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

Kirkegaard2017 - 16S rRNA gene amplicon survey of anaerobic digesters

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

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

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

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.

mmlong2-lite

Singularity container for mmlong2-lite workflow Intended to be used with Snakemake workflow manage

Methonotrophic Biomass Quant BUP part2

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. This is the second part of the dataset for the manuscript. The former set can be found in "Gregersen, Simon (2021), “Methonotrophic Biomass Quant BUP”, Mendeley Data, V1", doi: 10.17632/g45gbw5r7n.

E.denticulatum quant BUP

MaxQuant output files (txt folder) from quantitative bottom-up proteomics analysis of two pilot-scale hot-water extracts from E. denticulatum, described in the manuscript "Proteomic characterization of pilot scale hot-water extracts from the industrial carrageenan red seaweed Eucheuma denticulatum" Extract A is labelled "A-013-05e" and Extract B "A-022-05e". Data is organized as exploratory phase (unspecific analysis with 1%, 5%, and 10% FDR as well as semi-specific analysis with 1% and 5% FDR) and as final phase (for tryptic and semi-specific analysis with optimized search parameters). Raw MS data are available upon request. Repository also contains the reference protein database (in .fasta format) as well as qRNAseq data

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

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