Affymetrix Microarray Core
Customer Requirements: 
  1. Prepare total RNA samples using Affymetrix’s recommended isolation procedure and provide ~ 5 - 10μg of total RNA at a minimum concentration of ~1μg/μl.  RNA samples must be completely free of ethanol and phenol contamination.  The Core will not be responsible for incomplete reactions due to contamination.

  

  1. Bring Tissue or RNA (samples on dry ice) to RB-1 room 252.

 

  1. When you are notified that data analysis is completed, please be ready to pick up your CD, cRNA, and hyb samples.  Samples will be held at the facility in  (-80) for two months

 

Core Procedures:

 

  1. Run samples on the Bioanalyzer to check RNA quality.  Degraded RNA will not be processed and investigator will be notified immediately.  

 

  1. Perform all quality control procedures at each step.  

 

  1. cRNA target is prepared and hybridized on to chips.  Chips are washed, stained and scanned. 

 

  1. Perform image analysis and generate gene expression profiles.  

 

All data will be available on a CD.  Contact investigator once experiment is completed.

 

PRICING for LA Biomed users:

 

Service Name 

Service Type

Price
 RNA preparation

 Tissues - FastPrep

 Cells

$30 per sample

$20 per sample
 

Bioanalyzer

$80 per plate

Sample Prep

3’ Gene Expression Arrays

         (5 ug)

$800 per sample (chip included)

Whole Transcript Expression

          (100 ng)

$600 per sample (chip included)

Assisted

Microarray

Data Analysis

 Data quality evaluation

 $10 per array

 Data analysis I **

 Genespring

 $40 per hour

 $200 per experiment

* Includes:  Total RNA analysis, cRNA target preparation, fragmentation, hybridization, Data evaluation, Absolute and Comparison Analysis.

 

** Includes:  Data filtering, functional clustering, and additional annotations.

 

Data:
Experimental data will be available on CD.  When you are notified that your data is ready, please be ready to pick up your CD, cRNA and hyb samples

Contact:
Please contact Jennifer Dedes (mailto:Jdedes@labiomed.org) or call ext 8178 for latest pricing and service information.  Prices are subject to change based on chip, reagent, and labor costs.

 

Typical RNA Isolation Protocol:

 

1.     Homogenize tissue samples in ~1 ml of TRIzol reagent per 50-100 mg of tissue using FastPrep.

2.     After homogenization, remove insoluble material from the homogenate by centrifuging at 10,000 RPM for 10 min at 4°C.

3.     Transfer the top layer solution into a new tube and discard pellet

4.     Incubate homogenized samples for 5 min at room temp. To permit complete dissociation of nucleoprotein complexes.

5.     Add 0.250 ml of chloroform per 1 ml of TRIzol.

6.     Cap sample tubes and shake vigorously by hand for 15 sec.
Incubate samples at room temp for 5 min.

7.     Centrifuge samples at 10,000 RPM for 15 min at 4°C

8.     Remove the upper phase and transfer into new tube.

9.     Add 600ul of 100% EtOH to every 1ml of Trizol.

10. Add samples on Qiagen RNeasy spin columns. Follow clean up protocol.

 

Total RNA in the amount of 5 -10ug should be provided at a minimal concentration of 1ug/ul

RNA OD 260/280 ratio should be 2.1 (in TE buffer).

     All RNA provided must be eluted in Depc treated water. 

 

 

Other Pertinent Information:

 

Available Affymetrix Chips