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  • Baltic Sea; BED; Local adaptation; methylation call; population genomics; SNP; three-spined stickleback; Whole genome sequencing  (2)
  • Abundance; Abundance per volume; Biovolume; C. affinis; Calculated; Carbon, total, particulate/Nitrogen, total, particulate ratio; Cell biovolume; Cell surface area/cell volume ratio; Chaetoceros affinis; Chaetoceros affinis, biovolume; Chaetoceros affinis, cell biovolume; Chaetoceros affinis, growth rate; Chaetoceros affinis, surface area; Coccolithophores; Diatom; E. huxleyi; Eco-evolution; Emiliania huxleyi; Emiliania huxleyi, biovolume; Emiliania huxleyi, cell biovolume; Emiliania huxleyi, growth rate; Emiliania huxleyi, surface area; experimental data; Growth rate; Identification; Mean values; Number of batch; Number percentage; partition; Priority Programme 1704 DynaTrait: Flexibility Matters: Interplay between Trait Diversity and Ecological Dynamics Using Aquatic Communities as Model Systems; Replicate; size; SPP1704; Time in days; Treatment  (1)
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  • 1
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    Unknown
    High quality G-to-A SNPs from the genomes of 96 wild caught three-spine sticklebacks (2019)
    PANGAEA
    Details
    Publication Date: 2023-01-13
    Description: To improve the methylation estimates in our study, we corrected for SNPs, which could have led to a wrong methylation call. The excluded positions were derived with custom written perl scripts from C-to-T and G-to-A-SNPs with genotype quality of 20 and a minimum allele frequency of 0.005 from the 96 wild caught three-spined sticklebacks with a combination of custom written Perl and R-scripts using packages from methylkit and GenomicRanges. This BED-file contains the G-to-A-SNPs, in which the first field is the name of the chromosome; the second describes the start position and the third the end position of the feature in standard chromosomal coordinates.
    Keywords: Baltic Sea; BED; Local adaptation; methylation call; population genomics; SNP; three-spined stickleback; Whole genome sequencing
    Type: Dataset
    Format: application/zip, 5.8 MBytes
    Location Call Number Limitation Availability
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    DATA PANGAEA
  • 2
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    Unknown
    High quality C-to-T SNPs from the genomes of 96 wild caught three-spine sticklebacks (2019)
    PANGAEA
    Details
    Publication Date: 2023-01-13
    Description: To improve the methylation estimates in our study, we corrected for SNPs, which could have led to a wrong methylation call. The excluded positions were derived with custom written perl scripts from C-to-T and G-to-A-SNPs with genotype quality of 20 and a minimum allele frequency of 0.005 from the 96 wild caught three-spined sticklebacks with a combination of custom written Perl and R-scripts using packages from methylkit and GenomicRanges. This BED-file contains the C-to-T SNPs, in which the first field is the name of the chromosome; the second describes the start position and the third the end position of the feature in standard chromosomal coordinates.
    Keywords: Baltic Sea; BED; Local adaptation; methylation call; population genomics; SNP; three-spined stickleback; Whole genome sequencing
    Type: Dataset
    Format: application/zip, 5.8 MBytes
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    DATA PANGAEA
  • 3
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    Unknown
    Experiment on an artificial phytoplankton community in response to high CO2: relative importance assay and calculated relative importance (2022)
    PANGAEA
    Details
    Publication Date: 2024-03-22
    Description: This dataset includes information specific to the Eco-Evo assay applied to a long-term community selection experiment after 80,186, and 288 days. The community contained Emiliania huxleyi and Chaetoceros affinis (details about Species and genotypes used can be found in doi:10.1098/rsbl.2016.0774). The long-term community selection phase to ambient and high CO2 (400 and 1250ppm, respectively) started on the 10th of January 2017, details about the sorting phase in semi-continuous batch cycles can be found in doi:10.1594/PANGAEA.887780. Here, the raw data from the subsequent Eco-Evo assay are presented, as well as the calculated relative importance of species and genotype sorting.The first eco-evo Assay (after 80 days) previously served to validate the new method (https://doi.org/10.1111/1365-2435.13923) and Abundance (column 8) of Time 80 (first 25 rows) and the calculated relative contribution to total changes of that timepoint (column 28- first 4 rows) are also included in the previous dataset (https://doi.org/10.1594/PANGAEA.896220). Abundance-weighted means are calculated as the sum of each species' cell abundances multiplied with their respective trait, divided by the total cell abundance. Relative Importance of eco-evolutionary changes to the total change are calculated following the formula given in Hattich et al 2022 (https://doi.org/10.1111/1365-2435.13923).
    Keywords: Abundance; Abundance per volume; Biovolume; C. affinis; Calculated; Carbon, total, particulate/Nitrogen, total, particulate ratio; Cell biovolume; Cell surface area/cell volume ratio; Chaetoceros affinis; Chaetoceros affinis, biovolume; Chaetoceros affinis, cell biovolume; Chaetoceros affinis, growth rate; Chaetoceros affinis, surface area; Coccolithophores; Diatom; E. huxleyi; Eco-evolution; Emiliania huxleyi; Emiliania huxleyi, biovolume; Emiliania huxleyi, cell biovolume; Emiliania huxleyi, growth rate; Emiliania huxleyi, surface area; experimental data; Growth rate; Identification; Mean values; Number of batch; Number percentage; partition; Priority Programme 1704 DynaTrait: Flexibility Matters: Interplay between Trait Diversity and Ecological Dynamics Using Aquatic Communities as Model Systems; Replicate; size; SPP1704; Time in days; Treatment
    Type: Dataset
    Format: text/tab-separated-values, 1779 data points
    Location Call Number Limitation Availability
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    DATA PANGAEA
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