540701, 111.194726 -2.586794, 111.254876 -2.623877, 111.320056 -2.651038, 111.388661 -2.667608, 111.459 -2.673176, 111.529339 -2.667608, 111.597944 -2.651038, 111.663124 -2.623877, 111.723274 -2.586794, 111.776911 -2.540701, 111.822715 -2.486736, 111.859558 -2.426228, 111.886534 -2.360667, 111.90298 -2.291668, 111.908493 -2.220931, 111.902938 -2.150197, 111.886454 -2.081208, 111.859448 -2.015662, 111.822585 -1.955173, 111.776775 -1.901229, 111.723144 -1.855157, 111.663014 -1.818092, 111.597863 -1.790946, 111.529297 -1.774386, 111.459 -1.768821))"},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046851-251120083545085/datasets/export for details.
DOI: 10.21950/t0qjb5
title: El mundo editorial en Madrid a finales del siglo XVIII: datos georreferenciados de librerías, imprentas, bibliotecas y otros establecimientos y profesionales

description: Este dataset reúne los datos utilizados para la construcción del SIG histórico “El mundo editorial en Madrid a finales del siglo XVIII”, publicado como mapaweb interactivo mediante la tecnología de ArcGIS Online. Contiene información georreferenciada sobre la localización de establecimientos y profesionales vinculados al mundo del libro y la industria editorial en Madrid (imprentas, librerías, puestos de venta, estampadores, fundidores de letra, bibliotecas, etc.) procedente de avisos de prensa y otras fuentes impresas entre 1780 y 1808. El dataset aporta datos básicos de referencia sobre los negocios de diferentes impresores y libreros, sus localizaciones y fechas de actividad comercial.
DOI: 10.15468/dl.cm367w
title: Occurrence Download

description: A dataset containing 3179 records in GBIF matching the query:
SELECT
 '324' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 33.06103686093294
 AND decimalLatitude &lt;= 37.42857426825602
 AND decimalLongitude &gt;= 100.19009778061415
 AND decimalLongitude &lt;= 109.37183140870387
 AND "year" &gt;= 2015
 AND "year" &lt;= 2025
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 3179 records were derived from 122 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046840-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mweu9p
title: Occurrence Download

description: A dataset containing 64389 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-1000.0",
 "Geometry POLYGON((-6.25617 41.0851,27.48128 41.0851,27.48128 72.26782,-6.25617 72.26782,-6.25617 41.0851))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Linnaea borealis"
 ]
}

 The dataset includes 64389 records from 87 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046834-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/ccdc.csd.cc2pd99q
title: CCDC 2484473: Experimental Crystal Structure Determination

description: Related Article: Shen Wu, Shinjiro Takano, Tatsuya Tsukuda|2025|Phys.Chem.Chem.Phys.(PCCP)|27|25862|doi:10.1039/D5CP03444B
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2pd9br
title: CCDC 2484474: Experimental Crystal Structure Determination

description: Related Article: Shen Wu, Shinjiro Takano, Tatsuya Tsukuda|2025|Phys.Chem.Chem.Phys.(PCCP)|27|25862|doi:10.1039/D5CP03444B
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2pdmzq
title: CCDC 2484804: Experimental Crystal Structure Determination

description: Related Article: Austin J. Becksvoort, Gabrielle N. Shirley, Tess L. Bainbridge, Grace O. Hammers, Ian J. McGovern, Christopher R. Turlington|2025|Organometallics|||doi:10.1021/acs.organomet.5c00418
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2pmdk9
title: CCDC 2491301: Experimental Crystal Structure Determination

description: Related Article: Jiyong Li, Songyang Li, Cuijuan Zhang, Liankun Ai, Jiaxiang Chu|2025|Inorg.Chem.|||doi:10.1021/acs.inorgchem.5c04581
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2pmdlb
title: CCDC 2491302: Experimental Crystal Structure Determination

description: Related Article: Jiyong Li, Songyang Li, Cuijuan Zhang, Liankun Ai, Jiaxiang Chu|2025|Inorg.Chem.|||doi:10.1021/acs.inorgchem.5c04581
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2pmkhd
title: CCDC 2491454: Experimental Crystal Structure Determination

description: Related Article: A. Rostami-Vartooni, R. Kia, F. Abbasi, M. Kiamehr, P.R. Raithby|2025|Acta Crystallogr.,Sect.B:Struct.Sci.,Cryst.Eng. and Mat.|81|540|doi:10.1107/S2052520625008467
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2pmkjf
title: CCDC 2491455: Experimental Crystal Structure Determination

description: Related Article: A. Rostami-Vartooni, R. Kia, F. Abbasi, M. Kiamehr, P.R. Raithby|2025|Acta Crystallogr.,Sect.B:Struct.Sci.,Cryst.Eng. and Mat.|81|540|doi:10.1107/S2052520625008467
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2pmkkg
title: CCDC 2491456: Experimental Crystal Structure Determination

description: Related Article: A. Rostami-Vartooni, R. Kia, F. Abbasi, M. Kiamehr, P.R. Raithby|2025|Acta Crystallogr.,Sect.B:Struct.Sci.,Cryst.Eng. and Mat.|81|540|doi:10.1107/S2052520625008467
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2pmdg6
title: CCDC 2491298: Experimental Crystal Structure Determination

description: Related Article: Jiyong Li, Songyang Li, Cuijuan Zhang, Liankun Ai, Jiaxiang Chu|2025|Inorg.Chem.|||doi:10.1021/acs.inorgchem.5c04581
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2pmdf5
title: CCDC 2491297: Experimental Crystal Structure Determination

description: Related Article: Jiyong Li, Songyang Li, Cuijuan Zhang, Liankun Ai, Jiaxiang Chu|2025|Inorg.Chem.|||doi:10.1021/acs.inorgchem.5c04581
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2pmdj8
title: CCDC 2491300: Experimental Crystal Structure Determination

description: Related Article: Jiyong Li, Songyang Li, Cuijuan Zhang, Liankun Ai, Jiaxiang Chu|2025|Inorg.Chem.|||doi:10.1021/acs.inorgchem.5c04581
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2pn9ym
title: CCDC 2492181: Experimental Crystal Structure Determination

description: Related Article: Kristina A. Lotsman, Sofia S. Filippova, Vadim Yu. Kukushkin, Regina M. Islamova|2025|Polymers|17|2729|doi:10.3390/polym17202729
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.