Gene Expression Center NimbleGen Services

The Gene Expression Center provides full service NimbleGen array hybridization and sample   

labeling  for all Roche NimbleGen arrays, as well as cDNA synthesis for Roche NimbleGen

sample submission.

Roche NimbleGen / UW-Madsion Preferred Access Agreement

on-line survey: Here

Tell us about your experience with the Roche NimbleGen / UW-Madison preferred access agreement by October 31, 2008 by participating in 5-10 minute on-line survey.  All current and potiential users of the NimbleGen technology are asked to participate to enable us to better meet and serve your current and future array needs.

** Please note all NimbleGen services and prices listed here are available to University of Wisconsin - Madison researchers only**

Labeling does not include hybridization cost, which may vary depending on array format.

Additional hybridization costs include array mixer hyb chamber, Maui Hyb Station access fee and Axon Scanning fee per slide.  Please contact GEC for costs when experimental format is determined for pricing.

NimbleGen Full Labeling Service:  Researchers should bring their total RNA concentration (>200 ng/ul) , a photo of their samples with a MW std run on an agarose gel, and NimbleGen arrays to the GEC. When you bring over your samples please fill out a sample submission form (pdf) .  All your samples must be legibly labeled with a sample name, date, and P.I. name.  The amount of input RNA needed is dependent on the labeling protocol chosen.

The Center will confirm the quantity and quality of each sample by quanitation on the ND-1000 followed by analysis on the Agilent 2100 BioAnalyzer using a RNA6000 NanoChip. Following all appropriate protocols, your sample will be labeled and hybridized to your arrays. As soon as results are available, the researcher will be contacted via e-mail.  All files generated will be transferred to a PC formatted CD or DVD and given to the researcher. Basic data analysis support is available using Roche NimbleGen's Nimblescan, and DNASTAR's ArrayStar. Samples are processed in the order they are received.

Note: The researcher is responsible for purchasing all arrays. Arrays must be purchased directly from NimbleGen.

cDNA Synthesis Service for sample submission to Roche Nimblegen

$70.00/Sample  ($20.00 less than Roche NimbleGen !!!!)

GEC will verify RNA integrity of each sample by analyzing 400ng of each sample on the Agilent 2100 BioAnalyzer.  If there are any concerns or questions regarding the profile generated for a sample the user will be contacted. Samples that meet Roche NimbleGen QC standards will then be used for template in-put for first stand cDNA synthesis following NimbleGen recommended protocols. The GEC requires 10 ug total RNA in-put for first stand cDNA synthesis for both Eukaryotic and Prokaryotic source RNA. User will receive ready to go ds-cDNA for the Roche NimbleGen Gene Expression Service. Samples are processed in the order received. All material and a copy of the protocol sheet are returned to the user at the time of sample pickup.

RNA submission requirements:

Tubes clearly labeled with PI's name,date, and sample ID

12-15ug total RNA per sample

RNA conc. >  1ug/ul

Sample submission Form (pdf)

Independent Instrumentation Access:

Requires interested parties to contact the GEC to set up an account for instrument scheduling. A training session for all users will be mandated prior to using Center instrumentation.

NimbleGen Training :

Training is available for all NimbleGen array protocols and procedures at no charge. Please contact the Gene Expression Center for additional information, or to schedule a training session.

 Link to UW NimbleGen Contract service pricing

 Roche LightCycler 480

 A Roche LightCycler 480 is available on a fee for use basis.

Note: Users must use Roche LightCycler 480 plates and sealers when running samples on the Roche LightCycler 480. Plates may be purchased from the Roche supply cabinet housed in room 3455 of the GEC. Same day delivery is available on the following list  of products.  Please direct supply cabinet related questions to Beth Nigh at 1-800-845-7355 Ext. 28034, or email her at   beth.nigh@roche.com

Affymetrix Full Labeling Service:  Researchers should bring their total RNA , a photo of their samples with a MW std run on an agarose gel, and GeneChips to the GEC. Please refer to the Guidelines for Sample Submission sheet prior to bringing your total RNA samples to the GEC. When you bring over your samples please fill out a sample drop off sheet  (PDF) , and insure your samples are legibly labeled with a sample name and your P.I.'s name.  The amount of input RNA needed is dependent on the labeling protocol chosen. For new labeling projects the GEC has begun using the Ambion MessageAmp II-Biotin Enhanced kit. The  MessageAmp II kit supports a starting input of 1 ug of total RNA for labeling.  The GEC also supports the Affymetrix GeneChip IVT labeling kit.

