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Scientific Data

Hákon Jónsson, Patrick Sulem, Birte Kehr, Snaedis Kristmundsdottir, Florian Zink, Eirikur Hjartarson, Marteinn T Hardarson, Kristjan E Hjorleifsson, Hannes P Eggertsson, Sigurjon Axel Gudjonsson, Lucas D Ward, Gudny A Arnadottir, Einar A Helgason, Hannes Helgason, Arnaldur Gylfason, Adalbjorg Jonasdottir, Aslaug Jonasdottir, Thorunn Rafnar, Soren Besenbacher, Michael L Frigge, Simon N Stacey, Olafur Th Magnusson, Unnur Thorsteinsdottir, Gisli Masson, Augustine Kong, Bjarni V Halldorsson, Agnar Helgason, Daniel F Gudbjartsson, Kari Stefansson
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 GATK filters: 31,079,378 SNPs and 7,940,790 indels. Calling de novo mutations (DNMs) is a formidable challenge given the high false positive rate in sequencing datasets relative to the mutation rate...
September 21, 2017: Scientific Data
Dexter Hadley, James Pan, Osama El-Sayed, Jihad Aljabban, Imad Aljabban, Tej D Azad, Mohamad O Hadied, Shuaib Raza, Benjamin Abhishek Rayikanti, Bin Chen, Hyojung Paik, Dvir Aran, Jordan Spatz, Daniel Himmelstein, Maryam Panahiazar, Sanchita Bhattacharya, Marina Sirota, Mark A Musen, Atul J Butte
The Gene Expression Omnibus (GEO) contains more than two million digital samples from functional genomics experiments amassed over almost two decades. However, individual sample meta-data remains poorly described by unstructured free text attributes preventing its largescale reanalysis. We introduce the Search Tag Analyze Resource for GEO as a web application ( to curate better annotations of sample phenotypes uniformly across different studies, and to use these sample annotations to define robust genomic signatures of disease pathology by meta-analysis...
September 19, 2017: Scientific Data
Nicolas Gerber, Mauricio Reyes, Livia Barazzetti, Hans Martin Kjer, Sergio Vera, Martin Stauber, Pavel Mistrik, Mario Ceresa, Nerea Mangado, Wilhelm Wimmer, Thomas Stark, Rasmus R Paulsen, Stefan Weber, Marco Caversaccio, Miguel A González Ballester
Understanding the human inner ear anatomy and its internal structures is paramount to advance hearing implant technology. While the emergence of imaging devices allowed researchers to improve understanding of intracochlear structures, the difficulties to collect appropriate data has resulted in studies conducted with few samples. To assist the cochlear research community, a large collection of human temporal bone images is being made available. This data descriptor, therefore, describes a rich set of image volumes acquired using cone beam computed tomography and micro-CT modalities, accompanied by manual delineations of the cochlea and sub-compartments, a statistical shape model encoding its anatomical variability, and data for electrode insertion and electrical simulations...
September 19, 2017: Scientific Data
Fred Prior, Kirk Smith, Ashish Sharma, Justin Kirby, Lawrence Tarbox, Ken Clark, William Bennett, Tracy Nolan, John Freymann
The Cancer Imaging Archive (TCIA) is the U.S. National Cancer Institute's repository for cancer imaging and related information. TCIA contains 30.9 million radiology images representing data collected from approximately 37,568 subjects. This data is organized into collections by tumor-type with many collections also including analytic results or clinical data. TCIA staff carefully de-identify and curate all incoming collections prior to making the information available via web browser or programmatic interfaces...
