Data experimental design materials and methods

Data, experimental design, materials and methods
Conflict of interest
Acknowledgements We would like to acknowledge the BBSRC for support (grant BB/H001948/1), the Chemical Analysis Facility at the University of Reading for access to the Orbitrap instrument, the Centre for Advanced Microscopy at the University of Reading for their help with the ESEM analyses, and the PRIDE team for their help in depositing the proteomics data to the proteomeXchange public repository.
Value of the data
Data As an important model plant for biological research, rice also is one of the most important crops and food for human consumption [1]. We performed a systematic identification of the lysine acetylome in rice, recently [2]. Fig. 1 show the experimental and bioinformatics workflow of the rice lysine acetylome. A total of 1337 lysine-acetylation (Kac) sites on 716 proteins were identified, and data is presented in Supplementary Table S1. The raw data were available on PRIDE database with accession number http://www.ebi.ac.uk/pride/archive/projects/PXD002291. Most of the peptides contain 7–15 ppar pathway (Fig. 2A). Of the 716 proteins, 435, 143, and 55 contained 1, 2, and 3 Kac sites, respectively (Fig. 2B). The information on the Kac peptides and proteins were summarized in Table S1. Kac motif is listed in Supplementary Table S2. To better understand the global cellular functions of the acetylated proteins in rice, a GO functional classification was conducted in terms of their molecular functions, cellular components, and biological processes, the GO data is listed in Supplementary Table S3. KEGG also conducted and the detail data listed in Supplementary Table S4. We also used Cytoscape software to generate an interaction network for all of the acetylated proteins. When the threshold confidence score was set at 0.70, associations were detected among 347 proteins (Supplementary Table S5). As shown in Fig. 3, this network contained a number of acetylated proteins at key hubs. The detailed data were discussed by Xiong et al. [2]. The raw data about this research is available on PRIDE database, accession number is http://www.ebi.ac.uk/pride/archive/projects/PXD002291.
Experimental design, materials and methods
Data Data for Lymantria dispar male survival after topical application of different single-stranded DNA (ssDNA) fragments are presented in Fig. 1 as survived male imago frequency.
Experimental design, materials and methods
Data Tables 1–4 display raw model output and field data for populations of Undaria pinnatifida growing in a harbour setting. Model results are from simulations carried out using a spatially-explicit, individual-based model of U. pinnatifida population dynamics. A description of this model can be found in the associated research article [1]. Field data are from populations of invasive U. pinnatifida growing in Brest harbour, France, which were surveyed during 2005 and 2006 [2].
Experimental design, materials and methods Field data was collected from the port of Brest in France during the 2005/06 growing season: during this field experiment, 64 aluminium panels were set-up one metre below the surface, a depth optimal for the recruitment of the U.pinnatifida, and the settlement and length of each individual was recorded every month. Simulations were carried out using an individual-based model with environmental parameters (light, temperature and day length) representative of Brest harbour, France. Surface water temperature data for the port of Brest (2003–06) were obtained from a SOMLIT (Service d’Observation en Milieu Littoral, INSU-CNRS, Brest) buoy situated a few hundred metres from the marina [2,3]. Mean global solar irradiance data for the region were obtained using the CalSol online application (Institut National de L׳Energie Solaire, CEA-CNRS) [4].
Acknowledgements This research is supported by an Irish Research Council ELEVATE international career development fellowship, co-funded by Marie Curie Actions under the European Union’s Seventh Framework Programme. The data presented here that were collected in Brest were obtained as part of the PhD thesis of Marie Voisin who benefitted from a Ph.D. fellowship (“Renouvellement des Compétences” Program) from the Region Bretagne. MV and FV are thankful to the many people from the Department AD2M of the Station Biologique de Roscoff who provided help for the surveys carried out in the field.