cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.14278/rodare.1937
title: Reactivity Map Code

description: Matlab code to generate reactivity map of the galena particle
description: Funded by European Union's Horizon 2020 Research and Innovation Program under Grant Agreement 815748
DOI: 10.5281/zenodo.7357389
title: Table A2: RNA-seq Data for shRNA PRLR vs shRNA NTC for 2 samples each in PEO-1.

description: <strong>Table A2: RNA-seq Data for shRNA PRLR vs shRNA NTC for 2 samples each in PEO-1.</strong> A) Excel Workbooks for RNA seq analysis showing the differential expression results for shRNA PRLR vs shRNA NTC for 2 samples each in PEO-1. Samples F01_5 and F01_6 represent shRNA NTC PEO-1 and F01_7 to F01_8 represent shRNA PRLR PEO-1. Sheet 1: statistically significant up-regulated genes with log2fold change of &gt;= 1 (sorted by fold change). Sheet 2: statistically significant down-regulated genes with log2fold change of &lt;= -1 (sorted by fold change) Sheet 3: Statistically significant differentially expressed (DE) genes (p value =&lt; 0.05 and p adj =&lt; 0.05) including normalised counts for each sample (rounded values) Sheet 4: Differential expression analysis results (raw) including normalised counts for each sample. Sheet 5: Raw counts for the six samples (three replicates PEO-1 shRNA NTC and three replicates PEO-1 shRNA PRLR Sheet 6: Filtered normalised counts (all genes with row Sum less than one were removed) The data presented log2 fold change, lfcSE = standard error of the log2 Fold Change estimate, stat = Wald statistic and fold change are included. B) List of genes in the top up-regulated and down-regulated hallmark pathways, which were affected by PRLR knockdown in PEO-1 cells. Sheet 1: list of all (raw) hallmark pathways affected by knocking down PRLR generated by set enrichment analysis (GSEA) in R using the Bioconductor package fgsea. Sheet 2: list of significantly affected pathways with (p value =&lt; 0.05 and p adj =&lt; 0.05) Sheet 3: list of gene in Myc targets V1 pathway Sheet 4: list of gene in Myc targets V2 pathway Sheet 5: list of gene in epithelial mesenchymal transition pathway Sheet 6: list of gene in glycolysis pathway Sheet 7: list of gene in oxidative phosphorylation pathway. The data presented NES= normalised enrichment score, NE= enrichment score, n More Extreme= number of times a random gene set had a more extreme enrichment score value, log2 fold change, lfcSE = standard error of the log2 Fold Change estimate, stat = Wald statistic , fold change, p value, and read count are included.
DOI: 10.5281/zenodo.7357390
title: Table A2: RNA-seq Data for shRNA PRLR vs shRNA NTC for 2 samples each in PEO-1.

description: <strong>Table A2: RNA-seq Data for shRNA PRLR vs shRNA NTC for 2 samples each in PEO-1.</strong> A) Excel Workbooks for RNA seq analysis showing the differential expression results for shRNA PRLR vs shRNA NTC for 2 samples each in PEO-1. Samples F01_5 and F01_6 represent shRNA NTC PEO-1 and F01_7 to F01_8 represent shRNA PRLR PEO-1. Sheet 1: statistically significant up-regulated genes with log2fold change of &gt;= 1 (sorted by fold change). Sheet 2: statistically significant down-regulated genes with log2fold change of &lt;= -1 (sorted by fold change) Sheet 3: Statistically significant differentially expressed (DE) genes (p value =&lt; 0.05 and p adj =&lt; 0.05) including normalised counts for each sample (rounded values) Sheet 4: Differential expression analysis results (raw) including normalised counts for each sample. Sheet 5: Raw counts for the six samples (three replicates PEO-1 shRNA NTC and three replicates PEO-1 shRNA PRLR Sheet 6: Filtered normalised counts (all genes with row Sum less than one were removed) The data presented log2 fold change, lfcSE = standard error of the log2 Fold Change estimate, stat = Wald statistic and fold change are included. B) List of genes in the top up-regulated and down-regulated hallmark pathways, which were affected by PRLR knockdown in PEO-1 cells. Sheet 1: list of all (raw) hallmark pathways affected by knocking down PRLR generated by set enrichment analysis (GSEA) in R using the Bioconductor package fgsea. Sheet 2: list of significantly affected pathways with (p value =&lt; 0.05 and p adj =&lt; 0.05) Sheet 3: list of gene in Myc targets V1 pathway Sheet 4: list of gene in Myc targets V2 pathway Sheet 5: list of gene in epithelial mesenchymal transition pathway Sheet 6: list of gene in glycolysis pathway Sheet 7: list of gene in oxidative phosphorylation pathway. The data presented NES= normalised enrichment score, NE= enrichment score, n More Extreme= number of times a random gene set had a more extreme enrichment score value, log2 fold change, lfcSE = standard error of the log2 Fold Change estimate, stat = Wald statistic , fold change, p value, and read count are included.
DOI: 10.5281/zenodo.7357470
title: Table A2: RNA-seq Data for shRNA PRLR vs shRNA NTC for 2 samples each in PEO-1.

