The quality of the nucleic acid is essential to the overall success of the microarray analysis. Since the most appropriate protocol for the isolation of RNA or DNA is source dependent, we recommend using a protocol that has been established for the tissues or cells being used. In the absence of an established protocol, we recommend using one of the commercially available kits designed for nucleic acid isolation.

The 2100 bioanalyzer is Agilent's highly successful microfluidics-based platform for the analysis of DNA, RNA, proteins and cells. As the first commercial, analytical instrument based on lab-on-a-chip technology the Agilent 2100 bioanalyzer has proven to be an excellent alternative to messy and labor-intensive gel electrophoresis techniques; delivering fast, automated, high quality digital data instead of the subjective, time-consuming results associated with gels.

The process only takes 35 ~ 40 minutes for 12 samples: Load samples, run chip, view output.

The NanoDrop® ND-1000 UV-Vis Spectrophotometer enables highly accurate analyses of extremely small samples with remarkable reproducibility. The patented sample retention system eliminates the need for cuvettes and capillaries which decreases the measurement cycle time. The ND-1000 is designed for 1-2 ul undiluted samples.

• 1 to 5 µg of total RNA required for Affymetrix labeling protocol
• 5 to 10 µg of total RNA required for ENZO Biosciences labeling protocol
• 1st and 2nd strand cDNA synthesis from total RNA
• Generation of biotin-labeled cRNA
• Quantification and quality check
• cRNA fragmentation

• Total RNA quality assessment
• 1st and 2nd strand cDNA synthesis from total RNA
• in vitro transcription (IVT)
• Second round 1st and 2nd strand cDNA synthesis
• IVT with biotin
• Quantification and quality check
• cRNA fragmentation

• 0.25 µg of genomic DNA is required
• Restriction digestion of DNA
• Cleanup, and QC for the restriction digest
• Ligation
• PCR
• Fragmentation
• End-labeling

• Samples are loaded on to an expression or mapping array and hybridized overnight.
• The samples are removed to microfuge tubes,
• The arrays are then processed through the GeneChip® Fluidics Station 450.
• Each array is then scanned on the Affymetrix GeneChip® Scanner 3000.

CombiMatrix Corporation's CustomArray™ is a high quality, completely customizable array format that provides a cost effective and timely solution for microarray users. Oligonucleotide probes can be defined and designed by the user and supported by the open source CombiMatrix probe design system at no additional cost. CustomArray™ uses a specially modified "CMOS" semi-conductor to direct the molecular assembly of a specific sequence of DNA bases in response to a digital command. The 12,000 feature CustomArray™ chip available in 1 × 3 inch format to fit most spotted microarray scanners.

The NanoChip® Molecular Biology Workstation is an automated multi-purpose instrument that facilitates detection of known sequences, such as in the analysis of Single Nucleotide Polymorphisms (SNPs) and Short Tandem Repeats (STRs) using the NanoChip® Electronic Microarray. The unique, open-architecture design permits us to define, select and build our own test panels or use predefined analyte specific reagent packs (ASR's).

Basic Data Analysis: the core will run a pairwise comparision analysis (e.g., control vs. experimental) using Affymetrix GCOS data analysis software.
Extended Data Analysis: the core analyst will provide an indepth analysis of multivariate experiment data (e.g., 3 or more treatments, time-course experiment, etc.).

Core lab service cost
Affymetrix GeneChip® price list for UCHSC