The unsupervised analysis clusters together with remarkable precision sequences belonging to the same datasets, indicating that the integration sites of different vectors are defined by specific patterns of flanking TFBS motifs.
Primary PCR was performed using 200 ng ligated DNA, BW-1HR primer (5'-CCGGGAGATCTGAATTCGTGT-3') [24], primer specific for 3' flanking sequence of TCRAV2 (5'-AGATGATACAGAGACAAAATGTGAGC-3') and 2 U of AmpliTaq Gold DNA polymerase (Applied Biosystems, Foster City, CA).
A second PCR was performed using 1 µl of the first PCR product (diluted 1/100), BW-1HR, anestedted primer specific for 3' flanking sequence of TCRAV2 (5'-TATTGTGGATGCTAACAAGTGCTTTC-3').
Primer pairs specific for flanking sequences were designed for 481 of the SSR sequences (88.5%).
As our varietal SNPs were identified based on the presence of flanking genome-specific SNP s), some of them would have such genome-specific SNP s) overlapping with the assay primers, so a portion of these SNPs would, in practice, function as co-dominant SNP markers.
Polymerase chain reactions were carried out in the presence of specific primers flanking the sequence of two microsatellite markers D7S-1779 anD7S-246868 located athehe chromosomal region 7q32 34 (see Material and methods section for detail).
After microdissection and DNA extraction, polymerase chain reaction (PCR) was carried out in the presence of specific primers flanking the sequence of two microsatellite markers (D7S-1779 anD7S-246868) located athehe chromosomal region 7q32 34 (cytogenetic localization 150 152 cM) previously reported to be altered in thyroid cancer (Zhang et al, 1998; Roque et al, 2001).
Comparison of flanking regions supports the view that these loci produce unique transcripts with specific expression profiles.
Both motifs were separately analyzed to estimate the specific effect of flanking and of tandem mismatches in comparison with the standard triples.
The specific subset of flanking regions used in this analysis (1,385 upstream and 1,399 downstream flanking regions) should accurately represent the genome-wide effect of protein-coding LCRs on adjacent DNA.
