There are several downstream analysis goals for which RNA-seq is well suited. Main categories of these are described briefly below with reference to supporting materials. Refer to S2 Table for specific tools relevant to many of these areas. For each application, a basic data recommendation is provided. It is important to remember that these are simply examples. In addition to the varying demand...

Comment on reversibility We and others have observed differences in the reversibility measured by the QPatch instrument and by manual patch clamp: washout of lipophilic compounds is delayed in the QPatch. The probable reason for this is the presence of unrecorded cells within the chip. One major difference as compared to manual patch clamp is that QPatch does not allow continuous flow of extrac...

The basis for our score is a feature vector corresponding to a given input. In our case, the input is a sequence to be classified, and the features are going to be the output of certain tools (see workflow in Figure 1) we feed with the input sequence. In the following, we describe the two distinct steps necessary for the computation: as a prerequisite, we first establish distributions from our ...

Table B: One-tailed p-values for F̂ST based on WGS data. †With the exception of the compairison between MKK and MLA in 2014, all p-values are Monte Carlo estimates based on 1000 random permutations as described in Table A. The p-value for MKK and MLA in 2014 is exact, since there were fewer than 1000 possible permutations given nMKK = 4 parasite samples from MKK, and nMLA = 8 parasite samples fr...

n k − is the rate of constitutive degradation of lateral signaling. Lateral signaling is mediated by complexes of LIN-12-cyto with LAG-1 transcription factor. Silencing of lateral signaling occurs due to proteosomal degradation of LIN-12-cyto [1]. The mean half-life of proteins susceptible to proteolysis has been measured to be approximately 43 minutes [2]. Therefore, the reference value of par...