Agilent Bioanalyzer 2100
The Agilent bioanalyzer utilizes a microchannel based electrophoretic cell that allows rapid and sensitive investigation of nucleic acid samples. This instrument is routinely used in our core for measuring the integrity of total RNA samples, for analysis of labeled cRNA used in microarrays, and more recently as a quality control and quantitation device for Genome Analyzer sequencing libraries.
The instrument is available to trained users (for more information on core equipment use policies click the "Equipment" link on the left hand side of this page, for more information on getting trained see below). If you have already completed a formal training with facility personnel and have your own materials, please use the on-line calendar to reserve time during normal working hours at least 24 hours in advance.
Many sample types can be analyzed on the bioanalyzer, including total RNA, labeled RNA, small and micro RNAs, and small and large DNA fragments. In addition, there are "regular" and high-sensitivity options for many of these sample types that utilize specific kits. The core maintains some of these as materials that are available for purchase if you want to use the instrument yourself. We have available:
RNA 6000 Nano Kit: 5-500 ng/ul sensitivity, good for measuring RNA integrity, assessing labeled RNA or fragmented RNA size distribution, or polyA+ purification efficacy. OK, not great, for quantitation. Several typical examples of total RNA profiles run on the bioanalyzer can be found at this Ambion hosted web site.
DNA 1000 Kit: 0.1-50 ng/ul sensitivity claimed (we don't see much below 1 ng/ul), size range 25-1000 bp. Used primarily by us to look at sequencing libraries, very good for quantitation and QC (for example, to identify primer dimers and adapter dimers). Double strand specific.
DNA High Sensitivity Kit: 5-500 pg/ul sensitivity, 50-7000 bp size range. Good for accurate quantitation and QC of very dilute sequencing libraries. Double strand specific.
For information on other kits that are available to purchase, please consult the Agilent bioanalyzer site. You are welcome to use any of these products on our instrument following appropriate training.
Using the Bioanalyzer
You must have a Genome Center account to use the bioanalyzer, which you can create here if necessary.
Use of the Bioanalyzer conforms to the other guidelines for any equiment usage in the core. Please click the "Equipment" link to the left and familiarize yourself with these guidelines. One difference from the use of other equipment is that if you are using facility materials to carry out your analyses, you MUST contact us ahead of time to be sure we can provide you with the appropriate supplies. Please don't just sign up on the calendar and assume we will see it.
For the training session, first arrange a time with us to be trained. Training is always carried out in conjunction with an actual run, so it's most productive to have all samples that fit in a particular chip (up to 12) ready to go. Fellow labmates are not qualified to train you. There is a limit of four people during a training session and two separate training sessions can be done for the yearly fee. We recommend familiarizing yourself with the bioanalyzer troubleshooting and maintenance manual. Not only will it help with your initial training, but it will give you a more detailed overview of the functions and capabilities of the instrument beyond what we cover. This manual is available as a 4.7 Mb pdf download.
If you have already completed a formal training with facility personnel and have your own materials, please use the on-line calendar to reserve time during normal working hours at least 24 hours in advance. Put your name in the "subject" box, and phone number and laboratory PI in the "description" box. If your lab has a particular DaFIS # to be used for equipment use, please indicate this as well. To delete a scheduled calendar date, contact Charlie or Heather.
Please bring your own pipettors (0.5-10 ul volumes are used), tips, gloves, and ice bucket (we can provide ice, no extra charge). For RNA chips, we recommend bringing your samples over as 2 uL aliquots in 0.5 mL tubes for the denaturing step. A condensed instruction sheet summarizing the protocol is available and should be consulted before doing your run; among other things this document will further explain what you need to bring and what we provide.
Bioanalyzer Output
The software that runs the bioanalyzer has a number of useful analytic options. It is available on the computer that runs the instrument, but this computer also runs the heavily-utilized nanodrop so it is usually not feasible to do much analysis there. We have another copy of the software on a core workstation, which you're free to use if available. A demo version of the software is available from Agilent; you can do everything the normal software does except save or export your file. Typically we create a pdf of the file once it is fully analyzed, then put this on our web server for you to download locally.