Abstract:
:With the aim to uncover the molecular pathways underlying the regulation of sleep, we recently assembled an extensive and comprehensive systems genetics dataset interrogating a genetic reference population of mice at the levels of the genome, the brain and liver transcriptomes, the plasma metabolome, and the sleep-wake phenome. To facilitate a meaningful and efficient re-use of this public resource by others we designed, describe in detail, and made available a Digital Research Object (DRO), embedding data, documentation, and analytics. We present and discuss both the advantages and limitations of our multi-modal resource and analytic pipeline. The reproducibility of the results was tested by a bioinformatician not implicated in the original project and the robustness of results was assessed by re-annotating genetic and transcriptome data from the mm9 to the mm10 mouse genome assembly.
journal_name
Sci Datajournal_title
Scientific dataauthors
Jan M,Gobet N,Diessler S,Franken P,Xenarios Idoi
10.1038/s41597-019-0171-xsubject
Has Abstractpub_date
2019-10-31 00:00:00pages
258issue
1issn
2052-4463pii
10.1038/s41597-019-0171-xjournal_volume
6pub_type
杂志文章相关文献
Scientific Data文献大全abstract::Metadata that are structured using principled schemas and that use terms from ontologies are essential to making biomedical data findable and reusable for downstream analyses. The largest source of metadata that describes the experimental protocol, funding, and scientific leadership of clinical studies is ClinicalTria...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/s41597-020-00780-z
更新日期:2020-12-18 00:00:00
abstract::The use of hydrogen (H2) as a substitute for fossil fuel, which accounts for the majority of the world's energy, is environmentally the most benign option for the reduction of CO2 emissions. This will require gigawatt-scale storage systems and as such, H2 storage in porous rocks in the subsurface will be required. Acc...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/s41597-020-0568-6
更新日期:2020-07-09 00:00:00
abstract::The mammalian innate immune system senses many bacterial stimuli through the toll-like receptor (TLR) family. Activation of the TLR4 receptor by bacterial lipopolysaccharide (LPS) is the most widely studied TLR pathway due to its central role in host responses to gram-negative bacterial infection and its contribution ...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/sdata.2017.7
更新日期:2017-03-01 00:00:00
abstract::Phase contrast time-lapse microscopy is a non-destructive technique that generates large volumes of image-based information to quantify the behaviour of individual cells or cell populations. To guide the development of algorithms for computer-aided cell tracking and analysis, 48 time-lapse image sequences, each spanni...
journal_title:Scientific data
pub_type:
doi:10.1038/sdata.2018.237
更新日期:2018-11-13 00:00:00
abstract::Tardigrades are ubiquitous microscopic animals that play an important role in the study of metazoan phylogeny. Most terrestrial tardigrades can withstand extreme environments by entering an ametabolic desiccated state termed anhydrobiosis. Due to their small size and the non-axenic nature of laboratory cultures, molec...
journal_title:Scientific data
pub_type: 评论,杂志文章
doi:10.1038/sdata.2016.63
更新日期:2016-08-16 00:00:00
abstract::We performed whole-genome sequencing for eight inbred rat strains commonly used in genetic mapping studies. They are the founders of the NIH heterogeneous stock (HS) outbred colony. We provide their sequences and variant calls to the rat genomics community. When analyzing the variant calls we identified regions with u...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/s41597-019-0041-6
更新日期:2019-04-23 00:00:00
abstract::The nuclear receptor estrogen receptor 2 (ESR2, ERβ) modulates cancer cell proliferation and tumor growth, exerting an oncosuppressive role in breast cancer (BC). Interaction proteomics by tandem affinity purification coupled to mass spectrometry was previously applied in BC cells to identify proteins acting in concer...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/sdata.2018.31
更新日期:2018-03-06 00:00:00
abstract::Mesenchymal stem/stromal cells (MSCs) were identified in most tissues of an adult organism. MSCs mediate physiological renewal, as well as regulation of tissue homeostasis, reparation and regeneration. Functions of MSCs are regulated by endocrine and neuronal signals, and noradrenaline is one of the most important MSC...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/sdata.2018.196
更新日期:2018-10-02 00:00:00
abstract::Long-term exposure to air pollution is considered a major public health concern and has been related to overall mortality and various diseases such as respiratory and cardiovascular disease. Due to the spatial variability of air pollution concentrations, assessment of individual exposure to air pollution requires spat...
