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  • 1. Alneberg, Johannes
    et al.
    Sundh, John
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Bennke, Christin
    Beier, Sara
    Lundin, Daniel
    Hugerth, Luisa W.
    Pinhassi, Jarone
    Kisand, Veljo
    Riemann, Lasse
    Jürgens, Klaus
    Labrenz, Matthias
    Andersson, Anders F.
    BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea2018In: Scientific Data, E-ISSN 2052-4463, Vol. 5, article id 180146Article in journal (Refereed)
    Abstract [en]

    The Baltic Sea is one of the world's largest brackish water bodies and is characterised by pronounced physicochemical gradients where microbes are the main biogeochemical catalysts. Meta-omic methods provide rich information on the composition of, and activities within, microbial ecosystems, but are computationally heavy to perform. We here present the Baltic Sea Reference Metagenome (BARM), complete with annotated genes to facilitate further studies with much less computational effort. The assembly is constructed using 2.6 billion metagenomic reads from 81 water samples, spanning both spatial and temporal dimensions, and contains 6.8 million genes that have been annotated for function and taxonomy. The assembly is useful as a reference, facilitating taxonomic and functional annotation of additional samples by simply mapping their reads against the assembly. This capability is demonstrated by the successful mapping and annotation of 24 external samples. In addition, we present a public web interface, BalticMicrobeDB, for interactive exploratory analysis of the dataset. [GRAPHICS] .

  • 2.
    Burgos, María A.
    et al.
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Andrews, Elisabeth
    Titos, Gloria
    Alados-Arboledas, Lucas
    Baltensperger, Urs
    Day, Derek
    Jefferson, Anne
    Kalivitis, Nikos
    Mihalopoulos, Nikos
    Sherman, James
    Sun, Junying
    Weingartner, Ernest
    Zieger, Paul
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    A global view on the effect of water uptake on aerosol particle light scattering2019In: Scientific Data, E-ISSN 2052-4463, Vol. 6, article id 157Article in journal (Refereed)
    Abstract [en]

    A reference dataset of multi-wavelength particle light scattering and hemispheric backscattering coefficients for different relative humidities (RH) between RH = 30 and 95% and wavelengths between lambda = 450 nm and 700 nm is described in this work. Tandem-humidified nephelometer measurements from 26 ground-based sites around the globe, covering multiple aerosol types, have been re-analysed and harmonized into a single dataset. The dataset includes multi-annual measurements from long-term monitoring sites as well as short-term field campaign data. The result is a unique collection of RH-dependent aerosol light scattering properties, presented as a function of size cut. This dataset is important for climate and atmospheric model-measurement inter-comparisons, as a means to improve model performance, and may be useful for satellite and remote sensing evaluation using surface-based, in-situ measurements.

  • 3. Mukwaya, Anthony
    et al.
    Lindvall, Jessica M.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Xeroudaki, Maria
    Peebo, Beatrice
    Ali, Zaheer
    Lennikov, Anton
    Dahl Ejby Jensen, Lasse
    Lagali, Neil
    A microarray whole-genome gene expression dataset in a rat model of inflammatory corneal angiogenesis2016In: Scientific Data, E-ISSN 2052-4463, Vol. 3, article id 160103Article in journal (Refereed)
    Abstract [en]

    In angiogenesis with concurrent inflammation, many pathways are activated, some linked to VEGF and others largely VEGF-independent. Pathways involving inflammatory mediators, chemokines, and micro-RNAs may play important roles in maintaining a pro-angiogenic environment or mediating angiogenic regression. Here, we describe a gene expression dataset to facilitate exploration of pro-angiogenic, pro-inflammatory, and remodelling/normalization-associated genes during both an active capillary sprouting phase, and in the restoration of an avascular phenotype. The dataset was generated by microarray analysis of the whole transcriptome in a rat model of suture-induced inflammatory corneal neovascularisation. Regions of active capillary sprout growth or regression in the cornea were harvested and total RNA extracted from four biological replicates per group. High quality RNA was obtained for gene expression analysis using microarrays. Fold change of selected genes was validated by qPCR, and protein expression was evaluated by immunohistochemistry. We provide a gene expression dataset that may be re-used to investigate corneal neovascularisation, and may also have implications in other contexts of inflammation-mediated angiogenesis.

  • 4.
    Roquet, Fabien
    et al.
    Stockholm University, Faculty of Science, Department of Meteorology .
    Williams, Guy
    Hindell, Mark A.
    Harcourt, Rob
    McMahon, Clive
    Guinet, Christophe
    Charrassin, Jean-Benoit
    Reverdin, Gilles
    Boehme, Lars
    Lovell, Phil
    Fedak, Mike
    A Southern Indian Ocean database of hydrographic profiles obtained with instrumented elephant seals2014In: Scientific Data, E-ISSN 2052-4463, Vol. 1, article id 140028Article in journal (Refereed)
    Abstract [en]

    The instrumentation of southern elephant seals with satellite-linked CTD tags has offered unique temporal and spatial coverage of the Southern Indian Ocean since 2004. This includes extensive data from the Antarctic continental slope and shelf regions during the winter months, which is outside the conventional areas of Argo autonomous floats and ship-based studies. This landmark dataset of around 75,000 temperature and salinity profiles from 20–140 °E, concentrated on the sector between the Kerguelen Islands and Prydz Bay, continues to grow through the coordinated efforts of French and Australian marine research teams. The seal data are quality controlled and calibrated using delayed-mode techniques involving comparisons with other existing profiles as well as cross-comparisons similar to established protocols within the Argo community, with a resulting accuracy of ±0.03 °C in temperature and ±0.05 in salinity or better. The data offer invaluable new insights into the water masses, oceanographic processes and provides a vital tool for oceanographers seeking to advance our understanding of this key component of the global ocean climate.

  • 5. Schoffelen, Jan-Mathijs
    et al.
    Oostenveld, Robert
    Lam, Nietzsche H. L.
    Uddén, Julia
    Stockholm University, Faculty of Social Sciences, Department of Psychology. Stockholm University, Faculty of Humanities, Department of Linguistics. Radboud University, The Netherlands; Max Planck Institute for Psycholinguistics, The Netherlands; Swedish Collegium for Advanced Study, Sweden.
    Hultén, Annika
    Hagoort, Peter
    A 204-subject multimodal neuroimaging dataset to study language processing2019In: Scientific Data, E-ISSN 2052-4463, Vol. 6, article id 17Article in journal (Refereed)
    Abstract [en]

    This dataset, colloquially known as the Mother Of Unification Studies (MOUS) dataset, contains multimodal neuroimaging data that has been acquired from 204 healthy human subjects. The neuroimaging protocol consisted of magnetic resonance imaging (MRI) to derive information at high spatial resolution about brain anatomy and structural connections, and functional data during task, and at rest. In addition, magnetoencephalography (MEG) was used to obtain high temporal resolution electrophysiological measurements during task, and at rest. All subjects performed a language task, during which they processed linguistic utterances that either consisted of normal or scrambled sentences. Half of the subjects were reading the stimuli, the other half listened to the stimuli. The resting state measurements consisted of 5 minutes eyes-open for the MEG and 7 minutes eyes-closed for fMRI. The neuroimaging data, as well as the information about the experimental events are shared according to the Brain Imaging Data Structure (BIDS) format. This unprecedented neuroimaging language data collection allows for the investigation of various aspects of the neurobiological correlates of language.

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