Affymetrix Arrays

Agilent Bioanalyzer 2100

Most user supplied RNA or DNA samples (depending on the specific protocol followed and source material provided) are initially QC checked using the Agilent Bioanalyzer 2100 and/or the NanoDrop ND-1000 spectrophotometer.

Due to the instability of RNA and the near universal presence of RNases, performing an RNA integrity check prior to sample processing steps is essential for confidence in the final results of gene expression analysis studies. The Agilent Bioanalyzer 2100 offers a microfluidics-based platform for rapid analysis using only a very small portion of your provided total RNA samples. For further information on this instrument and its capabilities, please check the Agilent Bioanalyzer 2100 webpage.

NanoDrop ND-1000 Spectrophotometer

There are many brands of spectrophotometers (and infrequently calibrated) in use across laboratories, departments and institutions, each with varying degrees of accurate capabilities in reading small quantities of precious samples.

We strictly rely on our Facility's NanoDrop ND-1000 spectrophotometer when assessing the quantity/concentration levels of all user supplied samples. Our calibrated ND-1000 enables a uniform method for highly accurate analyses of extremely small samples with remarkable reproducibility. For further information on this instrument and its capabilities, please check the NanoDrop ND-1000 Spectrophotometer webpage.

Speed-Vac Concentrator System

Depending on the precise assay protocol being followed, we ask users to make available a specific amount of sample material at a defined concentration.

When users don't, or are unable to supply samples that meet established guidelines, the Facility's SDP Speed-Vac Concentrator with UVS400 Universal Vacuum System is used to concentrate provided nucleic acid materials. This method is preferred over EtOH precipitation approaches as there is no loss of precious material and no chance of added remaining salt contamination effecting downstream enzymatic processing steps.

Array Automation's ArrayPlex - Automated/Robotic Instrumentation

Specific Affymetrix Instrumentation

Affymetrix Instrumentation present within the UCI DNA & Protein MicroArray Facility consists of the following:

GeneChip Hybridization Ovens 640 and 320 - for overnight hybridization of target RNAs or DNAs with the DNA oligo probes found on an Expression, Exon, Tiling or Mapping/SNP GeneChip array.

Three GeneChip Fluidics Stations 450, each capable of processing up to four GeneChip arrays at a time, allowing for automated washing and staining protocols of the hybridized arrays.

GeneChip 3000 Scanner 7G with Autoloader installed and a dedicated dual processor computer workstation for scanning the resulting arrays and quantifying the amount of bound target at each probe cell site of an array; the unit additionally acts as the controller for the GeneChip Fluidics Stations and Scanner.