description: <strong>Table A2: RNA-seq Data for shRNA PRLR vs shRNA NTC for 2 samples each in PEO-1.</strong> A) Excel Workbooks for RNA seq analysis showing the differential expression results for shRNA PRLR vs shRNA NTC for 2 samples each in PEO-1. Samples F01_5 and F01_6 represent shRNA NTC PEO-1 and F01_7 to F01_8 represent shRNA PRLR PEO-1. Sheet 1: statistically significant up-regulated genes with log2fold change of &gt;= 1 (sorted by fold change). Sheet 2: statistically significant down-regulated genes with log2fold change of &lt;= -1 (sorted by fold change) Sheet 3: Statistically significant differentially expressed (DE) genes (p value =&lt; 0.05 and p adj =&lt; 0.05) including normalised counts for each sample (rounded values) Sheet 4: Differential expression analysis results (raw) including normalised counts for each sample. Sheet 5: Raw counts for the six samples (three replicates PEO-1 shRNA NTC and three replicates PEO-1 shRNA PRLR Sheet 6: Filtered normalised counts (all genes with row Sum less than one were removed) The data presented log2 fold change, lfcSE = standard error of the log2 Fold Change estimate, stat = Wald statistic and fold change are included. B) List of genes in the top up-regulated and down-regulated hallmark pathways, which were affected by PRLR knockdown in PEO-1 cells. Sheet 1: list of all (raw) hallmark pathways affected by knocking down PRLR generated by set enrichment analysis (GSEA) in R using the Bioconductor package fgsea. Sheet 2: list of significantly affected pathways with (p value =&lt; 0.05 and p adj =&lt; 0.05) Sheet 3: list of gene in Myc targets V1 pathway Sheet 4: list of gene in Myc targets V2 pathway Sheet 5: list of gene in epithelial mesenchymal transition pathway Sheet 6: list of gene in glycolysis pathway Sheet 7: list of gene in oxidative phosphorylation pathway. The data presented NES= normalised enrichment score, NE= enrichment score, n More Extreme= number of times a random gene set had a more extreme enrichment score value, log2 fold change, lfcSE = standard error of the log2 Fold Change estimate, stat = Wald statistic , fold change, p value, and read count are included.
DOI: 10.5281/zenodo.7357433
title: Datasets related to "Mannhardt et al. (2022): Overcoming the energy crisis in Europe: Collaborative and selfish mitigation strategies of the gas shortage"

description: Datasets for the submitted article: "Overcoming the energy crisis in Europe: Collaborative and selfish mitigation strategies of the gas shortage" by Jacob Mannhardt, Paolo Gabrielli, Giovanni Sansavini (sansavig@ethz.ch)<br> Reliability and Risk Engineering Lab, Institute of Energy and Process Engineering, ETH Zurich All rights lie with the authors. Refer to the README.txt for a description of the datasets and their usage in the article.
DOI: 10.5281/zenodo.7357434
title: Datasets related to "Mannhardt et al. (2022): Overcoming the energy crisis in Europe: Collaborative and selfish mitigation strategies of the gas shortage"