The Center will confirm the quantity and quality of each sample by quanitation on the ND-1000 followed by analysis on the Agilent 2100 BioAnalyzer using a RNA6000 NanoChip.   Following all appropriate protocols and procedures for Eukaryotic and Prokaryotic total RNA labeling, the Center will synthesize and fragment biotin labeled cRNA and synthesize cDNA, fragment and biotin end-terminus label cDNA, respectively. If appropriate, the sample will then be hybridized to a Test3 GeneChip.  Test3 arrays are relatively inexpensive and are used as an assessment tool for determining target quality and labeling efficiency.  Test3 array data will be analyzed by following the quality control parameters provided by Affymetrix.  If the data obtained from the Test3 array is satisfactory, the sample will then be hybridized to the expression array.  The images will be analyzed in GeneChip® Command Console, and the data is extracted using Affymetrix Expression Console.  As soon as results are available, the researcher will be contacted via e-mail.  All files generated will be transferred to a PC formatted CD or DVD and given to the researcher. 

  †Please contact Center Director for further information.

  *Researchers are responsible for purchasing all GeneChips®.  Individual Test3 GeneChips® 

    may be purchased from the Center at cost.  Please refer to the current UW-Madison                   Academic  Pricing Sheet for all GeneChip® prices.  To ensure academic pricing, when ordering      from Affymetrix (1-888-362-2447), please refer to UW Contract #27465.

GeneChip Hybridization and Scanning:  Researchers should bring their fragmented biotin labeled cRNA samples and GeneChips to the Center.  Please refer to the Guidelines for Sample Submission sheet prior to bringing your samples to the GEC. When you bring over your samples please fill out a sample drop off form, and insure your samples are legibly labeled with a sample name and your group name. Following all Affymetrix protocols and procedures, the Center will hybridize your samples to the appropriate array, post process the arrays, scan and extract data.  The Center strongly recommends all samples be hybridized to the Affymetrix Test3 array to ensure target quality and labeling efficiency. 

*Researchers are responsible for purchasing all GeneChips®.  Individual Test3 GeneChips® may be purchased from the Center at cost.  Please refer to the current UW-Madison Academic Pricing Sheet for all GeneChip® prices.  To ensure academic pricing, when ordering from Affymetrix     (1-888-362-2447), please refer to UW Contract #27465.

Please note:  No refund for poor results.  If a GeneChip® appears faulty at time of hybridization and/or analysis, a new GeneChip® will be requested from Affymetrix, but Center charges still apply. 

Frequently Asked Affymetrix Questions (PDF)

For additional information about the availability of Affymetrix GeneChips® please see:
www.affymetrix.com/products/products_list.html

UW-Madison Affymetrix Sales Representatives is Mike Anderson   1-800-223-5281 Ext.4256

UW-Madison Field Applications Specialist

The Agilent 2100 BioAnalyzer utilizes "Lab-on-a-Chip" technology to integrate sample preparation, fluid handling, separation, detection, and data analysis.  Agilent Technologies has Lab-on-a-Chip kits available that analyze RNA, DNA, and Proteins.

  Some examples of analysis that can be done are:

         • Quantitative analysis of PCR fragments

         • Restriction fragment sizing

         • Cy 5 labeled cRNA and cDNA

         • RNA analysis up to 6,000 bp

         • DNA analysis from 25 - 12,000 bp

         • Analyze protein samples (cell lysate, column factions, and purified proteins) ranging

            in size from 14 - 200 kDa.

 Affymetrix recommends the 2100 BioAnalyzer for qualifying total (eukaryotic and prokaryotic) or         messenger RNA.

Individuals must be trained satisfactorily by a Center Specialist prior to gaining access to the instrumentation.  There is a one time training fee of $90.00 per hour. The chip cost is not included in the cost of the training.  A maximum of 4 people maybe trained at one time.

Please contact the GEC at gecinfo@biotech.wisc.edu to schedule training.

Price includes the Agilent Chip, all consumables, reagents and RNA ladder.  

If a lab is planning on running a large number of samples it is recommended you purchase your own kit.

Custom microarrays will be printed using a Genomic Solutions GeneMachines OmniGrid arrayer and SMP3 pins from TeleChem International.   Each print project has a 100 slide maximum capacity.  Arrays may be printed on poly-lysine slides provided by the Center or on user supplied slides.   Researchers must supply material to be printed in either a Greiner 96 well V-bottom plate (catalog# T-3016-3) or a Genetix 384 microarray plate (catalog# G-3229-1).  We have determined these plates to be most suitable for printing and therefore will only accept material in these plates.  Both plate types may be purchased from ISC Bioexpress or you may purchase a desired amount from the Center. 

Please contact the Center at (608) 265-3029 to discuss printing preparation and details.  We will explain how the arrayer will print your array, the arrangement of samples to obtain the desired array layout and the desired file format out-put required for various data extraction softwares.

Quotes are available upon request from the Center  Director.

Microarray Scanners

A Molecular Dynamics Axon 4000B Scanner and a PerkinElmer ScanArray Express Scanner are available for scanning of slides at $10 per slide.