cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.3uyanv
title: Occurrence Download

description: A dataset containing 151 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chiroptera",
 "Geometry POLYGON ((-94.85175583\t16.46926027, -94.85175583\t16.69908919, -94.57596113\t16.69908919, -94.57596113\t16.46926027, -94.85175583\t16.46926027))",
 "Year is greater than or equal to 1900",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil)"
 ]
 }
 }
 ]
}

 The dataset includes 151 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023509-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11198585
title: Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 04

description: Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as Giardia parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded in situ on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of Giardia and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.

Data set 04 comprises an image series of 120 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 50 nm using the T1 detector of the SEM at high vacuum. Original pixel size was 10 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.
DOI: 10.5281/zenodo.11198586
title: Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 04

description: Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as Giardia parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded in situ on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of Giardia and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.

Data set 04 comprises an image series of 120 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 50 nm using the T1 detector of the SEM at high vacuum. Original pixel size was 10 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.
DOI: 10.5281/zenodo.11198690
title: Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 05

description: Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as Giardia parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded in situ on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of Giardia and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.

Data set 05 comprises an image series of 500 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 50 nm using the DBS detector of the SEM at low vacuum (0.4 mbar). Original pixel size was 6 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.
DOI: 10.5281/zenodo.11198691
title: Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 05

description: Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as Giardia parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded in situ on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of Giardia and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.

Data set 05 comprises an image series of 500 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 50 nm using the DBS detector of the SEM at low vacuum (0.4 mbar). Original pixel size was 6 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.
DOI: 10.5281/zenodo.11202405
title: Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 08

description: Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as Giardia parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded in situ on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of Giardia and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.

Data set 08 comprises an image series of 299 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 50 nm using the DBS detector of the SEM at low vacuum (0.4 mbar). Original pixel size was 3 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.
DOI: 10.5281/zenodo.11202406
title: Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 08

description: Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as Giardia parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded in situ on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of Giardia and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.

Data set 08 comprises an image series of 299 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 50 nm using the DBS detector of the SEM at low vacuum (0.4 mbar). Original pixel size was 3 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.
DOI: 10.5281/zenodo.11199432
title: Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 07

description: Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as Giardia parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded in situ on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of Giardia and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.

Data set 07 comprises an image series of 318 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 10 nm using the DBS detector of the SEM at low vacuum (0.4 mbar). Original pixel size was 8 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.
DOI: 10.5281/zenodo.11199433
title: Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 07

description: Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as Giardia parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded in situ on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of Giardia and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.

Data set 07 comprises an image series of 318 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 10 nm using the DBS detector of the SEM at low vacuum (0.4 mbar). Original pixel size was 8 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.
DOI: 10.5281/zenodo.11203781
title: Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 10

description: Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as Giardia parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded in situ on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of Giardia and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.

Data set 10 comprises an image series of 255 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 50 nm using the T1 detector of the SEM at high vacuum. Original pixel size was 10 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.
DOI: 10.5281/zenodo.11203782
title: Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 10

description: Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as Giardia parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded in situ on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of Giardia and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.

Data set 10 comprises an image series of 255 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 50 nm using the T1 detector of the SEM at high vacuum. Original pixel size was 10 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.
DOI: 10.5281/zenodo.11203026
title: Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 09

description: Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as Giardia parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded in situ on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of Giardia and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.

Data set 09 comprises an image series of 400 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 10 nm using the DBS detector of the SEM at low vacuum (0.4 mbar). Original pixel size was 10 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.
DOI: 10.5281/zenodo.11203027
title: Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 09

description: Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as Giardia parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded in situ on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of Giardia and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.

Data set 09 comprises an image series of 400 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 10 nm using the DBS detector of the SEM at low vacuum (0.4 mbar). Original pixel size was 10 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.
DOI: 10.5281/zenodo.11204454
title: Targeting non-canonical NF-κB signalling in CYLD cutaneous syndrome by selective inhibition of IκB kinase alpha

description: CYLD cutaneous syndrome (CCS)  skin tumours develop from puberty onwards, can number in the hundreds and progressively grow over time. CCS patients lack medical therapies and require repeated surgery to control tumour burden. CYLD loss of heterozygosity drives tumour growth, and CCS tumours have previously been shown to demonstrate increased canonical NF-KB and Wnt signalling.  Here, we demonstrate evidence of non-canonical NF-κB signalling in CCS tumours, with increased p100 to p52 processing and RelB protein expression. Utilising complementary transcriptomics and proteomics on patient derived CCS tumour cell fractions, we identify IκB kinase alpha (IKKα) as a candidate target in the non-canonical NF-κB signalling pathway. A novel, highly selective, IKKα inhibitor in patient derived CCS tumour spheroid cultures demonstrated that IKKα inhibition reduced tumour spheroid viability.  These data provide the pre-clinical rationale for the assessment of topical IKKα inhibitors as a novel treatment for CCS.