description: Datasets for the submitted article: "Overcoming the energy crisis in Europe: Collaborative and selfish mitigation strategies of the gas shortage" by Jacob Mannhardt, Paolo Gabrielli, Giovanni Sansavini (sansavig@ethz.ch)<br> Reliability and Risk Engineering Lab, Institute of Energy and Process Engineering, ETH Zurich All rights lie with the authors. Refer to the README.txt for a description of the datasets and their usage in the article.
DOI: 10.6084/m9.figshare.21618087.v1
title: Genome assembly and annotation

description: genome assembly and annotation
DOI: 10.5522/04/16930864
title: Tension at intercellular junctions is necessary for accurate orientation of cell division in the epithelium plane

description: In growing epithelia, divisions are typically oriented in the epithelial plane to drive tissue expansion. In some organs, divisions are then re-oriented so that they occur perpendicular to the epithelium plane to drive tissue stratification and cell differentiation. When uncontrolled, this switch in orientation can lead to defects in tissue organisation and, in the context of cancer, has been suggested to contribute to metastasis. While much is known about the molecular machinery guiding mitotic spindle orientation, less is known about the role of mechanical factors in this process. Here, we use mechanical and chemical perturbations to show that mechanics plays a role in controlling the plane of division. Overall, our data suggest that the orientation of spindles in the epithelium plane requires a threshold level of mechanical tension at intercellular junctions.
DOI: 10.5522/04/16930864.v1
title: Tension at intercellular junctions is necessary for accurate orientation of cell division in the epithelium plane

description: In growing epithelia, divisions are typically oriented in the epithelial plane to drive tissue expansion. In some organs, divisions are then re-oriented so that they occur perpendicular to the epithelium plane to drive tissue stratification and cell differentiation. When uncontrolled, this switch in orientation can lead to defects in tissue organisation and, in the context of cancer, has been suggested to contribute to metastasis. While much is known about the molecular machinery guiding mitotic spindle orientation, less is known about the role of mechanical factors in this process. Here, we use mechanical and chemical perturbations to show that mechanics plays a role in controlling the plane of division. Overall, our data suggest that the orientation of spindles in the epithelium plane requires a threshold level of mechanical tension at intercellular junctions.
DOI: 10.17031/1632
title: 1992 - Ongoing Plymouth Marine Laboratory (PML) Zooplankton and Phytoplankton data collected at L4

description: Dataset of zoo and phyto plankton collected from L4 by Plymouth Marine Laboratory.
DOI: 10.17031/1648
title: 2020 Marine Biological Association of the UK (MBA) CPR Data request Stella Alexandroff Exeter University

description: CPR dataset used to investigate the effects of changes in ocean circulation and water mass on cod growth and bivalve chronologies in the northern North Atlantic
DOI: 10.17031/1633
title: 1987-2015 Swedish Meteorological and Hydrological Institute (SMHI) Plankton Swedish West Coast
DOI: 10.17031/1634
title: 2000 to date North, Irish & Celtic Seas Centre for Environment, Fisheries and Aquaculture Science Smartbuoy marine monitoring
DOI: 10.17031/1636
title: 1924-2013 MBA L4 and E1 Young Fish Survey
DOI: 10.17031/1637
title: Phyto and zooplankton records provided by Marine Science Scotland (MSS) from Loch Ewe, Scalloway, Scapa and Stonehaven
DOI: 10.17031/1635
title: Phytoplankton Dataset provided by the Environment Agency (EA) 2000-2017
DOI: 10.17031/ykdq-wy51
title: Li partitioning in Emiliania huxleyi
DOI: 10.17031/1651
title: 2020 Marine Biological Association of the UK (MBA) CPR Data request Diana Caldarescu AWI

description: Area A6, total diatoms, total dinoflagellates, total large and total small Copepods as monthly means, 1958 to 2018.
DOI: 10.17031/1xhd-pg17
title: Plankton lifeform traits master list (v4)
DOI: 10.17031/1647
title: 2020 Marine Biological Association of the UK (MBA) CPR Data request Ryan Morse NOAA

description: Exploratory analysis in order to examine community level changes in diatom and dinoflagellate contribution to overall observed satellite chlorophyll levels on the northeast US continental shelf
DOI: 10.17031/1655
title: Plankton lifeform traits master list (v4:2020-07-27)
DOI: 10.17031/1656
title: 2020 Marine Biological Association of the UK (MBA) CPR Data request Jed Kempf September 2020

