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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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RNA Quality Control

Before RNA samples can be processed for microarray, sequencing, or any other technology platform they must be tested for quality on the Agilent 2100 Bioanalyzer, quantitated on the NanoDrop Spectrophotometer, and tested on the Qubit 2.0 Fluorometer when needed.

Examples of GARP Passing RNA Samples

The GARP recommends using a kit to isolate and extract total RNA samples. We have found that the RNeasy Kits from Qiagen work especially well. View the protocol and see actual results (PDF) from samples successfully run using the Agilent 2100 Bioanalyzer. GARP also recommends extraction kits from Zymo Research, Inc. In order to prevent false-positive results in downstream applications, RNA must be treated with DNAse incorporated into the isolation or clean-up protocols.

For RNA samples isolated from FFPE tissues, please use isolation kits specially designed for RNA isolation from FFPE tissues such as Qiagen FFPE, Zymo Research FFPE or NuGEN's Prelude FFPE RNA Isolation kit.

Instruments

The GARP uses two instruments to determine the quality and concentration of samples delivered for processing: Agilent 2100 Bioanalyzer and NanoDrop® Spectrophotometer.

Agilent 2100 Bioanalyzer

The Agilent 2100 Bioanalyzer uses Lab-on-a-chip technology and capillary electrophoresis to render an extremely accurate measurement of any RNA integrity. The Agilent 2100 Bioanalyzer software has been designed to be intuitive and easy to use. For more information, please see:

Agilent 2100 BioanalyzerLab Chips

NanoDrop® Spectrophotometer

The second instrument is the NanoDrop® Spectrophotometer. The instrument can precisely measure sample concentration using only 1.5 µL.

Significance of 260/230 ratio (PDF)

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

NanoDrop ND1000NanoDrop Measuring Sample

Please email us at microarray@bcm.edu if you are interested in using the Agilent BioAnalyzer to check the quality of your RNA samples.

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