The past decades have witnessed an era of data

The past decades have witnessed an era of data explosion that touches almost every aspects of modern science. Powerful technologies such as Next-gen DNA sequencing, high throughput/content screening platforms, the Large Hadron Collider and more, routinely generate copious amounts of data. At the same time, collaborations between different disciplines had never been so urgently needed to provide new insights that otherwise would not be possible. We are in need of a revolution in publication infrastructure towards supporting researchers with the means to preserve and gain access to research output. In this context, Elsevier has proudly launched , an open access journal that publishes data from a broad spectrum of disciplines including Biology, Chemistry, Economics, Psychology and Physics. strives to provide a platform for researchers to easily share and reuse each other׳s datasets, promote collaboration across disciplines and to showcase the benefits of data driven research.
Value of the data
Experimental design, materials and methods Chromatin fibers were reconstituted with purified chicken histone octamers and DNA fragments containing 601 sequences through salt dialysis described previously [11]. One extremity of a single Kinase Inhibitor Library fiber was attached to the surface of the cover slip and the other extremity is tethered to a paramagnetic bead with the diameter of 2.8µm [5]. Short DNA spacers of 251bp (SS) and long DNA spacers of 2360bp (LS) were applied to prevent chromatin fiber from sticking to the glass surface [12]. The exerted force is corresponding to the magnet position and calculated with the method described previously [13]. In order to capture the details of single nucleosome unwrapping events, we changed the constant magnet shift (CMS) to the programmed magnet shift (PMS). The rate of CMS is 10mm/180s and PMS contains three rates of 5mm/5s, 3.25mm/30s, and 1.75mm/200s. Figure 1 shows the details of the Force-Extension traces of the SS and LS chromatin fibers measured at CMS or PMS mode. These fibers showed no rapture events at the highest exerted force. However, the stepwise rupture events continued at the highest force in the chromatin fiber shown in Fig. 2. The process of chromatin refolding in the presence of decreasing force was recorded in Fig. 2.
Acknowledgements This work was financially supported by the Netherlands Organization for Scientific Research (NWO).
Experimental design Bacterial lysates were processed according to MED FASP protocol (Fig. 1). Peptides were analyzed by LC–MS/MS and the resulting spectra were handled by the MaxQuant software. All peptides and proteins identified in this study are listed in Supplementary Tables S1 and S2 (for table legend see ‘Legends to Tables 1 and 2’), respectively. Absolute protein contents and protein concentrations were calculated using the total protein approach (Table 2). DNA was digested with nuclease and the released nucleotides were quantified. The total protein content of the single bacterial cell was calculated from the total DNA and total protein of the sample as described in [1]. The total protein content of the single cell was used for computation of protein copy numbers per cell (Table S2). Table S3 shows a selection of proteins involved energy metabolism in Escherichia coli.
Material and methods
Data, experimental design, materials and methods In-gel protein digestion, in-solution protein digestion, SCX-HPLC of peptides and MS/MS were performed as described in [4]. Precursor ions with charges of 2+ and 3+ were examined. Peptide sequences were assigned using Mascot (Matrix Science) to search an EST database using the following search parameters: MS and MS/MS mass tolerances were set to ±1.2 and ±0.6Da, respectively. One missed cleavage was allowed and carbamidomethylcysteine and oxidized methionine were set as fixed and variable modifications, respectively. Searches were based on a significance threshold of p<0.05. MudPIT scoring was used to remove protein hits that had scores based purely on a large number of low-scoring peptide matches. Ion score cut-off was set at ≥25 and each protein hit was required to have at least one bold red (best match in database) peptide. False positive rates were calculated using the decoy option provided by Mascot and estimated as below 2%. Peptide sequences and inferred protein identities are compiled in Supplemental Table S1.