DNA Microarray and Bioinformatics - MUSC ProteoGenomics Facility

Services » DNA Microarray and Bioinformatics


The DNA Microarray Core Facility provides comprehensive resources to assist researchers in employing Affymetrix DNA microarray technology. Its personnel provide assistance to investigators in planning the scope of DNA microarray experimentation, as well as performing target preparation, hybridization, GeneChip scanning, and data analysis.


  • Detailed protocols for preparing biotin-labeled cRNA targets (e.g., isolation of RNA, synthesis of cDNA, in vitro transcription).
  • Preparation of biotin-labeled cRNA targets including synthesis of cDNA and in vitro transcription.
  • RNA, cRNA and fragmented cRNA quality control using Lab-on-a-chip technology.
  • Quality control tests on targets, including hybridization of cRNAs to test arrays to verify the suitability for subsequent full-array hybridization.
  • Hybridization of labeled cRNAs to full arrays and laser confocal scanning of the "hybridized" chips.

Bioinformatics Services

  • Assessment of hybridization quality and sample correlation using the AffyQC algorithm.
  • Normalization of data using one of the following procedures MAS5, RMA, gcRMA or MBEI (dChip).
  • Identification of differentially expressed genes using either a) fold change and/or t-test for two-sample experiments; b) 1-way ANOVA for 3- or more-sample experiments.
  • Significance analysis of gene ontology (GO) terms associated with differentially expressed genes.
  • Hierarchical clustering of differentially expressed genes and/or samples
  • Array data analysis is facilitated using the web-based DNA microarray analysis program, ArrayQuest™.

Fees for DNA Microarray and Bioinformatics Services

Academic/Core Non Academic
Bioanalyzer service: Agilent 2100 analysis of RNA or DNA $2.75/Sample $6
Bioanalyzer service: Agilent 2100 analysis of DNA high Sensitivety $55 79
Eukaryotic Target Preparation (per RNA sample) Standard
- Synthesis of cDNA
- Preparation of Biotin-labeled cRNA (IVT) or cDNA (NuGen)
$90 $220
Eukaryotic Target Preparation (per RNA sample) Low
- Synthesis of cDNA
- Preparation of Biotin-labeled cRNA (IVT) or cDNA (NuGen)
$180 $265
Affymetrix Target miRNA $55 $140
Affymetrix Target WT $110 $195
Affymetrix gene chip Hybridization $30 $90
Training in the use of ArrayQuest™ to perform DNA microarray analysis using methods currently held in the ArrayQuest Methods Library None Inquire

1, pricing does not include the cost of Affymetrix GeneChips. Contact facility personnel to obtain vendor pricing.

Facility personnel assist users in the performance of Affymetrix GeneChip hybridization, scanning and preliminary data analysis. On request, we will assist users in experimental design and will provide the necessary protocols and reference materials needed for preparation of hybridization samples. MUSC researchers, please contact the facility for information before ordering Reagents for Affymetrix GeneChip experimentation from Affymetrix, to ensure that you receive MUSC contract pricing.

Users can access all data files generated from their DNA microarray experimentation via the web-based MUSC DNA Microarray Database. This database was developed using uArrayDB™.



The facility is equipped with a complete Affymetrix system, comprising a GeneChip® Scanner 3000 7G with AutoLoader, hybridization oven and fluidics workstation. The Affymetrix system is complemented by a BioRad iCycler real time PCR machine and an Agilent 2100 Bioanalyzer.




Technical Information

  • Double-Stranded cDNA Synthesis (Invitrogen) PDF
  • RNA Transcript Biotin Labeling (Enzo) PDF
  • RNA Extraction and Isolation for Microarray Analysis: PDF
  • Eukaryotic Target Preparation for Microarray Analysis: PDF
  • Reagent List for Affymetrix GeneChip Experimentation: MS Excel