Whole Genome Profiling 2.0

For de-novo projects, we begin with a custom 6X to 8X to 10X genome coverage large insert genomic DNA BAC library (or we use available BAC clones). We pool BAC clones in a systematic manner, prepare highly purified NGS grade BAC DNA, digest the pooled DNA (EcoRI), add tags and perform Illumina NGS runs on the pooled BAC DNA. Finally, we assemble the sequence reads into BAC scaffolds (e.g. contigs) for a High Density Sequence Based Physical Map.The final deliverables for your team:

• A physical Map with Billions of 150bp sequence tags on average 20-40 per BAC at an estimated over sampling rate of at least 30-fold to 40-fold per fragment using the newest Illumina HiSeq (or newer platform).
• We expect two reads at every EcoRI site in all the BAC clones with ~100bp -150 bp of sequence info per site (billions of data points to build a BAC based Physical Map)!
• A modified version of FPC Software Program (a physical map/fingerprinting software) to study/analyze the WGP Physical Map data and the living BAC clones in 384-well plates.

In the FPC program you will see the BAC clones assembled into BAC scaffolds, but most importantly they are linked together by sequences, not by fragment lengths as with other fingerprinting technologies (like SnapShot or agarose gel fingerprinting). The WGP data are comprised of two Illumina reads every ~2 Kb to ~6 Kb (at each EcoRI site) on all BAC clone inserts. These data can be added directly/immediately to an existing or future Whole Genome Sequencing project.

When you find a region of interest in the data, you instantly have the BAC clone address (for deep sequencing or downstream experiments).

Amplicon Express and Keygene have generated over 40 physical maps for more than 27 different species of varying genome size (130 Mbp -5000 Mbp) and complexity.