Agilent Microarray Fluorescent Scanner
The Expression Analysis facility has an Agilent G2565BA fluorescent scanner available for use by trained individuals. The scanner has 5 um resolution, and can scan 1" x 3" microscope slide-based arrays in red, green, or both channels; compatible dyes include Cy3, Cy5, and Alexas 555, 647, and 660. The unit can scan 48 slides at a time with automatic laser scan adjustment. 10 um scans, sufficient resolution for most arrays, take about 8 minutes per slide and generate 50 Mb tif files. 5 um scans take about 20 minutes and generate 100 Mb files. After users complete training on the instrument, the scanner is available for use during normal working hours. Since Cy5 dye instability can be a problem, it is advisable to give a few days notice to facility personnel to reserve your place on the scanner. Be prepared to recover your data by flash drive or by CD. NO GUARANTEE ON DATA STORAGE IS MADE!
The scan computer also has a feature extraction program to generate intensity information on the scanned images. This program can be run while the scanner is collecting data on other arrays, and is available for use anytime there is no conflict with other users. The same program is installed on a computer in GBSF 4212 and can be used there. The tif file created by the scanner can also be transferred into other feature extraction programs, but be aware of the input file requirements for these program so you can modify your image post-scanning if necessary. Tools are available to generate properly configured design files that can be integrated with the scanned image.
You must have a Genome Center account (which you can create here) to cover training and scanning charges. Recharge rates for scanning and analysis will depend on whether users or facility personnel perform the scanning. For user-performed scans, rates are based on training fees (assessed annually) and a flat per slide rate. A sign up sheet is next to the instrument to register your scans. For more information regarding equipment use, please consult the "Equipment" link.
To reserve scanner time during normal working hours, please use the on line calendar. 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.
Molecular Devices GenePix 4000B Scanner
The GenePix (or Axon) scanner shares certain features with the Agilent scanner described above: 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). The GenePix Pro application is also installed on the workstation computer in 4212A, so images can be analyzed there as well. This scanner differs from the Agilent scanner in several important respects--it 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 is faster than the Agilent scanner, and 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. Another difference is that scans on the 4000B are generated by lasers scanning from the top of the slide, so there is more flexibility in the types of slides that can be used in this instrument (for example, the black Combimatrix slides can't be scanned in the Agilent scanner but can in the 4000B).
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" from plans on the internet (seen to the right). 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.
Once you have been trained on the instrument, please use the on-line calendar to reserve time during normal working hours at least 24 hours ahead of time to ensure availability. 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. For more information regarding equipment use, please consult the "Equipment" link.
A condensed instruction sheet summarizing the scanning protocol is available: we recommend printing this out and bringing it to your training. To delete a scheduled calendar date, contact Charlie or Heather.