September 19, 2017: Scientific Data
Tomaso Fortibuoni, Simone Libralato, Enrico Arneri, Otello Giovanardi, Cosimo Solidoro, Saša Raicevich
Historic data on biodiversity provide the context for present observations and allow studying long-term changes in marine populations. Here we present multiple datasets on fish and fisheries of the Adriatic Sea covering the last two centuries encompassing from qualitative observations to standardised scientific monitoring. The datasets consist of three groups: (1) early naturalists' descriptions of fish fauna, including information (e.g., presence, perceived abundance, size) on 255 fish species for the period 1818-1936; (2) historical landings from major Northern Adriatic fish markets (Venice, Trieste, Rijeka) for the period 1902-1968, Italian official landings for the Northern and Central Adriatic (1953-2012) and landings from the Lagoon of Venice (1945-2001); (3) trawl-survey data from seven surveys spanning the period 1948-1991 and including Catch per Unit of Effort data (kgh(-1) and/or nh(-1)) for 956 hauls performed at 301 stations...
September 12, 2017: Scientific Data
Sarah A Marley, Christine Erbe, Chandra P Salgado Kent
Dolphins use frequency-modulated whistles for a variety of social functions. Whistles vary in their characteristics according to context, such as activity state, group size, group composition, geographic location, and ambient noise levels. Therefore, comparison of whistle characteristics can be used to address numerous research questions regarding dolphin populations and behaviour. However, logistical and economic constraints on dolphin research have resulted in data collection biases, inconsistent analytical approaches, and knowledge gaps...
September 12, 2017: Scientific Data
Jesús M Ibáñez, Alejandro Díaz-Moreno, Janire Prudencio, Daria Zandomeneghi, William Wilcock, Andrew Barclay, Javier Almendros, Carmen Benítez, Araceli García-Yeguas, Gerardo Alguacil
Deception Island volcano (Antarctica) is one of the most closely monitored and studied volcanoes on the region. In January 2005, a multi-parametric international experiment was conducted that encompassed both Deception Island and its surrounding waters. We performed this experiment from aboard the Spanish oceanographic vessel 'Hespérides', and from five land-based locations on Deception Island (the Spanish scientific Antarctic base 'Gabriel de Castilla' and four temporary camps). This experiment allowed us to record active seismic signals using a large network of seismic stations that were deployed both on land and on the seafloor...
September 12, 2017: Scientific Data
Louise van der Weyden, Natasha A Karp, Agnieszka Swiatkowska, David J Adams, Anneliese O Speak
The process of metastasis is a multi-stage cascade with prior studies suggesting that the colonisation of the secondary site is the rate limiting step. This process involves contributions from the tumour cells and also non-tumour intrinsic factors such as the stroma and the haematopoietic system. In this study, we present data from screening 810 genetically-modified mouse lines with the experimental metastasis assay where intravenous delivery of murine metastatic melanoma B16-F10 cells was used to assess the formation of pulmonary metastasic foci...
September 12, 2017: Scientific Data
Edward Kim, Kevin Huang, Alex Tomala, Sara Matthews, Emma Strubell, Adam Saunders, Andrew McCallum, Elsa Olivetti
Predictive materials design has rapidly accelerated in recent years with the advent of large-scale resources, such as materials structure and property databases generated by ab initio computations. In the absence of analogous ab initio frameworks for materials synthesis, high-throughput and machine learning techniques have recently been harnessed to generate synthesis strategies for select materials of interest. Still, a community-accessible, autonomously-compiled synthesis planning resource which spans across materials systems has not yet been developed...
September 12, 2017: Scientific Data
Samuel J White, Brent Vadopalas, Katherine Silliman, Steven B Roberts
Olympia oysters are found along the west coast of North America and as the only native oyster species in the region, receive considerable attention with regard to restoration and conservation. Knowledge of genetic structure of this species is essential for resource managers. Here we provide genetic data for three distinct populations of Olympia oysters in Puget Sound, Washington, USA in the form of genotype-by-sequencing data (GBS). Specifically, this includes description of sequence data and a derived table that provides single nucleotide polymorphism (SNP) information for 10,363 loci...