description: From January 1989 to December 2020, monthly means of total large copepods and total small copepods for 15 selected standard areas (B4, B5, B6, C3, C4, C5, C6, D3, D4, D5, D6, E4, E5, E6 and F4).
DOI: 10.17031/1657
title: 2020 Marine Biological Association of the UK (MBA) CPR Data request Jed Kempf September 2020 (2)

description: From January 1989 to December 2018, monthly means of Phytoplankton Colour Index (PCI) for 15 standard areas (B4, B5, B6, C3, C4, C5, C6, D3, D4, D5, D6, E4, E5, E6 and F4).
DOI: 10.17031/1658
title: 2020 Marine Biological Association of the UK (MBA) CPR Data request Marc Taylor Thunen-Institute March 2020

description: CPR zooplankton data (100 taxa) for the periods 1958 to 2017, in the Standard Areas of the North Sea and adjacent waters (A1, B1, B2, B4, B5, C1, C2, C3, C4, C5, D1, D2, D3, D4, and D5)
DOI: 10.17031/1659
title: 2020 Marine Biological Association of the UK (MBA) CPR Data request Louis Perperzak NIOZ September 2020

description: From January 1970 to December 2018, monthly means of a selection of planktonic taxa (169 eyecount, 70 traverse, 176 phytoplankton) in 5 selected standard areas (C2, C1, D3, D2, D1).
DOI: 10.17031/w508-x849
title: Operational Oceanographic Products and Services (OOPS) CPR Survey Data Extract (2016)

description: Area Definitions [-20 62] [-13 62] [-13 74] [3 84] [21 67.5] [15 61] [17 53] [0.5 34] [-13 34] [-13 46.5] [-20 48.5] [-72.5 42.5] [-56 55] [-39 53] [-39 44.5] [-50 37.5] [-67 33] [-72 39] for Temora longicornis Acartia spp. (unidentified) Oithona spp. Calanus finmarchicus Calanus helgolandicus Metridia lucens Large Copepods Small Copepods
DOI: 10.17031/1660
title: CPR survey long-term dataset for Noctiluca abundance. Sample route Plymouth to Roscoff 1981-2018.
DOI: 10.17031/1663
title: Data for the UK Marine Strategy Framework Directive Article 8 biodiversity assessment: Condition of intertidal seagrass communities in coastal waters determined using Water Framework Directive methods

description: Water Framework Directive River Basin Management Plan Cycle 2 intertidal seagrass classification data used for the Marine Strategy Framework Directive Article 8 biodiversity assessments for the UK Regional Seas. The WFD seagrass method statement and classification tool ('Intertidal Seagrass Tool_SAILOR_v2.4_UKTAG.xlsx’) used to calculate WFD Ecological Quality Ratios are available at http://www.wfduk.org/resources%20/transitional-and-coastal-waters-intertidal-seagrass. Project coordinated by the Environment Agency and Joint Nature Conservation Committee. River Basin Management Plan Cycle 2 seagrass data held by the relevant WFD Agency.
DOI: 10.17031/1664
title: Data for the UK Marine Strategy Framework Directive Article 8 biodiversity assessment: Condition of intertidal rocky shore macroalgae (seaweed) communities in coastal waters determined using Water Framework Directive methods

description: Water Framework Directive River Basin Management Plan Cycle 2 intertidal rocky shore macroalgal index classification data used for the Marine Strategy Framework Directive Article 8 biodiversity assessments for the UK Regional Seas. The WFD rocky shore macroalgae method statement and classification tool (‘Precision In Rocky Shores_PIRATES_v04_UKTAG.xls’) used to calculate WFD Ecological Quality Ratios are available at http://www.wfduk.org/resources%20/coastal-waters-rocky-shore-macroalgae. Project coordinated by the Environment Agency and Joint Nature Conservation Committee. River Basin Management Plan Cycle 2 rocky shore macroalgae data held by the relevant WFD Agency.
DOI: 10.17031/1665
title: Data for the UK Marine Strategy Framework Directive Article 8 biodiversity assessment: Condition of soft sediment invertebrate communities in coastal waters determined using Water Framework Directive methods