journal_title:Scientific data
pub_type:
doi:10.1038/sdata.2019.35
更新日期:2019-03-12 00:00:00
abstract::Hydrologic soil groups (HSGs) are a fundamental component of the USDA curve-number (CN) method for estimation of rainfall runoff; yet these data are not readily available in a format or spatial-resolution suitable for regional- and global-scale modeling applications. We developed a globally consistent, gridded dataset...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/sdata.2018.91
更新日期:2018-05-15 00:00:00
abstract::A synthesis of phenotypic and quantitative genomic traits is provided for bacteria and archaea, in the form of a scripted, reproducible workflow that standardizes and merges 26 sources. The resulting unified dataset covers 14 phenotypic traits, 5 quantitative genomic traits, and 4 environmental characteristics for app...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/s41597-020-0497-4
更新日期:2020-06-05 00:00:00
abstract::Understanding of sequence diversity is the cornerstone of analysis of genetic disorders, population genetics, and evolutionary biology. Here, we present an update of our sequencing set to 15,220 Icelanders who we sequenced to an average genome-wide coverage of 34X. We identified 39,020,168 autosomal variants passing G...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/sdata.2017.115
更新日期:2017-09-21 00:00:00
abstract::Neural microarchitecture is heterogeneous, varying both across and within brain regions. The consistent identification of regions of interest is one of the most critical aspects in examining neurocircuitry, as these structures serve as the vital landmarks with which to map brain pathways. Access to continuous, three-d...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/s41597-020-00692-y
更新日期:2020-10-20 00:00:00
abstract::Lysosomes are the main degradative organelles of cells and involved in a variety of processes including the recycling of macromolecules, storage of compounds, and metabolic signaling. Despite an increasing interest in the proteomic analysis of lysosomes, no systematic study of sample preparation protocols for lysosome...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/s41597-020-0399-5
更新日期:2020-02-26 00:00:00
abstract::RAS genes are frequently mutated in cancer and have for decades eluded effective therapeutic attack. The National Cancer Institute's RAS Initiative has a focus on understanding pathways and discovering therapies for RAS-driven cancers. Part of these efforts is the generation of novel reagents to enable the quantificat...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/s41597-019-0166-7
更新日期:2019-08-29 00:00:00
abstract::Efficient energy consumption at the building level is vital for sustainability. Providing energy efficient systems and solutions requires an understanding of how energy gets consumed. However, there is a general lack of large-scale open datasets about the energy consumption of buildings, which hinders the research. Th...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/sdata.2019.15
更新日期:2019-02-19 00:00:00
abstract::Larval fishes are a useful metric of marine ecosystem state and change, as well as species-specific patterns in phenology. The high level of taxonomic expertise required to identify larval fishes to species level, and the considerable effort required to collect samples, make these data very valuable. Here we collate 3...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/sdata.2018.207
更新日期:2018-10-16 00:00:00
abstract::The experimental dataset presented was collected in an 18 m long and 1 m wide laboratory flume. Low to high flood flows through an urbanized floodplain were modelled. The floodplain bed is rough, modelled with dense artificial grass. A square cylinder array, representing house models, was set on the rough bed. The cyl...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/s41597-020-00791-w
更新日期:2021-01-11 00:00:00
abstract::Transparent evaluations of FAIRness are increasingly required by a wide range of stakeholders, from scientists to publishers, funding agencies and policy makers. We propose a scalable, automatable framework to evaluate digital resources that encompasses measurable indicators, open source tools, and participation guide...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/s41597-019-0184-5
更新日期:2019-09-20 00:00:00