September 12, 2017: Scientific Data
Dirk Nikolaus Karger, Olaf Conrad, Jürgen Böhner, Tobias Kawohl, Holger Kreft, Rodrigo Wilber Soria-Auza, Niklaus E Zimmermann, H Peter Linder, Michael Kessler
High-resolution information on climatic conditions is essential to many applications in environmental and ecological sciences. Here we present the CHELSA (Climatologies at high resolution for the earth's land surface areas) data of downscaled model output temperature and precipitation estimates of the ERA-Interim climatic reanalysis to a high resolution of 30 arc sec. The temperature algorithm is based on statistical downscaling of atmospheric temperatures. The precipitation algorithm incorporates orographic predictors including wind fields, valley exposition, and boundary layer height, with a subsequent bias correction...
September 5, 2017: Scientific Data
Fantina Madricardo, Federica Foglini, Aleksandra Kruss, Christian Ferrarin, Nicola Marco Pizzeghello, Chiara Murri, Monica Rossi, Marco Bajo, Debora Bellafiore, Elisabetta Campiani, Stefano Fogarin, Valentina Grande, Lukasz Janowski, Erica Keppel, Elisa Leidi, Giuliano Lorenzetti, Francesco Maicu, Vittorio Maselli, Alessandra Mercorella, Giacomo Montereale Gavazzi, Tiziano Minuzzo, Claudio Pellegrini, Antonio Petrizzo, Mariacristina Prampolini, Alessandro Remia, Federica Rizzetto, Marzia Rovere, Alessandro Sarretta, Marco Sigovini, Luigi Sinapi, Georg Umgiesser, Fabio Trincardi
Tidal channels are crucial for the functioning of wetlands, though their morphological properties, which are relevant for seafloor habitats and flow, have been understudied so far. Here, we release a dataset composed of Digital Terrain Models (DTMs) extracted from a total of 2,500 linear kilometres of high-resolution multibeam echosounder (MBES) data collected in 2013 covering the entire network of tidal channels and inlets of the Venice Lagoon, Italy. The dataset comprises also the backscatter (BS) data, which reflect the acoustic properties of the seafloor, and the tidal current fields simulated by means of a high-resolution three-dimensional unstructured hydrodynamic model...
September 5, 2017: Scientific Data
Alexander J Cole, Ying Zhu, Trisha Dwight, Bing Yu, Kristie-Ann Dickson, Gregory B Gard, Jayne Maidens, Susan Valmadre, Anthony J Gill, Roderick Clifton-Bligh, Deborah J Marsh
Somatic mutation of the tumor suppressor gene TP53 is reported in at least 50% of human malignancies. Most high-grade serous ovarian cancers (HGSC) have a mutant TP53 allele. Accurate detection of these mutants in heterogeneous tumor tissue is paramount as therapies emerge to target mutant p53. We used a Fluidigm Access Array™ System with Massively Parallel Sequencing (MPS) to analyze DNA extracted from 76 serous ovarian tumors. This dataset has been made available to researchers through the European Genome-phenome Archive (EGA; EGAS00001002200)...
September 5, 2017: Scientific Data
Spyridon Bakas, Hamed Akbari, Aristeidis Sotiras, Michel Bilello, Martin Rozycki, Justin S Kirby, John B Freymann, Keyvan Farahani, Christos Davatzikos
Gliomas belong to a group of central nervous system tumors, and consist of various sub-regions. Gold standard labeling of these sub-regions in radiographic imaging is essential for both clinical and computational studies, including radiomic and radiogenomic analyses. Towards this end, we release segmentation labels and radiomic features for all pre-operative multimodal magnetic resonance imaging (MRI) (n=243) of the multi-institutional glioma collections of The Cancer Genome Atlas (TCGA), publicly available in The Cancer Imaging Archive (TCIA)...
