Array Scanner

Molecular Devices (Axon) GenePix 4000B Scanner

The GenePix (or Axon) scanner has the following features: 5 um resolution scanning capability, 635 nm and 532 nm dual laser excitation wavelengths (compatible dyes include Cy3, Cy5, and Alexas 555, 647, and 660), barcode reading capacity, and accompanying fluorescent feature analysis software (GenePix Pro 6.0).  This scanner scans one slide at a time, so typically a user has to be around to “feed” the machine if multiple slides need to be analyzed. It  displays the acquired image in real time so the operator very quickly knows if the scan is worth continuing, or whether the process should be halted. The data are generated by lasers scanning from the top of the slide, so there is flexibility in the types of slides that can be used in this instrument.  According to the specs, the scanner should be suitable to analyze the Spatial Transcriptomics tissue optimization slides.  For more scanner specs please see this information.

The Axon scanner is housed in an ozone-scrubbed chamber.  In the central valley of California, ozone levels in the summer can have a substantial impact on the stability of the Cy5 dye used in array experiments.  The dye is particularly vulnerable to ozone degradation in its excited state during the laser scan.  To minimize these effects, we built the “ozone annihilator”.  Air is drawn in through a series of metallic catalytic converter grids, which break down the ozone.  This air is then directed to a chamber housing the scanner, so there is a constant positive pressure flow of ozone free air.  Just turn on the air flow a few minutes prior to starting the scan and you’ll be all set.

As with the Agilent scanner, user costs will be based on annual training fees and per slide scanning charges.  You must have a Genome Center account (which you can create here) to cover training and scanning charges.  It is necessary to log on in order to access the computer controlling the scanner. If you (or your lab) has an account at the School of Medicine (SOM), your account name and Kerberos password will log you on, and will also automatically map your lab’s School of Medicine servers onto the computer.  It is recommended that you copy your images to these servers as a backup. If you don’t have an SOM account, log on to the computer as a guest, as follows:

Username:  GenomeUser2
Password: scanner1!
Domain: UCDSOM

You should then create a folder for yourself on that desktop and deposit your data there since you’ll be sharing this desktop.  If desired, your data can be subsequently transferred to the Genome Center server, backup and archiving policies still to be determined.
If you have never used the Axon Scanner, you must arrange a time with us to be trained. Training is most effectively done with your actual microarray.  Because arrays should be scanned as soon as possible following processing, make sure you have your appointment slot before starting your array experiment.  Facility instruments that require user training involve training with facility personnel, not fellow labmates. There is a limit of four people during a training session and two separate training sessions can be done for the yearly fee.  A condensed instruction sheet summarizing the scanning protocol is available:  we recommend printing this out and bringing it to your training.  Please contact Vanessa to make arrangements for training and scanner use.

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