Kirkegaard2017 - 16S rRNA gene amplicon survey of anaerobic digesters

RData file with OTUtables and metadata for a comprehensive survey of anaerobic digester

CodfishHydrolysatesMS

MS raw data, MaxQuant output files, and Table S4 for the manuscript "Biofunctionality of enzymatically derived peptides from codfish (Gadus morhua) frame; Bulk in vitro properties, quantitative proteomics, and bioinformatic prediction

UPLIFT Plastic Upcycling project

This repository will collect the datasets, public deliverables and published articles of the UPLIFT project, funded European Union’s Horizon 2020 research and innovation programme under grant agreement Nº 953073

Interview protocol for the elicitation of community preferences

This is the standardized protocol based on the Swing method that was used to elicit weight preferences for first-level and second-level management objectives with the overall goal of developing a collaborative management plan for Blueskin Bay estuary (Aotearoa New Zealand) together with the local community

mmlong2-lite: a lightweight workflow for microbial genome recovery with long-read sequencing data

Code and files for the mmlong2-lite workflow See https://github.com/Serka-M/mmlong2-lite for more detail

MASPOT tetraploid potato clone population - GBS and phenotype data

GBS and phenotype data for MASPOT population, a panel of tetraploit potato clone

Data from: To Be or Not to Be Tetraploid - The Impact of Marker Ploidy on Genomic Prediction and GWAS of Potato

Data analyzed in the study "To Be or Not to Be Tetraploid - The Impact of Marker Ploidy on Genomic Prediction and GWAS of Potato" (Aalborg and Nielsen, 2024), including GBS data, across-year-corrected phenotype data of 762 MASPOT panel clones and 18 parents of five phenotypes chipping quality, length/width ratio, senescence, dry matter content, and yield, the parentage of the 762 MASPOT clones (incomplete 18-parent full-diallel cross). The GBS data includes the MQ30 filtered tetraploid and allele frequency genotypes of the full panel with SNPEff annotation (relative to the DMv4.03 S. tuberosum reference genome), the SNP depth at each position, a file of positions analyzed in the study (31,007 markers), and genotype matrices of the filtered (complete filtration strategy in study) tetraploid and allele frequency markers

Methonotrophic Biomass Quant BUP

Raw LC-MS/MS data and MaxQuant output files (txt folder) from quantitative bottom-up proteomics analysis of the fermeted biomass from methanotrophic bacteria described in the manuscript "Emulsifier peptides derived from seaweed, methanotrophic bacteria, and potato proteins identified by quantitative proteomics and bioinformatics". The biomass was pre-fractionated by SDS-PAGE and subsequently in-gel digested as described in M&M. The remaining two raw data files can be found in "Gregersen, Simon (2021), “Methonotrophic Biomass Quant BUP part2”, Mendeley Data, V1", doi: 10.17632/76v7mnmyr3.

Strong isolation by distance among local populations of an endangered butterfly species (Euphydryas aurinia)

The marsh fritillary (Euphydryas aurinia) is a critically endangered butterfly species in Denmark known to be particularly vulnerable to habitat fragmentation due to its poor dispersal capacity. We identified and genotyped 318 novel SNP loci across 273 individuals obtained from 10 small and fragmented populations in Denmark using a genotyping-by-sequencing (GBS) approach to investigate its population genetic structure. Our results showed clear genetic substructuring and highly significant population differentiation based on genetic divergence (FST) among the 10 populations. The populations clustered in three overall clusters and due to further substructuring among these, it was possible to clearly distinguish six clusters in total. We found highly significant deviations from Hardy-Weinberg equilibrium due to heterozygote deficiency within every population investigated which indicates substructuring and/or inbreeding (due to mating among closely related individuals). The stringent filtering procedure that we have applied to our genotype quality could have overestimated the heterozygote deficiency and the degree of substructuring of our clusters but is allowing relative comparisons of the genetic parameters among clusters. Genetic divergence increased significantly with geographic distance, suggesting limited gene flow at spatial scales comparable to the dispersal distance of individual butterflies and strong isolation by distance. Altogether, our results clearly indicate that the marsh fritillary populations are genetically isolated. Further, our results highlight that the relevant spatial scale for conservation of rare, low mobile species may be smaller than previously anticipated

Impact of substrate moisture content on growth and performance of black soldier fly larvae

Experimental data and data analyses growth, respiration and performance of black soldier fly larvae grown at different substrate moisture content