Since all experiments were performed by transfecting equal amounts of vector DNA - and not equal molar ratios of vector molecules,- to exclude side effects of stuffer DNA, some of the differences within the increased transient transfection efficiencies of the smaller plasmids are caused by this.
All bait and prey chimeric proteins have been controlled, then they have been transformed with the corresponding empty vector in order to exclude auto-activation problems.
Multiple sequence alignment were performed to exclude vector sequences and to identify redundant (not unique) sequences using the program AlignX (Vector NTI Suite V 8.0, InforMax, Invitrogen, Carisbad, CA, USA) with an engine based on the Clustal W algorithm.
Thus, sequences from each group of strain-specific SSH libraries were trimmed, in order to exclude vector sequences and poor quality regions (Phred < 20), and aligned with the aid of CAP3 [ 74].
For each of the 6 strains, the sequenced clones have been trimmed, in order to exclude vector sequences and poor quality regions (Phred < 20), and aligned with the aid of CAP3, generating 1,063 contigs, which contained 6,712 sequences overall.
Equal amounts of vector DNA were used to exclude undesired effects of any added stuffer DNA, as for example sonicated salmon sperm DNA or any other small plasmid DNA with varying CpG contents.
RefSeq entries are classified as reviewed, provisional and predicted with those designated "reviewed" indicating an extensive manual review process to exclude contaminating or vector sequences and to ensure that the gene or protein sequence is not truncated.
Briefly, sequences were processed (to exclude low quality, contaminating vector sequences and poly A+ tracts) using Trace2dbEST [ 81].
Next, we wanted to exclude the possibility that integration of shRNA lentiviral vector showed off-target effects.
To exclude potential nonspecific effects, cells were also infected with an empty lentiviral vector (EV) or a lentiviral vector expressing a human DLK shRNA (hDLK).
