Facility Introduction:

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: Linda Prince, Ph.D., conservation botanist

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:

• Request for Sequencing
• Sample Submission Sheet
• Helpful Hints

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 Biosystems – PeakScanner Free software to view, edit, analyze and print fragment analysis data. Windows only.

Applied Biosystems – Sequence 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.