The Applied Genomic Technologies Core

Description of Microarray Services

RNA Quality Control Assessment

• RNA quality control using Agilent 2100 Bioanalyzer. All RNA samples for microarray analysis must be run on the bioanalyzer to assess sample quality.

Affymetrix GeneChip Microarrays

• 3' Expression Array Analysis
• Full service of Affymetrix GeneChip 3' Expression Analysis including RNA labeling, hybridization and scanning using eukaryotic and prokaryotic GeneChip arrays.
• Whole Transcript Expression Array Analysis
• Full service of Affymetrix GeneChip exon and gene level expression analysis including labeling, hybridization and scanning using Exon 1.0 ST and Gene 1.0 ST arrays.
• miRNA Array Analysis
• Full service of Affymetrix miRNA Array Analysis including RNA labeling using Genisphere Flashtag Labeling kit, hybridization and scanning.
• Resequencing Array Analysis
• Full service of Affymetrix resequencing analysis including PCR, labeling, hybridization and scanning using Affymetrix Resequencing arrays and CustomSeq Resequencing arrays.
• Tiling Array Analysis
• Full service of Affymetrix Tiling Analysis including sample labeling, hybridization and scanning using Affymetrix GeneChip Tiling arrays.

All Affymetrix services above are performed on the Affymetrix GeneChip® Instrument System

• Hybridization Oven 640
• Fluidics Station 450
• GeneChip® Scanner 3000 7G with autoLoader
• Computer workstation with Affymetrix GeneChip® Command Console Software (AGCC).

Agilent DNA Microarrays

Provide full service of one or two-color target labeling, hybridization and scanning using Agilent DNA microarrays including gene expression microarray, CHIP-on-chip microarray, custom microarray, etc.

Spotted arrays

Provide full service of two-color target labeling, hybridization and scanning using spotted glass slide arrays.

Agilent DNA microarray and spotted array are performed on Agilent DNA Microarray Processing System

• Agilent G2545A hybridization oven
• Agilent microarray hybridization chamber
• Agilent G2565BA microarray scanner: measure fluorescence from two dyes simultaneously; can read any mix of 1" x 3" glass slide microarrays (both Agilent and non-Agilent)
• Agilent Feature Extraction Software: automatically finds and places microarray grids, rejects outlier pixels, accurately determines feature intensities and ratios, flags outlier pixels, and calculates statistical confidences