Here we provide CellRanger processed data and an annotated anndata object (.h5ad).
DOI: 10.5281/zenodo.11204455
title: Targeting non-canonical NF-κB signalling in CYLD cutaneous syndrome by selective inhibition of IκB kinase alpha

description: CYLD cutaneous syndrome (CCS)  skin tumours develop from puberty onwards, can number in the hundreds and progressively grow over time. CCS patients lack medical therapies and require repeated surgery to control tumour burden. CYLD loss of heterozygosity drives tumour growth, and CCS tumours have previously been shown to demonstrate increased canonical NF-KB and Wnt signalling.  Here, we demonstrate evidence of non-canonical NF-κB signalling in CCS tumours, with increased p100 to p52 processing and RelB protein expression. Utilising complementary transcriptomics and proteomics on patient derived CCS tumour cell fractions, we identify IκB kinase alpha (IKKα) as a candidate target in the non-canonical NF-κB signalling pathway. A novel, highly selective, IKKα inhibitor in patient derived CCS tumour spheroid cultures demonstrated that IKKα inhibition reduced tumour spheroid viability.  These data provide the pre-clinical rationale for the assessment of topical IKKα inhibitors as a novel treatment for CCS.

Here we provide CellRanger processed data and an annotated anndata object (.h5ad).
DOI: 10.15468/dl.hhkptx
title: Occurrence Download

description: A dataset containing 72078 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is one of (Lepus yarkandensis Günther, 1875, Lepus timidus Linnaeus, 1758, Lepus hainanus Swinhoe, 1870, Caprolagus hispidus (Pearson, 1839), Ochotona iliensis Li & Ma, 1986, Ochotona argentata Howell, 1928)",
 "Year 1980-2024"
 ]
}

 The dataset includes 72078 records from 216 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021473-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s55b63
title: Occurrence Download

description: A dataset containing 236427 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is one of (Ratufa bicolor (Sparrman, 1778), Castor fiber Linnaeus, 1758)",
 "Year 1980-2024"
 ]
}

 The dataset includes 236427 records from 500 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021471-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bvcsrj
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Botanical Collections of the Åbo Akademi",
 "Country is Croatia"
 ]
}

 The dataset includes 10 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028212-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.29153042
title: R_code, data and supplementary materials associated with the manuscript "<b>Deciphering the patterns and drivers of tardigrade diversity along altitudinal gradients</b>"

description: This dataset accompanies the study <i>"Deciphering the patterns and drivers of tardigrade diversity along altitudinal gradients."</i> It includes metadata, environmental variables, bryophyte trait data, tardigrade trait assignments, and bioinformatics outputs from a DNA metabarcoding survey of 546 bryophyte samples collected across altitudinal gradients in the Italian Alps. Tardigrade communities were identified using high-throughput COI sequencing, and diversity was analyzed at taxonomic, phylogenetic, and functional levels. The data support analyses of alpha/beta diversity, trait-environment relationships, and community assembly in meiofaunal taxa.Dataset comprises:<b>SM.1: </b>Sample information: collection data and all tested variable.<b>SM.2: </b>Models’ results and additional figures supporting the analyses. Includes: Figure S2:1 - 4 and Table S2:1 - 18.<b>SM.3: </b>Archive including pipelines and raw data used for the analysis (Metabarcoding_pipeline.html, Statistical_procedures.html, Phylogenetic_tree_calculation.docx, Phylogenetic_tree.tre, OTU_table.xlsx, OTU_x_trait_matrix.xlsx, Sample_data.xlsx, Metadata.xlsx).<b>SM.4: </b>Tardigrade traits data and list of all data sources.<br><b>The data are associated with the following paper:</b>Surmacz, B., D. Fontaneto, G. Vončina, and D. Stec. 2025. “Deciphering the Patterns and Drivers of Tardigrade Diversity Along Altitudinal Gradients.” <i>Molecular Ecology</i> e70196. https://doi.org/10.1111/mec.70196