Microarray and Q-PCR Instruments
Microarray
The Illumina BeadStation 500X is the centerpiece of current microarray analysis. This instrumentation and BeadStudio software, when used with Illumina BeadChips representing nearly all transcribed genes, provides powerful yet economical analysis of global gene expression. An Illumina technical bulletin gives a good overview of how gene expression analysis with this system works. For information on the process of labeling RNA, the types of arrays and their processing, and downstream data analysis, see the Microarray Service page
Links to old microarray equipment
Q-PCR
The Stratagene Mx3000p is currently used for all real-time PCR analysis in the Facility. This instrument is based on a peltier 96-well block system and has an overhead scanning optics system. The four installed filters allow reading of SYBR/FAM (492nm-516nm); HEX/VIC/JOE (535nm-555nm); Rox/Texas Red (585nm-610nm); and Cy5 (635nm-665nm). Thus, while the vast majority of analysis is performed with SYBR green (w/ROX normalization), nearly any assays can be done. This includes the >300,000 predesigned ABI TaqMan® Gene Expression Assays (formerly “Assays on Demand”) for mouse, human, rat and drosophila. The MX3000 software provides powerful analysis such as determining relative concentration of replicate unknowns, by linking them to specific standard curves.
The ND-1000 reads very small samples (1-2 µl) using surface tension rather than cuvettes. It is highly sensitive, yet the signal does not easily saturate, giving a wide dynamic range (~2 ng/µl to 3 µg/µl of DNA or RNA) without dilution. A full Spectrum reading (220-750nm) takes about 10 seconds, with the data directly transferred and analyzed on a PC.
Bioanalyzer (Bio-Rad Experion)
This automated electrophoresis unit analyzes samples on chips, similar to (or better than) the Agilent bioanalyzer 2100. For RNA, this provides quantitation and information on the integrity of the RNA, with orders of magnitude less sample than required than for agarose gel electrophoresis. There are two types of Experion kits for RNA analysis: normal sensitivity, for 1-12 samples at 5-500 ng/u; and high sensitivity, for for 1-11 samples at 100-5,000 pg/ul of RNA.