GENOME TECHNOLOGY ACCESS CENTER • DEPARTMENT OF GENETICS • WASHINGTON UNIVERSITY SCHOOL OF MEDICINE

Microarray

At the discretion of our clients, the microarray team can be involved in every step of a microarray project, and is equipped to run all major array formats including Illumina, Affymetrix, and Agilent.  We help with study design, preparing samples, we run the hybridizations, and can analyze the results.

How to Get Started

You may submit a project proposal via our microarray proposal form.  If you would like to submit a sample, please review our sample submission guidelines at the bottom of this page and contact us for submission instructions.  Below you will find more information about our microarray services, applications and analysis.

Microarray Applications

GTAC offers RNA , DNA and protein analysis onThermo Fisher Microarray Instruments, Software, and ServicesIllumina, and Agilent platforms.  Below is a list of applications that we support.  For further information about these applications and/or a consultation with our team to discuss experimental design, please contact genetics-gtac@email.wustl.edu

  • SOMAscan 1.3K
  • Gene expression
  • miRNA expression
  • SNP and copy number
  • DNA methylation

Gene Expression

Thermo Fisher Microarray Instruments, Software, and Services

  • Human, Mouse, Rat Gene ST
  • Human, Mouse, Rat Exon ST
  • Human, Mouse, Rat Clariom D
  • Human, Mouse, Rat Clariom S

Samples are prepared using WT Pico, WT Plus or NuGen Ovation and Pico amplification kits.  As little as 100 pg of total RNA can be used. This strategy can be used with partially degraded or FFPE RNA.

Agilent

  • Human, Mouse, Rat 8x60K, 4 X 44K
  • Model organism and custom

Samples are standardly prepared using LifeTechnologies MessageAmpII kits. Amplified RNA is labeled with Kreatech ULS kits. If total RNA mass is limited (less than 200 nanograms), Sigma WTA2 amplification kits can be used with Agilent microarrays. Amplified cDNA is labeled with Kreatech ULS. A minimum of 2 nanograms of total RNA is recommended. This strategy can be used with partially degraded RNA.


Protein Measurement

SOMAscan® Proteomic Assay

SOMAscan is a microarray based assay which measures more than 1,300 protein analytes in serum, plasma or cerebrospinal fluid, urine or equally small amounts of a variety of other biological matrices, such as lysates. The assay offers 8 logs of dynamic range, quantifying proteins from femtomolar to micromolar, with reproducibility of 4.6 median %CV for plasma.

The SOMAscan proteomic assay is enabled by protein-capture SOMAmers® (Slow Off-rate Modified Aptamer) reagents. The SOMAscan assay measures native proteins in complex matrices by transforming each individual protein concentration into a corresponding SOMAmer reagent concentration, which is then quantified by standard DNA microarray. To date, the SOMAscan assay has been applied successfully to biomarker discovery and validation in many pharmaceutical research and development projects, diagnostics discovery and development projects, and academic research projects.

How it works

  • Depending on the sample type, one SOMAscan kit is used to characterize 24 or up to 28 samples. Therefore submitting in multiples of 24 or 28 , while not required, is the most economic batch-size. It is optimal if you can submit >200ul/sample.
  • Use for our online submission form and sample handling instructions. 
  • Once you have confirmed the submission form and number of samples you wish to run, please let us know.  Reagent kits are always ordered new.  There’s typically  a ~2-3 week lead-time to receive the kits. 
  • For each 24-sample kit, there are four array substrates (slides) representing 8 identical oligonucleotide microarrays.  On each of the four substrates, 2 of the arrays are utilized as calibrators and controls for the serum or plasma SomaScan assay; therefore 24 arrays remain to accommodate your processed samples. To address microarray positional effect, we recommend that you randomize the samples/groups/conditions across the tubes or plate for submission. 
  • For non-Washington University researchers, once you have confirmed the number of samples you wish to process, we will issue a quote. A PO from you will be needed.