September 5, 2017: Scientific Data
Brunno Freire Oliveira, Vinícius Avelar São-Pedro, Georgina Santos-Barrera, Caterina Penone, Gabriel C Costa
Current ecological and evolutionary research are increasingly moving from species- to trait-based approaches because traits provide a stronger link to organism's function and fitness. Trait databases covering a large number of species are becoming available, but such data remains scarce for certain groups. Amphibians are among the most diverse vertebrate groups on Earth, and constitute an abundant component of major terrestrial and freshwater ecosystems. They are also facing rapid population declines worldwide, which is likely to affect trait composition in local communities, thereby impacting ecosystem processes and services...
September 5, 2017: Scientific Data
Thomas Pasquier, Matthew K Lau, Ana Trisovic, Emery R Boose, Ben Couturier, Mercè Crosas, Aaron M Ellison, Valerie Gibson, Chris R Jones, Margo Seltzer
In the last few decades, data-driven methods have come to dominate many fields of scientific inquiry. Open data and open-source software have enabled the rapid implementation of novel methods to manage and analyze the growing flood of data. However, it has become apparent that many scientific fields exhibit distressingly low rates of reproducibility. Although there are many dimensions to this issue, we believe that there is a lack of formalism used when describing end-to-end published results, from the data source to the analysis to the final published results...
September 5, 2017: Scientific Data
Lothar C Dieterich, Luca Ducoli, Jay W Shin, Michael Detmar
Vascular endothelial growth factors (VEGFs) and their receptors play crucial roles in the formation of blood and lymphatic vessels during embryogenesis, and also under pathologic conditions in the adult. Despite intensive efforts over the last decades to elucidate the precise functions of VEGFs, transcriptional responses to VEGF receptor stimulation are still not fully characterized. To investigate the specific transcriptional effects of VEGFR-2 and VEGFR-3 activation, we performed a correlation analysis of previously published CAGE sequencing and microarray data of human lymphatic endothelial cells (LECs) stimulated with distinct VEGFs acting through either VEGFR-2 or VEGFR-3...
August 29, 2017: Scientific Data
Hiromasa Ono, Osamu Ogasawara, Kosaku Okubo, Hidemasa Bono
Gene expression data are exponentially accumulating; thus, the functional annotation of such sequence data from metadata is urgently required. However, life scientists have difficulty utilizing the available data due to its sheer magnitude and complicated access. We have developed a web tool for browsing reference gene expression pattern of mammalian tissues and cell lines measured using different methods, which should facilitate the reuse of the precious data archived in several public databases. The web tool is called Reference Expression dataset (RefEx), and RefEx allows users to search by the gene name, various types of IDs, chromosomal regions in genetic maps, gene family based on InterPro, gene expression patterns, or biological categories based on Gene Ontology...
August 29, 2017: Scientific Data
Hideya Kawaji, Takeya Kasukawa, Alistair Forrest, Piero Carninci, Yoshihide Hayashizaki
The latest project from the FANTOM consortium, an international collaborative effort initiated by RIKEN, generated atlases of transcriptomes, in particular promoters, transcribed enhancers, and long-noncoding RNAs, across a diverse set of mammalian cell types. Here, we introduce the FANTOM5 collection, bringing together data descriptors, articles and analyses of FANTOM5 data published across the Nature Research journals. Associated data are openly available for reuse by all.
