To assign open reading frames and repair potential indels inserted during transcript assembly we used the pipeline prot4EST [ 48].
Differentiated Caco-2/15 cells, cultured on polycarbonate Transwell filter inserts, exhibited transcripts of the 3 PONs whereas Western blot revealed the protein expression of PON2 and PON3 only.
One of the features of the SREK kit and its replacement SOLiD Total RNA-Seq kit is that both retain the strandedness of the inserted RNA transcripts in the library.
Over a period of 11 weeks, cellular uptake of the DNA vaccine was examined by PCR, transcription of the insert by reverse transcript-PCR (RT-PCR) and mRNA translation by immunofluorescence staining of muscle biopsies.
Within Clone Mapper, the length used to search for possible matches between clone insert and target transcript can be defined by the user, with a minimum of 6 bp, so that it can be used to identify potential seed regions for miRNAs (Grosswendt et al. 2014) in complete C. elegans transcripts.
For nhr-46, gfp inserted after the transcript a specific start codon, in the proximal of the two unique exons, gave the same expression pattern as when gfp was inserted before the termination codon common to all transcripts; again a broad distribution but peaking this time in the L2 stage (WBIDs Expr9816/9835).
The MOS/POS ratio represents the overall sequence similarity between an RNAi clone insert and its target transcript.
To simulate a realistic sample of novel human genome insertions, we sampled substrings of varying length from the set of insertion sequences reported in a novel insertion characterization study (Kidd et al., 2010), and inserted them to the transcript sequences at random exon breakpoints.
To rule out the possibility that this enhanced activity is due to read-through of the first cistron, it was inserted into the dicistronic transcript in a inverted orientation (Fig. 3, H).
All inserts of a particular transcript size were found to be of identical sequence, except for a single heterozygous site in transcript 78 (table 2).
