Core Genetics Facility

The Laboratory for Molecular Systematics and Evolution at Rancho Santa Ana Botanic Garden is home to the Core Genetics Facility, established in 2000 thanks to a joint NSF equipment grant among RSABG, Pomona College and Harvey Mudd College.

We provide DNA sequencing and genotyping for members of the Claremont University Consortium.

Contact Information:
Email: Loraine Washburn This email address is being protected from spambots. You need JavaScript enabled to view it.
Phone: (909) 625-8767 ext. 265
FAX: (909) 626-7670

Submission Location:

The bench-top freezer just inside the Laboratory for Molecular Systematics and Evolution, in the main administrative building, second floor.

Submit samples by 4 p.m. on Monday. For Monday holidays, please have samples in by noon on Tuesday.


Services using Applied Biosystems 3130xl Genetic Analyzers:

  • DNA sequencing in tube or plate format.

  • Fragment analysis genotyping runs (plate format only).

  • Other Services: If you are interested in other services not listed, please contact us.

Downloadable Documents:

DNA Sequencing Basics:

  • Cycle Sequencing on MJ-PT100 (tube format) or on AB 9700 (plate format) thermal cyclers. Dye Terminator sequencing with BigDye version 3.1 (Applied Biosystems).
  • Sample purification using G50 medium Sephadex in CENTRI•SEP Spin Columns (Princeton Separations, Freehold, New Jersey, USA) for tubes, or filter plates (Phenix Research Products, Candler, North Carolina, USA).
  • Visualization on a 3130xl Genetic Analyzer (Applied Biosystems/Life Technologies Corporation, Carlsbad, California, USA). 50 cm array with POP-7 polymer. 750-850 bp read length.
  • Cost is currently $9 per sample. Discounts also available for half- and full plates.
  • Output is a digital file (.ab1) zipped up and emailed to you by noon on Wednesdays.

Genotyping Basics:

  • Visualization on a 3130xl Genetic Analyzer (Applied Biosystems/Life Technologies Corporation, Carlsbad, California, USA). 50 cm array with POP-7 polymer. 600 bp read length.
  • Cost is currently $150 per plate.
  • Output is a digital file (.fsa) zipped up and emailed to you.

 

Useful Links:

Applied Biosystems — Sequencing/genotyping equipment, chemistries, software.

Applied BiosystemsPeakScanner Free software to view, edit, analyze and print fragment analysis data. Windows only.

Applied BiosystemsSequence Scanner Free software to view, edit and print sequencing analysis files. Windows only.

Geneious — Moderately priced Software to manage sequence data from assembly through analysis to presentation.

4Peaks — Free software to view and edit sequence trace files. Mac OS only.

Phenix Research Products — lab supply vendor. Semi-skirted plates and thin walled tubes for submission of templates. Plate product number MPS-3580, tube product number MPX-600.

Sequencher — Premium sequence assembly software. Windows or Mac.

SoftGenetics — Moderately priced software packages for sequence analysis, genotyping, etc.