University of Chicago Genomics Core

Illumina Micro-array Gene Expression Experiments:

Available arrays: HumanHT12 (48,000 probes, RefSeq plus EST) *Please note: Illumina no longer offers Mouse arrays.

Before starting an experiment Read these guidelines and contact Dr. Faber ([email protected]) for an initial consult.

Sample submission (standard protocol) - Please submit 1 microgram of Total RNA (10 ul @ 100 ng/ul) in 1.5 ml tube. After diluting samples please re-measure before submitting. - Please label the samples with simple names (for instance AB1-12 for 12 samples on human HT12 array where AB corresponds to the PI’s initials). - Please randomize the samples before assigning names so that the AB1-12 order is the order in which the arrays will be hybridized to the human HT12 array. - Submit Total RNA samples to Dr. Siming Shou ([email protected]; please CC [email protected]) Bring a hard copy of the order form.

RNA isolation No particular procedure is recommended but we have observed that Qiagen products, or Trizol followed by a Qiagen product historically produces good results (the optional DNAse treatment is recommend). Follow the manufacturer’s directions! Do not overload columns.

Experimental design It is recommended to discuss the experimental design with your data analysis professional. Historically we have observed that for most tissue culture experiments an n of 2-3 and for most animal experiments an n of 4-6 is an adequate starting point.

Data output The data output can be tailored to a client’s needs and can range from the raw scan data (compatible with the Lumi analysis program in R) to an excel data file. Discuss this with your analysis professional. Also, the University of Chicago has an institutional license for the Illumina GenomeStudio module for gene expression analysis and can install that on a PC in your lab (once a paid experiment has been completed).

Pricing Check http://fgf.uchicago.edu/microarray_fees.php for latest fee structure.