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GeneChip Essentials - How Affymetrix Genechip® Gene Expression Microarrays Work

The Human Genome Project revealed our genetic sequence and discovered everyone's DNA to be 99.9% identical. So, how are we so different from each other? The answer is that identical genes can be very differently expressed, resulting in big biological differences.
Gene Expression Analysis

The 0.1% difference in our DNA sequence certainly contribute, but environmental influences...
Understanding Disease

Gene expression arrays have been used to study virtually every type of disease. For simplicity's...
Genes and Disease

To find a treatment, researchers first have to find some sort of genetic malfunction that...
How the Array Works

While that may sound simple enough, it's been a long road to figure out just what genes...
Natural Attraction

GeneChip microarrays use the natural chemical attraction between DNA and RNA molecules to...
C Pairs with G and A Pairs with T or U

There are only four molecules, or "bases", in every DNA chain: adenine (A), guanine...
A Good Match Sticks, a Bad Match Doesn't

When a single strand of DNA (ATCATG) matches a strand of RNA (UAGUAC), the two strands are...
The Basic Principle

Affymetrix microarrays use this base pairing attraction — known as hybridization —...
From a Gene to a Probe

Affymetrix microarrays can measure the expression of every known human gene, or any other...
More Probes are Better

In the example above, we built one probe to detect one short section of RNA. However, Affymetrix...
The Probe Pair

The probes we just talked about are seeking a "Perfect Match" to the RNA that is...
Matchmaker, Matchmaker

In a perfect world, the perfect match probe would only bind to its matched sequence and...
22 Probes in a Set

In all, there are 22 different probes, or data points, used to make sure that the microarray...
Features and probes

The surface of the Affymetrix array is like a giant checkerboard that has been shrunk down...
Extract and Prepare RNA

Now that we have a probe designed to measure expressed RNA, we have to extract the RNA from...
Chop up the RNA

Using another chemical process, we fragment the RNA chains up into millions of short pieces...
Wash Sample Over the Array

All of the prepared RNA sample is washed over the array for 14 to 16 hours. The number...
A Committed Relationship

But somewhere, in the tagged sample of RNA washing over the array, a match will be made....
Determining a Match

Let's assume that we have a match and that RNA in our sample bound to the probes built...
Making Glow in the Dark RNA

Because we can't see RNA, we can't directly figure out how much of it has stuck...
An Expressed Gene

Researchers wash the fluorescent stain over the array, and the glow in the dark molecules...
No Match at All

If the sample RNA doesn't match, it will be rejected by the probe on the array. It's...
When it Doesn't Work Out

Scientists will know that no match was made when they shine the laser on the probes and...
Measuring All Gene Expression at Once

So far we've been looking at expression from just one gene. And although GeneChip expression...
Comparing Gene Expression

The whole point of microarray gene expression analysis is to compare expression levels between...
Classifying Disease

Having found a gene expression pattern for rude behavior, our scientists explore if those...
An Actual Gene Expression Image

In reality, human expression arrays have over 1.3 million different probes used to detect...
Drug Discovery

Ultimately, the goal of identifying a disease pathway, like RUDE, is to develop a treatment...
From Chemical to Drug

After identifying and validating a target, drug companies begin the long and expensive task...
Treating People

Different people respond to drugs in different ways. Often, those responses are a result...
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