LMT Services

If you would like to submit a request for one or more of the following services, please use our Service Request Form.  

Gene Expression

The Laboratory of Microarray Technology (LMT) at Van Andel Institute offers gene expression analysis services using Agilent oligonucleotide microarrays as well as home brewed cDNA arrays. The formats of the arrays include 8 X 15K (8 arrays on one glass slide), 4 X 44K, and 244K. Each array on the slide contains 15,000 probes, 44,000 probes, or 244,000 probes, respectively. The 60-mer oligonucleotide probes are printed using Agilent’s SurePrint technology that is related to conventional “Inkjet” printing technology. This method of printing ensures quality controlled probe integrity and consistency. The 8 X 15K array is customizable, which enables you to tailor the probe set to meet your specific research need. We perform all labeling, hybridizations, and array scanning according to the standard protocols set forth by Agilent Technologies.   

Aligent Technologies Dual-Mode Gene Expression Analysis Solution 

CGH Arrays (2-color)

The LMT offers Agilent’s Comparative Genomic Hybridization (CGH) arrays. CGH arrays investigate genomic DNA aberrations relating to the cytological sample. DNA from the control sample and the experimental sample are labeled and hybridized to a 60-mer, 44,000 probe array. Analysis of the array shows the losses, gains and amplifications of the gene copy numbers at the chromosomal level. 

Press Release: Aligent Technologies Human Genome CGH Microarray 

miRNA Expression Arrays

The LMT can also perform Agilent microRNA (miRNA) expression arrays. MicroRNAs are single-stranded RNA molecules approximately 20-25 nucleotides long, which regulate gene expression, but are not translated into protein (non-coding RNA). This array method allows for quantitative estimates of the miRNA content within the tissues studied. Only 120ng of input Total RNA is needed to hybridize to a unique miRNA probe set with both sequence and size discrimination, resulting in highly specific detection of closely related mature miRNAs (capable of binding and regulating mRNA sequences).

Aligent Technologies miRNA Analysis Solution 

Bioanalyzer Assays

The Agilent Bioanalyzer utilizes microfluidics and fluorescent detection to analyze biological samples for the integrity and viability of mRNA, total RNA, DNA, and proteins.  The Bioanalyzer determines RNA quality and concentration through the generation of electropherograms and pseudo-gel images depicting the 18s/28s ribosomal bands.  Low-protein, high integrity RNA is essential when using microarrays for global gene expression profiling.  Pre-screening one’s samples with the Bioanalyzer insures sample reliability and saves on potential reagent costs the project may incur.  Bioanalyzer DNA assays reliably determine DNA fragment size and quantity with high resolution (band separation).   The Protein assay can quickly determine protein quantity and purity.

Aligent Technologies 2100 Bioanalyzer 

RNA Isolation

The primary RNA isolation method used by the LMT is by homogenizing cells or tissue with TRIzol Reagent.  TRIzol is a phenol-based lysis and stabilization reagent that disrupts cellular components while guanidine isothiocyanate preserves RNA molecules.  Addition of Chloroform to the homogenous mixture allows separation of the aqueous (RNA containing) and organic phases by centrifugation.  Precipitation of the aqueous phase with isopropanol and purification with lithium chloride concentrates and purifies the RNA. 

Invitrogen TRIzol(R) Reagent 

RNA Amplification

The Ambion MessageAmp 2 kit is the primary kit used by the LMT to amplify small amounts of RNA.  The process uses reverse transcription with an oligo(dT) primer tagged with a T7 promoter to synthesize cDNA.  T7 RNA polymerase then linearly amplifies the cDNA to create thousands of antisense RNA (aRNA or cRNA) copies of the original mRNA sequences in the sample.       

MessageAmpTM II aRNA Amplification Instruction Manual (PDF) 

DNA Isolation (from whole blood)

We perform isolation of DNA from whole blood using the Qiagen QiaAmp DNA Maxi kit.  After proteins are denatured, the blood lysate is spun through a DNA binding column.  The DNA is then eluted with elution buffer and quantified using the NanoDrop ND-1000 Spectrophotometer.     

Custom cDNA or Protein Printing

The LMT is also a high-throughput spotted microarray production facility.  The state-of-the-art Microarray robot, made by Beta Integrated Concepts (MI), can print up to 200 human, mouse, rat, and canine cDNA microarrays from purified clone libraries stored at -20C.  Whole library genome or custom microarrays can be printed upon request.