Finally after the last step response), by allowing for expression of GFP, the additional elements appended to design the decoder include, the expression of protein cI from the P ara and P lac promoters and the expression of proteins tetR and GFP from the P λ promoter.
The results of all three case studies are summarized in Table 2 which prove the robustness and efficiency of the ChemEngine program in recognizing patterns and developing regular expression for the typical cases dealt (Additional files 4, 5).
A heat map of the expression profiles for the three additional clusters was shown in Supplementary Figure 2. We ran a total of 24 000 iterations and convergence of the loss function is shown in Supplementary Figure 4. We let the lower bound of the weight be P=0.3.
For the additional expression verification of five germline-specific genes identified by our bioinformatic screen, we performed RT-qPCR (see Supplementary Information) using the GoTaq PCR Mastermix (Promega, Madison, WI) and the ABI 7300 qPCR machine.
Then, 0.5 mM isopropyl-β d-thiogalactopyranoside was added to the culture to induce protein expression for an additional 6 h.
Next, cells were grown at 28°C (the optimal temperature for OleTJE expression) for an additional 20 h at 220 rpm (in LB medium) or 40 h at 250 rpm (in the defined mineral medium).
In contrast to the viscous effects, the modeling of shrinkage effects does not require any further extension of the expression for the energy density, but an additional decomposition of the deformation into a shrinkage and a mechanical part.
In contrast to the protein count results, read count analyses revealed significant decreases in transcription and amino acid metabolism expression for KN (Additional file 3: Table S3).
Remarkably, by qRT-PCR we also observed a higher expression for an additional gene coding for ASC1 in anthers (Table 4).
Cultures were shifted to 20 °C for protein expression for an additional 6, 12, or 21 h with shaking at 250 rpm.
This also agrees with the high expression of TLK2 in luminal cell lines MCF7, MDA-MB-361 and SUM52PE which do not show high expression for PIK3CA (Additional file 1).
