Shared Resources


Genomics Facility

Director: Donald Baldwin, Ph.D.

The Genomics Facility enables researchers to observe global nucleic acid patterns including expression levels of all RNA transcripts in a sample, genetic variability throughout the genomic DNA sequence of an individual or tumor, and epigenetic modifications across the genome. These patterns, whether genome-wide or targeted to a specific set of markers, can be compared between normal, pre-malignant, cancer, and metastatic cell types in experiments that range from cell cultures to diagnostic or prognostic patient samples. The services include assistance with experimental design and resource assessment, sample preparation, assay performance, and data management and analysis.

Mission

The mission of the Genomics Facility is to provide quality services for molecular biology assays that are conducted with highly parallel or high-throughput technologies.

Contact

Don A. Baldwin, Ph.D.
215-898-3675
Fax: 898-4227
Email: dbaldwin@mail.med.upenn.edu

Locations

The Genomics Facility is located in adjacent laboratories in the basement (for minimal structural vibration) of the John Morgan Building and bioinformatics offices in Blockley Hall, which is adjacent to John Morgan and connected by a bridging hallway. Facility laboratories occupy 2220 sq. ft., plus 800 sq. ft. of office space including self-service bioinformatics work areas.

Fees

Usage Category Description Unit Price
DNA/RNA Extraction RNA isolation, PAXgene blood reagents $8.25
DNA/RNA Extraction RNA isolation, Qiagen column $6.60
RNA Amp/Label Affymetrix WT target labeling reagents $50.00
RNA Amp/Label NuGEN WT-Ovation Pico amplification, biotinylation $143.00
RNA Profiling GeneChip Affymetrix Human Gene 1.0ST Array $175.00
Microarray processing Affymetrix hybridization cocktail $38.00
SNP Genotyping GeneChip Affymetrix GeneChip, human SNP 6.0 $300.00
microRNA Profiling miRNA assay reagents, Exiqon $22.00
microRNA Profiling Exiqon miRCURY miRNA array $280.00
Other Arrays Agilent mouse CGH microarray 244A $402.50
Other Arrays Agilent CGH assay reagents $52.25
Microarray processing Agilent CGH array hybridization reagents $25.30
Molecular diagnostic CDR3 Spectratyping $345.00
Molecular diagnostic PCR Based Assay $30.00
Molecular diagnostic Twin Zygosity Testing $300.00
DNA/RNA Extraction DNA from 0.3 ml blood, avg yield 8 ug, batch = 96 $10.00
DNA/RNA Extraction DNA from 3.0 ml blood, avg yield 60 ug, batch = 12 $21.00
DNA/RNA Extraction DNA from 10.0 ml blood, avg yield 200 ug, batch = 12 $32.00
DNA/RNA Extraction DNA from 4 ml Oragene saliva, avg yield 50 ug, batch = 12 $21.00
Custom TaqMan genotype TaqMan SNP Assay validation using Coriell controls $75.00
Custom TaqMan genotype TaqMan genotyping, per assay $0.50
Custom TaqMan RNA TaqMan Gene Expression Assay validation, 1-16 specimens $100.00
Custom TaqMan RNA Gene Expression Assay set-up, per assay plate used $225.00
Custom TaqMan RNA Gene Expression Assay, per sample in quadruplicate $0.55
Self Service GenePix scanner, per session $20.00
Self Service Nanodrop spectrophotometer, per session $10.00
Self Service Agilent Bioanalyzer session $15.00
Service Lab work, per hour $70.00
Service Training, per hour $70.00
Bioinformatics Consulting Data analysis session, 0.5-4 hours $180.00
Bioinformatics Consulting Programming, data analysis or sys admin; per hour $90.00
Self Service Use of public computer, per hour $15.00
Bioinformatics Software Partek Genomics Suite shared license, per year $1,200.00

Equipment

  • The Affymetrix instrument with six FS450 fluidics stations
  • Two GCS3000 7G scanners
  • Affymetrix GeneTitan
  • GeneMachines OmniGrid robot with 48 pins
  • Tecan HS4800 Hybridization Station
  • SciGene Little Dipper
  • Axon GenePix 4000B scanner
  • Illumina Solexa GA IIx sequencer
  • ABI 7900 HT TaqMan
  • Beckman SNPstream
  • MJ Research tetrad thermalcyclers
  • ABI 3100 capillary electrophoresis instrument
  • Illumina GoldenGate
  • Sequenom
  • Luminex
  • High-Throughput Genomics
  • Illumina BeadStation
  • Biomek FX
  • Biomek 2000
  • Biomek FX
  • Qiagen M48 BioRobot
  • Chemagen Magnetic Separation Module I
  • TissueLyser bead mill
  • Qiagen QIAcube
  • Agilent Bioanalyzers, Nanodrop and Amersham GeneQuant spectrophotometers
  • Nanodrop fluorimeter
  • Software packages including: Agilent GeneSpring, Spotfire Decision Site, Partek Genomics Suite, Illumina GenomeStudio, BioConductor, Ingenuity and others.

User Logs

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