The remaining reads were combined into files based on the insert size of the library (irrespective of the prior biological treatment) and assembled using an additive multiple- k-mer (35, 39, 43, 47, 51, 55, 59, 63, and 67) approach [ 28, 29] with the Velvet/Oases assembler (Velvet version 1.1.04 and Oases version 0.1.21) [ 30].
Nine spherical VOIs were delineated based on the insert volumes and physical boundaries seen in the CT images.
An additional feature of this method is the capacity of determining the orientation of inserts, using an internal primer based on the insert sequence.
Primer sequences employed in this study are listed in Additional file 4. The first round of PCR was performed using 100 nM of the following primers: a gene specific primer-S1, 5'-CCACCCACCACCACCAATGnnnnnnnnnnnnnnnnnnn (n denotes the sequence complementary to the first 20 bp in the coding region of the target gene), and AODA2306 or AODS based on the insert orientation.
Less than 1% of the paired reads were inverted (one of the reads in other orientation than expected) or everted (both reads in other orientation resulting in wrong order of tags) and approximately 10% were mapped remotely (i.e., to a distant genomic position, significantly deviating from what is expected based on the insert-size distribution).
The average number of clones recognized by a single probe was 6.9, in good accordance with the assessment of the library redundancy based on the average insert size. 1 mm5 assembly, UCSC To characterize the inserts of the PWD/Ph BAC library at the DNA sequence level we sequenced and manually edited 87 BAC ends from 47 BAC clones (total 38,339 nucleotides).
Another 35 clones that were classified as discordant because the distance between the paired BESs was smaller 45-866 kb) or greater (201-329 kb) than expected based on the BAC insert sizes, presumably due to local insertions or deletions, could also be assigned to a single orthologous location in the mouse genome.
Based on the average insert size of 140 kb, one CB was estimated to be 1.13 kb (Table 1).
The parameters are calculated as annual averages based on the number of inserted pigs.
The administered activities were based on the package insert for the treatment device: ~120 Gy to treatment volume for glass microspheres.