SNP And Copy Number

Illumina
Infinium catalog and custom
Samples are prepared using Illumina’s Infinium HD Assay. Using robotics, GTAC can process as many as 1152 samples per week. Illumina provides a broad spectrum of arrays to address various facets of human genomic research.  Additionally, Illumina provides a wealth of Infinium arrays to address the needs of non-human genomics research.

Thermo Fisher Microarray Instruments, Software, and Services


Cytoscan HD

Together, CytoScan™ HD Array Solution along with the Command Console and Chromosome Analysis Suite software, enable you to perform high-resolution genome-wide DNA copy number analysis. The combined high resolution DNA copy number data and the ability to detect gains, losses, and UPDs on a single array makes the CytoScan™ HD Array Solution a great tool for next generation cytogenetics studies.

The Chromosome Analysis Suite (ChAS) software for cytogenetic analysis enables you to view and summarize chromosomal aberrations across the genome. Chromosomal aberrations may include copy number gain or loss, mosaicism, or loss of heterozygosity (LOH).


DNA Methylation

Illumina
Infinium HumanMethylation EPIC
With the Infinium MethylationEPIC BeadChip, researchers can screen over 850,000 methylation sites quantitatively across the genome at single-nucleotide resolution. Samples are prepared using Illumina’s Infinium HD Assay. DNA samples must first undergo bi-sulfite conversion in our laboratory. Please contact us for details.


MiRNA Expression

Thermo Fisher Microarray Instruments, Software, and Services

Genechip miRNA
The GeneChip miRNA 4.0 array contains content to screen for all mature miRs from miRBase Release 20.  Samples are prepared using Flashtag labeling kits. A minimum of 130  nanograms of total RNA is recommended. Unlike miRNA sequencing applications that require high integrity total cellular RNA, the Genechip miRNA assay can be successful with samples exhibiting RNA degradation.

RNA and DNA Sample Submissions Guidelines

Methodology Array RNA/DNA requirements Quantity used for QC Quality based on QC
Thermo Fisher WT Pico SL Human, Mouse, Rat Gene 1.0/2.0 ST 1-50 ng/ul 2 ul 260/280 :1.8 to 2.0
Human, Mouse, Rat Clariom D 10-15 ul 28s:18s : degraded samples
Human, Mouse, Rat Clariom S 2-50 ng input into assay No DNA contamination
Thermo Fisher WT Plus Human, Mouse, Rat Gene 1.0/2.0 ST 20-175 ng/ul 2 ul 260/280 :1.8 to 2.0
Human, Mouse, Rat Clariom D 10-15 ul 28s:18s :  RIN>7
Human, Mouse, Rat Clariom S 50 ng-500 ng input into assay No DNA contamination
Thermo Fisher miRNA miRNA vs 4.0 40-50 ng/ul 2 ul 260/280 :1.8 to 2.0
10-15 ul 28s:18s :  degraded samples
200-500 ng input into assay No DNA contamination
MessageAmp II Agilent 8x60K Human, Mouse, Rat 20-200 ng/ul 2 ul 260/280 :1.8 to 2.1
Agilent 4x44K Human, Mouse, Rat 12-30 ul 28s:18s :  RIN>7
Agilent custom or model 200-500 ng input into assay No DNA contamination
Sigma WTA2 Agilent 8x60K Human, Mouse, Rat 1-20 ng/ul 2 ul 260/280 :1.8 to 2.1
Agilent 4x44K Human, Mouse, Rat 10-15 ul 28s:18s :  degraded samples
Agilent custom or model 2-20 ng input into assay No DNA contamination
Infinium Omni-Express 50 ng/ul NO QC performed (investigator responsibility)
Global Screening Array 12-20 ul
other Infinium SNP arrays 200 ng input into assay
Thermo Fisher Cytoscan_HD Cytoscan_HD 50 ng/ul 2 ul 260/280 :1.8 to 2.0
15ul Highly intact DNA
250 ng input into assay No RNA contamination