description: Water Framework Directive River Basin Management Plan Cycle 2 Infaunal Quality Index classification data used for the Marine Strategy Framework Directive Article 8 biodiversity assessments for the UK Regional Seas. The WFD Infaunal Quality Index method statement and classification tool (‘IQI Workbook UKTAG v01 20140311.xlsm’) used to calculate WFD Ecological Quality Ratios are available at http://www.wfduk.org/resources%20/coastal-and-transitional-waters-benthic-invertebrate-fauna. Project coordinated by the Environment Agency and Joint Nature Conservation Committee. River Basin Management Plan Cycle 2 benthic invertebrate data held by the relevant WFD Agency.
DOI: 10.17031/1666
title: Data for the UK Marine Strategy Framework Directive Article 8 biodiversity assessment: Condition of intertidal saltmarsh communities in coastal waters determined using Water Framework Directive methods

description: Water Framework Directive River Basin Management Plan Cycle 2 intertidal saltmarsh classification data used for the Marine Strategy Framework Directive Article 8 biodiversity assessments for the UK Regional Seas. The WFD saltmarsh method statement and classification tool (‘Saltmarsh Tool_SKIPPER_ v1.0_UKTAG.xls’) used to calculate WFD Ecological Quality Ratios are available at http://www.wfduk.org/resources/transitional-and-coastal-waters-saltmarsh. Project coordinated by the Environment Agency and Joint Nature Conservation Committee. River Basin Management Plan Cycle 2 saltmarsh data held by the relevant WFD Agency
DOI: 10.17031/1667
title: Infaunal Quality Index Calculation Workbook (MSFD Offshore Draft v01: 18/03/2016 update)

description: This worksheet calculates the EQR (Ecological Quality Ratio) and Confidence of Class for the Water Framework Directive (WFD) transitional and coastal (TraC) macrobenthic infaunal samples using the infaunal quality index (IQI version IV). The worksheet calculates the average EQR and corresponding Confidence of Class (CofC) for groups of samples used for assessment. Acknowledgements to Angel Borja at AZTI Tecnalia (www.azti.es) for the AZTI Marine Biotic Index (AMBI) and associated ecological group sensitivity scores. The AZTI Marine Biotic Index and associated ecological group scores remain the intellectual property of Angel Borja, AZTI Tecnalia (www.azti.es).
DOI: 10.17031/1668
title: FlowCam Macro Noctiluca scintillans library, Station L4, 2018, sample run #1

description:  FlowCam Macro library of Noctiluca scintillans from vertical plankton net hauls collected in 2018 from station L4 using 335um mesh plankton net, 50cm diameter.  Fluid Imaging VisualSpreadsheet software required.
DOI: 10.17031/1669
title: Assembled contigs

