The DNA sequencing facility provides access to automated sequencing technology for researchers at the Institute for Systems Biology(ISB), collaborators and affiliated companies in the surrounding community. High quality sequence reads are produced at relatively low cost with a rapid turn-around time.
Services offered:
- Restriction digest fingerprinting
- Shotgun library construction
- DNA template preparation
- PCR (Polymerase Chain Reaction)
- Sequencing of BAC (bacterial artificial chromosome), plasmid or PCR product templates
- Sequence assembly and finishing using Phred, Phrap and Consed
- Database searches
- Genomic analyses
Equipment and procedures:
The sequencing facility is equipped with:
- an ABI 3730 XL sequencer,
- a Brinkman Instruments high-throughput plasmid prep robot,
- an AutoGen for preparing BAC DNA,
- several Applied Biosystems thermocyclers,
- Robbins Hydra liquid transfer robots,
- electrophoresis equipment, and
- a Molecular Dynamics fluorimager for fingerprinting.
Requests for services are entered through an in-house database (Kuch-Kar), and data are accessible to clients from the ISB collaborator server.
Figure 1: Improvements in sequencing technology have led to longer read lengths and higher quality data. The graph shows the improvement in sequence quality over the time that the ISB sequencing facility has been in operation.
Example(s) of projects that use the services of the facility:
- SNP (Single Nucleotide Polymorphism) discovery in toll receptor genes
- Discovery of putative regulatory regions through cross-species comparisons
- Identification of novel transcription factors in mouse T cell development
Representative publication(s):
Zody MCetal (2006) Analysis of the DNA Sequence and duplication history of human chromosome 15 Nature 440: 671-675
Daza-Vamenta R., Glusman G, Rowen L, Guthrie B, and Geraghty D (2004) Genetic divergence of the rhesus macaque major histocompatibility complex. Genome Research 14: 1501-1515.
Glusman G, Kaur A, Hood L, Rowen L. (2004) An enigmatic fourth runt domain gene in the fugu genome: ancestral gene loss versus accelerated evolution. BMC Evol Biol. 4:43.
Davidson EH, Rast JP, Oliveri P, Ransick A, Calestani C, Yuh CH, Minokawa T, Amore G, Hinman V, Arenas-Mena C, Otim O, Brown CT, Livi CB, Lee PY, Revilla R, Rust AG, Pan Z, Schilstra MJ, Clarke PJ, Arnone MI, Rowen L, Cameron RA, McClay DR, Hood L, Bolouri H. (2002) A genomic regulatory network for development. Science 295: 1669-78. Review.
|
home
