Is useful research data usually shared? An investigation of genome-wide association study summary statistics

AbstractPrimary data collected during a research study is increasingly shared and may be re-used for new studies. To assess the extent of data sharing in favourable circumstances and whether such checks can be automated, this article investigates the summary statistics of primary human genome-wide association studies (GWAS). This type of data is highly suitable for sharing because it is a standard research output, is straightforward to use in future studies (e.g., for secondary analysis), and may be already stored in a standard format for internal sharing within multi-site research projects. Manual checks of 1799 articles from 2010 and 2017 matching a simple PubMed query for molecular epidemiology GWAS were used to identify 330 primary human GWAS papers. Of these, only 10.6% reported the location of a complete set of GWAS summary data, increasing from 4.3% in 2010 to 16.8% in 2017. Whilst information about whether data was shared was usually located clearly within a data availability statement, the exact nature of the shared data was usually unspecified. Thus, data sharing is the exception even in suitable research fields with relatively strong norms regarding data sharing. Moreover, the lack of clear data descriptions within data sharing statements greatly complicates the task of automatically characterising shared data sets.</jats:p

Proteomic and transcriptomic analysis of rice tranglutaminase and chloroplast-related proteins

The recently cloned rice transglutaminase gene (tgo) is the second plant transglutaminase identified to date (Campos et al. Plant Sci. 205–206 (2013) 97–110). Similarly to its counterpart in maize (tgz), this rice TGase was localized in the chloroplast, although in this case not exclusively. To further characterise plastidial tgo functionality, proteomic and transcriptomic studies were carried out to identify possible TGO-related proteins. Some LHCII antenna proteins were identified as TGO related using an in vitro proteomic approach, as well as ATPase and some PSII core proteins by mass spectrometry. To study the relationship between TGO and other plastidial proteins, a transcriptomic in vivo Dynamic Array (Fluidigm™) was used to analyse the mRNA expression of 30 plastidial genes with respect to that of tgo, in rice plants subjected to different periods of continuous illumination. The results indicated a gene-dependent tendency in the expression pattern that was related to tgo expression and to the illumination cycle. For certain genes, including tgo, significant differences between treatments, principally at the initiation and/or at the end of the illumination period, connected with the day/night cycling of gene expression, were observed. The tgo expression was especially related to plastidial proteins involved in photoprotection and the thylakoid electrochemical gradient.This study was supported by the Spanish projects MEC BFU2006-15115-01/BMC, BFU2009-08575 and a collaborative project (TRANSBIO 2011) with the Biotechnology Department of Neiker Technalia, financed by the Environmental, Territorial Planification, Agriculture and Fish Dept., basque Gov, Spain. N. Campos had a pre-doctoral fellowship from the Agencia Española de Cooperación Internacional para el Desarrollo (AECID). The authors would especially like to thank Oriol Casagran (CRAG Genomic Services), Sami Irar (CRAG Proteomic Services), and Shirley Burgess (English correction). The authors would also like to thank the Spanish Ministry of Science and Innovation, Consolider-Ingenio 2010 Programme. CSD2007-00036 “CRAG” and the Xarxa de Referencia en Biotecnologia of the Generalitat de Catalunya.Peer reviewe