NimbleGen Services

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

The Gene Expression Center is now supporting the full range of NimbleGen Products. These arrays are produced using Maskless Array Synthesis (MAS) technology giving the researcher the highest level of flexibility possible in array design.

NimbleGen products are available for

DNA Methylation Analysis

Whole-Genome & Custom  Fine-tiling Array CGH

ChIP-chip

Gene Expression

Comparative Genome Sequencing

Guidelines for Accessing NimbleGen's Array Services

NimbleGen Product Options

*$230.00 per plex (4x $230.00=$920.00 per slide)

Descriptions:

Service- User sends NimbleGen the target sample for the specific array application method

interested in and NimbleGen will send User data extracted from the hybridized array.

Target sample submission requirements from NimbleGen may vary depending on the

application method service being sought.  NimbleGen will send results within 30 days of the samples passing QC.

Array- User orders the array directly from NimbleGen and NimbleGen will send the array

directly to user. Many arrays are "strippable" for reuse. Expression arrays cannot be stripped and reused.  A list of arrays and the protocol for stripping arrays is available from NimbleGen.

The UW-Madison NimbleGen account manager is JohnTrumbull   1-847-726-0382

Gene Expression Center NimbleGen Services

Synthesis of cDNA from total RNA

$70.00/Sample

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 NimbleGen QC standards will then be used for template in-put for first stand cDNA synthesis following NimbleGen recommended protocols. The GEC requires 12 ug total RNA in-put for first stand cDNA synthesis for both Eukaryotic and Prokaryotic source RNA. User will receive ready to go cDNA for the NimbleGen Gene Expression Service. Estimated turn around time per sample(s) submission is three business days or less. 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 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 reserve a date/time for instrumentation usage. A training session for all users will be mandated prior to using Center instrumentation.

 Additional NimbleGen support services coming soon...

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 group 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 using the GeneChip Operating Software (GCOS) and comparison analysis will be performed according the Researchers request.  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

UW-Madison Field Applications Specialist is John Bon 1-800-223-5281 Ext. 4201

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.  

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

Price includes the Agilent Chip, reagents and RNA ladder.  

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

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.