Shared Resources


DNA Sequencing Facility

Director: Tapan Ganguly, Ph.D.

The DNA Sequencing Facility was founded in 1994. The DNA Sequencing Facility provides: reliable, long read, automated Sanger sequencing with fast turnaround; microsatellite-based genotyping and fragment analysis; plasmid and BAC DNA preparation and purification; and related molecular biological services including PCR, cloning, sub-cloning, site-directed mutagenesis, and preparation of targeting vector for gene targeting in mice. It also provides services and support for analysis and interpretation of sequence data as well as the design of approaches to complex sequencing projects. Recently an ultra-high throughput Roche/454 sequencing service has been introduced at the facility. These services are essential to investigators who study the involvement of specific genes in normal cellular and developmental processes or abnormal processes that are found in cancer cells and tumors. With the availability of an integrated service for both Sanger and new generation sequencing, microsatellite-based genotyping, and various molecular biological services, researchers can easily obtain fast, reliable data on genes of interest, whether they are doing a targeted tumor genome sequence, screening clones for sequences of interest, establishing the identity of new clones, or searching for mutations in specific genes.

Contact

D6 Richards Building
3700 Hamilton Walk
Philadelphia, PA 19104

Office: 215-573-7238

Email: gangulyt@mail.med.upenn.edu

Locations

The DNA Sequencing Facility occupies 2,000 sq ft of space in the renovated area in the B tower of Richards basement.

Fees

Service

ACC Members

Other PENN, CHOP Faculty

Sanger Sequencing (collection of samples from different PI's)

$6

$6.65

Sanger  Sequencing, Ready to Load (RTL) , Full plate

$80

$89

Sanger  High Throughput Sequencing, Full Plate 

$300

$333

Sanger High Throughput Sequencing of plasmids from Bacterial Culture, Full Plate

$370

$405

     

Roche/454 Sequencing 1/2 Pico Titer Plate

$4,500

$5,000

Roche/454 Sequencing 1/4 Pico Titer Plate

$2,700

$3,000

Roche/454 Sequencing 1/8 Pico Titer Plate

$1,750

$1,945

     

Genotyping/Fragment Analysis  Full Plate (96 samples)  with Genotyping

$100

$110

Transgenic Mouse Genotyping by PCR 

$1.80 

$2.00 

     

PCR Amplification of Template

$6.80

$7.50

PCR Product Purification (gel )

$20

$22

Transformation

$27

$30

Site-directed Mutagenesis

$225

$250

Cloning / Sub-cloning

$131

$145

     

Plasmid Miniprep

$4.50

$5.00

Plasmid or Phage Maxiprep

$36

$40

Equipment

Equipment list

  • ABI 3730 96 capillary Sequencer (1)
  • Qiagen Qiacube for plasmid DNA preparation
  • ABI 3100 16 capillary Sequencer (3)
  • Beckman NX-8 Robot
  • Autogen AGF 3000 DNA Extractor
  • Kodak Gel Imaging System
  • Perkin-Elmer 9700 thermal cycler (1)
  • Beckman DU 640 spectrophotometer
  • Perkin-Elmer 2700 thermal cycler (4)
  • ThermoFisher NanoDrop spectrophotometer
  • Perkin-Elmer 9600 thermal cycler (1)
  • Beckman Allegra X15R tabletop centrifuge
  • Perkin-Elmer 2400 thermal cycler (2)
  • Low speed/general purpose centrifuge (3)
  • Vertical / horizontal electrophoresis systems
  • Savant Speed Vac system (2)
  • -80 °C Freezer, -20 °C Freezer, 3 Refrigerators
  • Millipore Milli-Q water purification system
  • Thermo Electron Shaking Water Bath
  • Fisher Bacterial Incubators
  • NBS Incubator Shaker

Equipment for 454 sequencing service

  • Roche/454 GS FLX sequencer
  • Fluorometer, TBS 380 w/mini cell adaptor
  • Agilent Bioanalyzer 2100 w/DNA 1000 kit
  • PCR workstation
  • Qiagen Tissuelyser w/tube rack assemblies for making water-in-oil emulsion
  • Nexcelom Cellometer w/slides for bead counting
  • Server (Data Rig) for 454 data storage and analysis

User Logs

https://bmic.upenn/dag/index.php

For more information, you can also visit the Core's website: http://www.med.upenn.edu/genetics/core-facs/dna-seq/