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Background: Given the high technical reproducibility and orders of magnitude greater resolution than microarrays, next-generation sequencing of mRNA (RNA-Seq) is quickly becoming the de facto standard for measuring levels of gene expression in biological experiments. Two important questions must be taken into consideration when designing a particular experiment, namely, 1) how deep does one need to sequence? and, 2) how many biological replicates are necessary to observe a significant change in expression?Results: Based on the gene expression distributions from 127 RNA-Seq experiments, we find evidence that 91% -4% of all annotated genes are sequenced at a frequency of 0.1 times per million bases mapped, regardless of sample source. Based on this observation, and combining this information with other parameters such as biological variation and technical variation that we empirically estimate from our large datasets, we developed a model to estimate the statistical power needed to identify differentially expressed genes from RNASeq experiments.Conclusions: Our results provide a needed reference for ensuring RNA-Seq gene expression studies are conducted with the optimally sample size, power, and sequencing depth. We also make available both R code and an Excel worksheet for investigators to calculate for their own experiments.

Ovarian cancer is a clinically and molecularly heterogeneous disease. The driving forces behind this variability are unknown. Here we report wide variation in expression of the DNA cytosine deaminase APOBEC3B, with elevated expression in a majority of ovarian cancer cell lines (3 standard deviations above the mean of normal ovarian surface epithelial cells) and high grade primary ovarian cancers. APOBEC3B is active in the nucleus of several ovarian cancer cell lines and elicits a biochemical preference for deamination of cytosines in 5′TC dinucleotides. Importantly, examination of whole-genome sequence from 16 ovarian cancers reveals that APOBEC3B expression correlates with total mutation load as well as elevated levels of transversion mutations. In particular, high APOBEC3B expression correlates with C-to-A and C-to-G transversion mutations within 5′TC dinucleotide motifs in early-stage high grade serous ovarian cancer genomes, suggesting that APOBEC3B-catalyzed genomic uracil lesions are further processed by downstream DNA ‘repair’ enzymes including error-prone translesion polymerases. These data identify a potential role for APOBEC3B in serous ovarian cancer genomic instability.

Reflectins are a unique group of structural proteins involved in dynamic optical systems in cephalopods that modulate incident light or bioluminescence. We describe cloning, structural characterization, and optical properties of a reflectin‐based domain, refCBA, from reflectin 1a of Hawaiian bobtail squid, Euprymna scolopes. Thin films created from the recombinant protein refCBA display interesting optical features when the recombinant protein is appropriately organized. RefCBA was cloned and expressed as a soluble protein enabling purification, with little structural organization found using Fourier transform infrared spectroscopy and circular dichroism. Single‐layer and multi‐layer thin films of refCBA were then produced by flow coating and spin coating, and displayed colors due to thin film interference. Diffraction experiments showed the assemblies were ordered enough to work as diffraction gratings to generate diffraction patterns. Nano‐spheres and lamellar microstructures of refCBA samples were observed by scanning electron microscopy and atomic force microscopy. Despite the reduced complexity of the refCBA protein compared to natural reflectins, unique biomaterials with similar properties to reflectins were generated by self‐assembled reflectin‐based refCBA molecules. © 2012 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2013