Model establishment, training, and testing were performed as before and the same four feature sets were considered (Tables 2 and 3).
Acrylamide gradient gels (8 and 16%) were prepared and electrophoresis performed as before [47].
Co-precipitation assays were performed as before, using FLAG antibody for immunoprecipitation followed by Western blotting with MYC- or HA-antibody to detect co-precipitated proteins.
K-means clustering of samples was performed as before, leaving out 15% of proteins (7 out of 44) with each of 10,000 iterations.
RT reactions were performed as before, with oligo dT-priming, and 0 20 ng of the in vitro RNA transcript as template, alone or diluted into 3 µg total mouse liver RNA.
The IP experiments were performed as before with the exception that 40 µL of synbody coated beads were used and the beads were washed seven times with PBST prior to elution.
Incubation and detection were performed as before, using Dako Monoclonal Rat Anti-Mouse KI-67 Antigen TEC-3 IgG2a primary at 1∶50 dilution for 1 hour at 37°C and Biolegend Biotin Goat Anti-Rat IgG Poly 4054 secondary at 1∶200 dilution for 30 minutes at room temperature.
Energetic analysis was performed as before, following affinity measurements (Supplementary Table 3).
Ethanol series dehydration was performed as before and the slides were air dried in darkness.
Alignments were performed as before and all unconserved positions were identified.
Relative quantitation was performed as before, taking duplicates to ensure reproducibility.