description: Processed reads from each sample were mapped to the S. ciliatum genome by using HISAT2. Next, the mapped reads were passed to StringTie for transcript assembly. After initial assembly, all assembled transcripts from regeneration and development were merged by using StringTie's merge module, which merges all the gene structures found in any of the samples.
DOI: 10.17031/nz24-br35
title: Plankton dataset provided by Scottish Association for Marine Science (SAMS) from the Lorn Pelagic Observatory (LPO)
DOI: 10.17031/1687
title: 2020 Marine Biological Association - Custom CPR Spatially Discrete Data Extract
DOI: 10.17031/b84a-7951
title: Photo- and Zooplankton dataset provided by Scottish Environment Protection Agency (SEPA) collected from the Forth and Clyde
DOI: 10.17031/1685
title: Selected CPR Meroplankton data_NEAtlantic
DOI: 10.17031/1707
title: Total diatoms, total dinoflagellates and coccolithophores for CPR Standard areas around UK
DOI: 10.17031/1709
title: Plankton lifeform traits master list (v4:2021-03-17)
DOI: 10.17031/1708
title: Continuous Plankton Recorder Dataset
DOI: 10.17031/1712
title: Selected CPR zooplankton for ICES regions 4a and 4b
DOI: 10.17031/1713
title: Copepods to species level for the North Atlantic - CPR data 2009 to 2018
DOI: 10.17031/1716
title: Spindelei records in the CPR Survey
DOI: 10.17031/1721
title: S3 Eurohab Selected CPR Taxa
DOI: 10.17031/1720
title: Phytoplankton Colour Index in the North Atlantic from 1958 to 2018
DOI: 10.17031/1723
title: Gridded Phytoplankton Colour Index 1958 - 2018
DOI: 10.17031/1735
title: CPR Records of Prorocentrum North Atlantic 1958 to 2018
DOI: 10.17031/1736
title: GMIT Unlocking the archive CPR dataset
DOI: 10.17031/1737
title: WGEAWESS Atlantic ITA CPR data
DOI: 10.17031/1738
title: Selected CPR Phytoplankton taxa
DOI: 10.17031/1739
title: CPR Thecosomes
DOI: 10.17031/1740
title: North Sea CPR select functional groups
DOI: 10.17031/1741
title: 2009-2019 University of Plymouth Lyme Bay Baited Remote Underwater Video system Metrics
DOI: 10.17031/1744
title: Shelf waters CPR assorted plankton data
DOI: 10.17031/1749
title: CPR example dataset
DOI: 10.17031/1673
title: CPR data NE Atlantic selected taxa
DOI: 10.17031/1751
title: CPR Thecosome and Euphausiid data for Grand Banks and Labrador Sea, 1991 to 2019
DOI: 10.17031/1752
title: Celtic Sea selected CPR zooplankton
DOI: 10.17031/1756
title: CPR selected zooplankton and total diatoms_dinos from NE Atlantic Shelf Standard areas
DOI: 10.17031/1757
title: Selected CPR taxa data from standard areas C4 and C5
DOI: 10.17031/1758
title: North Sea CPR Calanus and selected zooplankton
DOI: 10.17031/1760
title: 2015 Scottish Environment Protection Agency (SEPA) Outer Cromarty Firth Intertidal Seagrass Survey
DOI: 10.17031/1768
title: 2006 Essex Wildlife Trust Essex Undaria pinnatifida records
DOI: 10.17031/1778
title: Selected CPR zooplankton for Ireland
DOI: 10.17031/1779
title: NW Atlantic CPR Thecosomata
DOI: 10.17031/mu7fpl
title: Infaunal abundance and biomass data from surveys of the East Antrim Maerl bed in 2004

description: This dataset contains information on infaunal abundance and biomass from sediment grabs in Red Bay, Co. Antrim in 2004 on the RV Lough Foyle. The data from this survey was used to help support the Special Area of Conservation (SAC) site designation for Red Bay, Co. Antrim. A day grab was used to collect the samples, in total there were 20 samples taken and analysed. Particle Size Analysis (PSA) and Carbon & Nitrogen analysis was carried out on the sediments from the grab. The presence and absence of Maerl (alive or dead) was also recorded. The most abundant species found was Calcarea sp. and the most frequently recorded was the polychaete Glycera lapidium.
DOI: 10.17031/1718
title: 2009-2018 University of Plymouth Lyme Bay Benthic Video Survey metrics

description: Functional diversity, number of taxa and Cummulative weighted means of trait proportions from 2009 to 2018 derived from a combination of Baited Remote Underwater Video and Towed Underwater Video data. Calculation of metrics utilised the r programming language and the funrar and FD r Packages. The current resource available is version 2, a summary of the changes applied to the previous version: Within the creation of thesis univariate metrics the inclusion of species measured by their cover (such as mat forming species) were not included, while all abundance measured species were. This meant that all species came from the same underlying abundance distributions. For access to version 1 of this resource visit: https://dassh.ac.uk/downloads/DASSHDT00000472_v1
DOI: 10.17031/1799
title: NERC Grant NE/N011708/1. An unexpected requirement for silicon in coccolithophore calcification
DOI: 10.17031/1803
title: 2013 Scottish Environment Protection Agency (SEPA) Eden Estuary Intertidal Seagrass Survey
DOI: 10.17031/1804
title: 1991 Marine Biological Association (MBA) Witch Ground Basin RRS Challenger Cruise 82 sediment cores and gas sampling
DOI: 10.17031/1805
title: 2010 Natural England (NE) Flamborough Head SAC, biotope mapping of the intertidal reef feature
DOI: 10.17031/1809
title: 2004 Scottish Environment Protection Agency (SEPA) Irvine bay Grab Survey