abstract::In response to the COVID-19 pandemic, governments have implemented a wide range of non-pharmaceutical interventions (NPIs). Monitoring and documenting government strategies during the COVID-19 crisis is crucial to understand the progression of the epidemic. Following a content analysis strategy of existing public info...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/s41597-020-00609-9
更新日期:2020-08-27 00:00:00
abstract::Orchids are renowned for their spectacular flowers and ecological adaptations. After the sequencing of the genome of the tropical epiphytic orchid Phalaenopsis equestris, we combined Illumina HiSeq2000 for RNA-Seq and Trinity for de novo assembly to characterize the transcriptomes for 11 diverse P. equestris tissues r...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/sdata.2016.83
更新日期:2016-09-27 00:00:00
abstract::This paper describes the release of the detailed building operation data, including electricity consumption and indoor environmental measurements, of the seven-story 11,700-m2 office building located in Bangkok, Thailand. The electricity consumption data (kW) are that of individual air conditioning units, lighting, an...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/s41597-020-00582-3
更新日期:2020-07-20 00:00:00
abstract::As a World Health Organization Research and Development Blueprint priority pathogen, there is a need to better understand the geographic distribution of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) and its potential to infect mammals and humans. This database documents cases of MERS-CoV globally, with speci...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/s41597-019-0330-0
更新日期:2019-12-13 00:00:00
abstract::While tick-borne zoonoses, such as Lyme disease and tick-borne encephalitis, present an increasing global concern, knowledge of their vectors' distribution remains limited, especially for China. In this paper, we present the first comprehensive dataset of known tick species and their distributions in China, derived fr...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/s41597-019-0115-5
更新日期:2019-07-01 00:00:00
abstract::Preterm birth, or the delivery of an infant prior to 37 weeks of gestation, is a significant cause of infant morbidity and mortality. In the last decade, the advent and continued development of molecular profiling technologies has enabled researchers to generate vast amount of 'omics' data, which together with integra...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/sdata.2018.219
更新日期:2018-11-06 00:00:00
abstract::Social network analysis is an invaluable tool to understand the patterns, evolution, and consequences of sociality. Comparative studies over a range of social systems across multiple taxonomic groups are particularly valuable. Such studies however require quantitative social association or interaction data across mult...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/s41597-019-0056-z
更新日期:2019-04-29 00:00:00
abstract::Asymptomatic ebolavirus infection could greatly influence transmission dynamics, but there is little consensus on how frequently it occurs or even if it exists. This paper summarises the available evidence on seroprevalence of Ebola, Sudan and Bundibugyo virus IgG in people without known ebolavirus disease. Through sy...
journal_title:Scientific data
pub_type: 杂志文章,meta分析,评审
doi:10.1038/sdata.2016.133
更新日期:2017-01-31 00:00:00
abstract::Future highly renewable energy systems will couple to complex weather and climate dynamics. This coupling is generally not captured in detail by the open models developed in the power and energy system communities, where such open models exist. To enable modeling such a future energy system, we describe a dedicated la...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/sdata.2017.175
更新日期:2017-11-28 00:00:00
abstract::The quantity and condition of downed dead wood (DDW) is emerging as a major factor governing forest ecosystem processes such as carbon cycling, fire behavior, and tree regeneration. Despite this, systematic inventories of DDW are sparse if not absent across major forest biomes. The Forest Inventory and Analysis progra...
journal_title:Scientific data
pub_type:
doi:10.1038/sdata.2018.303
更新日期:2019-01-08 00:00:00
abstract::The Systems Biology for Infectious Diseases Research program was established by the U.S. National Institute of Allergy and Infectious Diseases to investigate host-pathogen interactions at a systems level. This program generated 47 transcriptomic and proteomic datasets from 30 studies that investigate in vivo and in vi...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/sdata.2014.33
更新日期:2014-10-14 00:00:00