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.  Below, one can find a flowchart which can help determine which service will be appropriate for an expression experiment.

NEW PRICING IS EFFECTIVE MAY 1ST, 2009

In addition to detailed descriptions further below, the following illustration shows our new pricing scheme.  The fees for each step are now divided as described below.

*User provides 4-plex mixer

cDNA Synthesis Service for Sample Submission to Roche NimbleGen, Iceland

RNA submission requirements

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

Print-out of Nanodrop concentrations, if available

12-15ug total RNA per sample

RNA conc. > 1ug/ul.  If concentration is needed, a speedvac is available for use at our facility or we charge a $40/hour fee for concentration.

A260/230 > 1.8

A260/280 > 1.8

Completed sample submission form

The RNA integrity of each sample is assessed by analyzing 4-400ng on the Agilent 2100 BioAnalyzer.  If there are any concerns or questions regarding the profile generated for a sample the user will be contacted. Researchers should bring their total RNA concentration (>1 ug/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.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 total RNA. User will receive ready to go ds-cDNA for the Roche NimbleGen Gene Expression Service. Samples are processed in the order received. The user will be notified by email when the samples are ready.  All material, a copy of the protocol sheet, and an electronic copy of both Agilent profiles will be given to the user at the time of sample pickup.

NimbleGen cDNA Synthesis and Labeling Service 

RNA submission requirements

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

Print-out of Nanodrop concentrations, if available

12-15ug total RNA per sample

RNA conc. > 1ug/ul.  If concentration is needed, a speedvac is available for use at our facility or we charge a $40/hour fee for concentration.

A260/230 > 1.8

A260/280 > 1.8

Completed sample submission form

Researchers should bring their total RNA concentration (>1 ug/ul), a photo of their samples with a MW std run on an agarose gel, and NimbleGen arrays to the GEC.  When you bring your samples to the GEC please fill out a sample submission form (pdf).  All your samples must be legibly labeled with a sample name, date, and P.I. name.  As with cDNA synthesis service, 10 ug is needed for input.

The Center will confirm the quantity and quality of each sample by quantification on the ND-1000 followed by analysis on the Agilent 2100 BioAnalyzer using a RNA6000 NanoChip or PicoChip. Following appropriate protocols, your samples will be labeled and hybridized to your arrays.  Data extraction and normalization is performed using Roche NimbleGen's Nimblescan.  Users will be contacted via e-mail that all files are available on the UWBC Facility File Transfer page for download.  In addition, assistance with DNASTAR's ArrayStar is available for simple comparison.  Samples are processed in the order they are received.  Please note there are additional fees related to hybridization, post-processing, and array scanning. Please see below.

Note: The researcher is responsible for purchasing all arrays. Arrays must be purchased directly from NimbleGen.  If using 4-plex arrays, please include the X4 mixers with your array order.  The GEC does not stock these mixers due to their limited shelf life.

Amino Allyl aRNA Synthesis and Fluorophore Coupling

RNA submission requirements

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

Print-out of Nanodrop concentrations, if available

2-5ug total RNA per sample

RNA conc. > 1ug/ul.  If concentration is needed, a speedvac is available for use at our facility or we charge a $40/hour fee for concentration.

A260/230 > 1.8

A260/280 > 1.8

Completed sample submission form

Researchers should bring their total RNA concentration (>100 ng/ul for a 1 ug input), a photo of their samples with a MW std run on an agarose gel, and NimbleGen arrays to the GEC.  When you bring your samples to the GEC please fill out a sample submission form (pdf).  All of your samples must be legibly labeled with a sample name, date, and P.I. name.  For the amino allyl kit, the recommended input range is 1-5 ug.  Smaller quantities are viable, but 2 round amplification may be more appropriate in that case.  Contact the GEC for experimental and pricing details about 2 round amplification.

The Center will confirm the quantity and quality of each sample by quantification on the ND-1000 followed by analysis on the Agilent 2100 BioAnalyzer using a RNA6000 NanoChip or PicoChip. Following appropriate protocols, your samples will be labeled and hybridized to your arrays.  Data extraction and normalization is performed using Roche NimbleGen's Nimblescan.  Users will be contacted via e-mail that all files are available on the UWBC Facility File Transfer page for download.  In addition, assistance with DNASTAR's ArrayStar is available for simple comparison.  Samples are processed in the order they are received.  Please note there are additional fees related to hybridization, post-processing, and array scanning. Please see below.

Note: The researcher is responsible for purchasing all arrays. Arrays must be purchased directly from NimbleGen.  If using 4-plex arrays, please include the X4 mixers with your array order.  The GEC does not stock these mixers due to their limited shelf life.

Hybridization Service

When a researcher uses either the NimbleGen or Amino Allyl labeling service, it is typically intended for a NimbleGen Microarray.  With this service, the researcher's samples will be hybridized to a NimbleGen 1-plex or 4-plex array following NimbleGen's hybridization, washing, and scanning protocol (found here at chapter 4). 

The fees listed here are in addition to any previous fees associated with labeling the samples. 

                      *User provides X4 array mixers

If interested in using 12-plex or HD2 arrays please contact the GEC for further information.

Post Processing and Scanning Service

This service includes the washing, scanning, and data extraction for each hybridized array (protocol here in chapters 4,5, and 6).  As soon as results are available, the files will be transferred to the UWBC Facility File Transfer page for download and the researcher will be notified by email.

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

                   *If handled by one of our technician, the facility charges a 40$/hour fee

Training is available for all NimbleGen array protocols and procedures at the Gene Expression Center.  Please contact the Gene Expression Center for costs involved, additional information, or to schedule a training session.

 Link to UW NimbleGen Contract service pricing