The Huck Institutes of the Life Sciences

Microarray sample preparation recommendations

Recommendations for preparing total RNA samples for use in microarrays

The key to successfully performing microarray experiments is to provide the core facility with total RNA of sufficient quality and quantity.

The quality of the initial samples is by far the single most important factor in the whole process.

 

Tissue and cell isolation

Investigators need to carefully choose their methods of tissue and cell isolation as the choice of these methods have a direct impact on the quality and quantity of RNA subsequently obtained.

If possible total RNA purification should follow tissue/cell isolation as quickly as possible to prevent alterations in the transcript profile.

In some cases immediate RNA purification is not possible.

If tissues/cells must be stored prior to RNA isolation then the use of products such as RNALater from Qiagen or similar reagents is recommended to prevent RNA degradation.

The core facility strongly encourages pilot projects to confirm that the chosen methods will reproducibly produce sufficient quantities of cells/tissues to ultimately yield the required amount of high quality RNA.

Once an isolation protocol or a storage and isolation protocol is established it is important that all of the samples collected for a given project be collected with this same protocol.

Variance in these techniques may result in differences in the transcript profile which may later be misidentified as changes due to experimental treatment while in reality they are artifacts of varying isolation and storage methodology.

 

RNA isolation

The facility does not perform total RNA purification nor does it DNAse samples prior to labeling.

These processes are the sole responsibility of the customer.

For Affymetrix arrays we require a minimum of 300 ng of total RNA for determination of sample concentration, purity, quality and labeling.

For NimbleGen arrays we require a minimum of 2 ug of total RNA.

If you believe you will have a difficult time meeting these requirements please contact the facility prior to beginning your project.

There are a number of well established commercial kits and protocols for a variety of species and tissue/cell types.

Investigators need to carefully determine the most appropriate methods for their tissue/cell type.

The core facility strongly encourages pilot projects to confirm that the chosen method will reproducibly produce sufficient quantities of high quality total RNA from the tissue/cell of interest.

Given the tremendous variety of tissue/cell types it is difficult for us to give specific recommendations.

For anyone not sure of what product to choose we strongly encourage you to examine the products from Qiagen and Ambion (LifeTech) as a starting point.

These companies have a large variety of products with decision charts to help you in choosing the right one.

Also if you need more detailed advice there are people in tech support at these companies who truly are experts in RNA isolation and have a broad experience in helping customers isolate RNA from every conceivable species/tissue/cell.

We do however have a few general recommendations regarding RNA isolation techniques based upon our experience.

We do not recommend the use of Trizol alone for total RNA isolation as the use of Trizol often results in samples that are contaminated by proteins and organics which can inhibit the sample labeling process.

We do recommend products like RNeasy which is a column based purification method resulting in very pure preparations of total RNA.

Many of our customers have found though that they get superior yield with Trizol so they perform an initial isolation with Trizol followed by a further cleanup using the RNeasy kit.

We have observed that this results in very pure RNA and this method has been used successfully for RealTime PCR, microarrays, and RNA-Seq.

 

Accurate Determination of RNA Concentration and Purity

RNA concentration is routinely determined by measuring absorbance at 260 nm.

However it should be noted that all nucleic acids have a peak absorbance at approximately 250 -260 nm, this includes RNA, DNA, and free nucleotides.

If your RNA preparation contains contaminating DNA or free nucleotides it will affect your ability to accurately determine the RNA concentration in your sample with a spectrophotometer.

RNA purity is determined by measuring the 260/280 and 260/230 ratios using a spectrophotometer.

Excessive absorbance at 280 nm indicates the presence of protein in your sample while excessive absorbance at 230 nm may indicate the presence of residual phenol in your sample.

The 260/280 ratio for RNA should be approximately 2.0 and the 260/230 ration should be 2.0 – 2.2.

These ratios can be affected by pH so we are comfortable with all ratios over approximately 1.8.

Ratios that differ significantly from that measure should undergo further purification.

We recommend the use of a NanoDrop to determine RNA purity and for an initial estimate of RNA concentration.

This device is easy to use and less prone to error than traditional spectrophotometers because sample dilution is usually unnecessary and pipetting errors have no effect on correct determination of concentration.

All facility customers may use the one we provide in 411 Chandlee Lab free of charge, but please bring your own pipettor and tips.

This instrument is regularly calibrated so that customers may be assured it provides an accurate measurement.

We regularly see sample concentrations reported to us that are in wide variance from the true concentration measured by our facility with calibrated NanoDrops or other techniques such as Bioanalzyer or Qubit discussed below.

If you are using your own spectrophotometer please check that it is calibrated by measuring the concentration of commercially obtained standards, use calibrated pipettors, and be careful in calculating and performing your dilutions.

As noted above DNA may affect the accurate determination of RNA concentration.

If you believe your total RNA has significant contamination with DNA we encourage the use of a Qubit which uses the specific binding of fluorescently labeled dyes to determine DNA and RNA concentration.

In our experience most RNA preparations will contain some DNA contamination, often 5% or less.

This level of contamination should not affect microarray analysis.

The Qubit is a relatively inexpensive device and we recommend any labs routinely preparing samples for microarrays or Next-Gen sequencing to obtain one.

 

RNA Sample Quality

It is essential to determine the quality of RNA samples prior to microarray analysis to ensure that differential degradation of samples is not later mistaken for differential expression.

Sample quality is determined using an Agilent Bioanalzyer and we provide this as a service at the Genomics Core Facility.

The Bioanalyzer will produce an RNA Integrity Number or RIN which is an objective measure of RNA quality.

RIN scores vary from 1-10 with 10 being the highest quality samples showing the least degradation.

We not only like to see high RIN scores (7-10) but we like to see a reasonably narrow distribution of the scores which is typically 1-1.5.

We recommend re-isolation of samples that have low RIN (6 or below) or are large outliers from the average RIN of a group of samples.

Once the total RNA samples have passed these quality measures they are ready for labeling and subsequent hybridization to microarrays.

 

Summary

High sample quality is essential for successful microarray experiments.

Customers are responsible for total RNA isolation.

We encourage customers to perform pilot projects to determine the best tissue/cell isolation technique and RNA purification technique for their sample type.

Once a tissue/cell isolation technique and RNA purification technique has been established it should be adhered to for all samples in a project.

Determine total RNA sample purity and estimate sample concentration with a NanoDrop.

The 260/280 and 260/230 ratios need to be greater than 1.8.

The Genomics Core will determine total RNA quality prior to sample labeling by assessing the sample using the Agilent Bioanalzyer.

RIN of 7-10 and ranges of RIN from 1 – 1.5 for a group of samples are preferred.