August 29, 2017: Scientific Data
Shuhei Noguchi, Takahiro Arakawa, Shiro Fukuda, Masaaki Furuno, Akira Hasegawa, Fumi Hori, Sachi Ishikawa-Kato, Kaoru Kaida, Ai Kaiho, Mutsumi Kanamori-Katayama, Tsugumi Kawashima, Miki Kojima, Atsutaka Kubosaki, Ri-Ichiroh Manabe, Mitsuyoshi Murata, Sayaka Nagao-Sato, Kenichi Nakazato, Noriko Ninomiya, Hiromi Nishiyori-Sueki, Shohei Noma, Eri Saijyo, Akiko Saka, Mizuho Sakai, Christophe Simon, Naoko Suzuki, Michihira Tagami, Shoko Watanabe, Shigehiro Yoshida, Peter Arner, Richard A Axton, Magda Babina, J Kenneth Baillie, Timothy C Barnett, Anthony G Beckhouse, Antje Blumenthal, Beatrice Bodega, Alessandro Bonetti, James Briggs, Frank Brombacher, Ailsa J Carlisle, Hans C Clevers, Carrie A Davis, Michael Detmar, Taeko Dohi, Albert S B Edge, Matthias Edinger, Anna Ehrlund, Karl Ekwall, Mitsuhiro Endoh, Hideki Enomoto, Afsaneh Eslami, Michela Fagiolini, Lynsey Fairbairn, Mary C Farach-Carson, Geoffrey J Faulkner, Carmelo Ferrai, Malcolm E Fisher, Lesley M Forrester, Rie Fujita, Jun-Ichi Furusawa, Teunis B Geijtenbeek, Thomas Gingeras, Daniel Goldowitz, Sven Guhl, Reto Guler, Stefano Gustincich, Thomas J Ha, Masahide Hamaguchi, Mitsuko Hara, Yuki Hasegawa, Meenhard Herlyn, Peter Heutink, Kelly J Hitchens, David A Hume, Tomokatsu Ikawa, Yuri Ishizu, Chieko Kai, Hiroshi Kawamoto, Yuki I Kawamura, Judith S Kempfle, Tony J Kenna, Juha Kere, Levon M Khachigian, Toshio Kitamura, Sarah Klein, S Peter Klinken, Alan J Knox, Soichi Kojima, Haruhiko Koseki, Shigeo Koyasu, Weonju Lee, Andreas Lennartsson, Alan Mackay-Sim, Niklas Mejhert, Yosuke Mizuno, Hiromasa Morikawa, Mitsuru Morimoto, Kazuyo Moro, Kelly J Morris, Hozumi Motohashi, Christine L Mummery, Yutaka Nakachi, Fumio Nakahara, Toshiyuki Nakamura, Yukio Nakamura, Tadasuke Nozaki, Soichi Ogishima, Naganari Ohkura, Hiroshi Ohno, Mitsuhiro Ohshima, Mariko Okada-Hatakeyama, Yasushi Okazaki, Valerio Orlando, Dmitry A Ovchinnikov, Robert Passier, Margaret Patrikakis, Ana Pombo, Swati Pradhan-Bhatt, Xian-Yang Qin, Michael Rehli, Patrizia Rizzu, Sugata Roy, Antti Sajantila, Shimon Sakaguchi, Hiroki Sato, Hironori Satoh, Suzana Savvi, Alka Saxena, Christian Schmidl, Claudio Schneider, Gundula G Schulze-Tanzil, Anita Schwegmann, Guojun Sheng, Jay W Shin, Daisuke Sugiyama, Takaaki Sugiyama, Kim M Summers, Naoko Takahashi, Jun Takai, Hiroshi Tanaka, Hideki Tatsukawa, Andru Tomoiu, Hiroo Toyoda, Marc van de Wetering, Linda M van den Berg, Roberto Verardo, Dipti Vijayan, Christine A Wells, Louise N Winteringham, Ernst Wolvetang, Yoko Yamaguchi, Masayuki Yamamoto, Chiyo Yanagi-Mizuochi, Misako Yoneda, Yohei Yonekura, Peter G Zhang, Silvia Zucchelli, Imad Abugessaisa, Erik Arner, Jayson Harshbarger, Atsushi Kondo, Timo Lassmann, Marina Lizio, Serkan Sahin, Thierry Sengstag, Jessica Severin, Hisashi Shimoji, Masanori Suzuki, Harukazu Suzuki, Jun Kawai, Naoto Kondo, Masayoshi Itoh, Carsten O Daub, Takeya Kasukawa, Hideya Kawaji, Piero Carninci, Alistair R R Forrest, Yoshihide Hayashizaki
In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation...
August 29, 2017: Scientific Data
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