An overview of the sub-themes drawn out from the transcript material is presented in Table 4.
A voice recording of all the sessions was made, and both RJ and JA took written notes which were used to help clarify the transcript material where necessary.
Subsequently, 30% of the transcript material will be reviewed by experts recruited from members of the follow-up committee to confirm the results of the categorization.
An embarrassment intensity rating scale was devised in which Ss were rated by the first and second authors from 0 = "no embarrassment" to 1 = "little", 2 = "some", 3 = "much" and 4 = "very much embarrassment or principal problem" based on clinical records and transcript material.
Hence, we further developed a metric to characterize the overall splice site usage for every exon intron boundary based on an expression-weighted average of its inclusion ratio in all transcripts (Materials and Methods).
Matrices were developed to facilitate comparisons across the transcripts material and to retain the context of the data (i.e. which focus group, characteristics of the interviewee) [ 13].
Hits with E-values <10− over at least 30 bp were manually examined and categorized based on how Helitrons altered the structure of the transcript (supplementary materials and methods, Supplementary Material online).
Restriction enzymes and cRNA transcript preparation materials were from Invitrogen Burlingtonn, ON, Canada), Promega (Madison, WI, USA) or New England Biolabs (Pickering, ON, Canada).
We repeated these experiments for several mutants using cDNAs synthesized from specific, rather than random, primers to eliminate the possibility that the RNA spanning the poly(A) site arose from an antisense transcript (see Materials and Methods).
Interestingly, Drosophila ets21c and ftz-f1 gene loci themselves contain AP-1 motifs and qualify as polarity response transcriptional signature transcripts (supplementary material Table S1).
