Sequence of the 5′-proximal promoter region of KLKB1 was obtained by shotgun cloning of genomic fragments from a bacterial artificial clone containing the KLKB1 gene, followed by screening of the clones using exon 1-specific probes.
Data from spike-in experiments (where the mRNA-ratios of a set of artificial clones are known) can be used to determine the relative merits of a set of analysis methods [13], [14].
Bacterial artificial clone (BAC) probes for KIT were prepared as described elsewhere (11), and applied onto the slides.
Here, an artificial clone with 165 CAG/CAA repeat encoding a 165-Q-stretch (extremely expanded; Q165) was also generated, as previously described [ 34].
To rule out the possibility of false-negative looping occurrence caused by unsuccessful 3C assay, we pooled three human bacterial artificial clones (BAC), mapping the interested regions as the positive control to the 3C assay.
The other 4,647 Trinity contigs that did not match ME49 genes produced significant matches against mouse and human bacterial artificial clone (BAC) sequences available in the NCBI non-redundant nucleotide database, and none mapped to known mouse or human genes.
In addition, emerging physical maps and bacterial artificial clone sequence data serve as template to investigate genetic variation within the cultivated germplasm pool with the goal to manipulate agriculturally important traits.
For BamHI- and Sau3A-digested libraries, some artificial clones from ligation of unrelated DNA fragments were identified and trimmed accordingly after Blast search of the mismatched sequences against the parasite genome sequence.
The positions (bp) of the BACs (bacterial artificial clones), RP11-398K22, RP-202D23, RP-332O9 and RP11-203D6 (1), alsoalshownown according to the UCSC database (hg19 assembly) (http://genome.ucsc.edu/cgi-bin/hgGateway?org=human).
To overexpress 9RKe and NRKe in rice, these two genes were amplified using polymerase chain reaction (PCR) primers NRKe-F and NRKe-R (Additional file 1, Table S1) and genomic DNA from indica rice variety 93-11 (Oryza sativa L. ssp. indica) and bacterial artificial clone (BAC) OSJNBa0004O15 from japonica variety Nipponbare (O. sativa L. ssp. japonica) as template, respectively.
It should be noted that the breeding structure of Quarter Horses and Thoroughbreds, as well as the differences in sequencing technology (i.e., next-generation sequencing of DNA fragments vs. Sanger sequencing of bacterial artificial clones) most likely contributed to the increased amount of genetic variation identified in this study.
