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Genomic and RNA Profiling Core Facility

Houston, Texas

BCM faculty, staff and trainees are the heart of the organization.
Genomic and RNA Profiling Core
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NanoDrop ND-1000 Spectrophotometer

The GARP uses a few instruments to determine the quality and concentration of samples delivered for processing. The first is the Agilent 2100 Bioanalyzer which can give an extremely accurate reading of any nucleic acid sample and give a readout showing the 18S and 28S peaks, along with degradation of any kind.

Another useful tool is the NanoDrop® ND-1000 Spectrophotometer. With only 1.5 microliters, it can give a precise concentration to any nucleic acid sample. Although the Agilent bioanalyzer gives a concentration, the NanoDrop® gives a more accurate reading.

NanoDrop® ND-1000 Spectrophotometer

The NanoDrop® uses uses this small amount of recoverable sample to detect accurate concentration as well as to produce a 260/280 and a 260/230 nm ratio giving further sample quality information. RNA, DNA, and any other nucleic acid sample can be run on the machine.

The NanoDrop® ND-3300 Fluorospectrometer has the unique ability to measure multiple fluorophores simultaneously through a new technique called virtual filtering. We use this instrument to detect accurate concentrations of samples too small to be accurately measured by the NanoDrop® ND-1000 Spectrophotometer.

Significance of 260/230 ratio (PDF)

Effects of Contaminants (ethanol, isopropanol, trizol and Qiagen's Buffer RLT) on 260/230 ratio (PDF)

The GARP will be using the NanoDrop® for accurate measurements of IVT and cRNA samples for Affymetrix reactions, as well as for measuring the concentration of dye incorporation in cDNA microarray samples. The NanoDrop® software comes with a special protocol for microarray samples labeled with Cy3®, Cy5®, and any other fluorescently dye-labeled samples. For more information on the NanoDrop® visit the NanoDrop® Technologies website.

If you have any questions about the NanoDrop® ND-1000 Spectrophotometer, please email us at microarray@bcm.edu.

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