The incorporation of the Cy-dyes in the labeled target sequences was measured with a NanoDrop spectrophotometer (NanoDrop Technologies).
Crude estimates of the amount of sequence collinearity between RH BAC tiling paths and DM sequences were measured from the graphical sequence alignment plots with the formula C = 2*O/(L1 + L2), where C is the fraction of collinear sequence, O is the total length of the overlapping sequence segments, and L1 and L2 are the lengths of sequences (or sequence intervals) being compared.
The coincidence of a given residue with the alignment of the rest of the family members, and the differences regarding the sequences outside the subfamily, were measured with an f-score as described in the Methods.
Two-dimensional TOCSY, ROESY, and NOESY spectra and band-selective, homonuclear-decoupled (BASHD TOCSYY, BASHD ROESY, and BASHD NOESY spectra were measured with standard pulse sequences [ 28, 29].
N R1, R2 and H N heteronuclear NOE values were measured with TROSY-based sequences collected on a 0.4 mM N, C-labeled S1R Δ35) sample at 600 MHz using the following relaxation delays: 10, 175, 350 and 525 ms (R1), and 0, 17, 51 and 85 ms (R2).
Conformational changes were measured with DymDom [55].
Absorbance values were measured with SpectraMax Plus384Spectrophotometer.
mRNAs were measured with oligonucleotide arrays (Affymetrix).
These integrated hairpins are then subsequently retrieved from the genomic DNA by PCR amplification, and the abundance of each shRNA sequence can be measured with microarray hybridization (Luo et al, 2008) or with next-generation sequencing technology (Sims et al, 2011).
Binding of the NF-kB p65 subunit to the NF-kB binding consensus sequence 5'- GGGACTTTCC-3' was measured with the ELISA-based Trans Am NF-kB kit (Active Motif, Carlsbad, CA, USA) using whole cell lysates prepared from chondrocyte cultures.
Average levels of sequence identity between orthologs were computed as follows: Each orthologous pair was aligned with MUSCLE v3.7 and the level of sequence identity was measured with trimAl V1.3 [ 89] as the number of identical residues over the length of the shortest protein.
