Guide to Utilization of Microarray System

1. System Utilization Flowchart

1-1. Send an e-mail to the Microarray Center with a hybridization request 
(application for utilization)
Contact the Microarray Center by sending an e-mail stating your request for a microarray 
experiment. The address is  The e-mail must contain the five 
following items.

Assignment Number (if you have it)
Requested time of hybridization
Number of samples
Your e-mail address
Abstract describing purpose of your research

There is a limit to the number of RNA samples you can submit with your application.
Up to twelve RNA samples may be submitted when the one-dye method is used, or six pairs 
if the two-dye method is used.

Please consider allowing for repeated experiments in a single "application" 
(example: experiments conducted twice for each of six different types of samples 
when using the one-dye method). We ask that e-mails with applications for utilization 
of the facilities be sent at least one month prior to the desired testing date.

1-2. When a reply is mailed from the Microarray Center
When you receive an e-mail in reply acknowledging "receipt of application for 
experiment" and accepting the application (including Assignment Number if you had not 
had it before you sent the e-mail stating your request to the Microarray Center), 
please send the following four items (a-d) to the address provided.  
a. Quality-checked RNA (checking procedures described below)
b. Document with attached photograph of the electrophoresis-checked total RNA and 
   description of the RNA in the photograph (single A4-sized page) 
c. Document with photograph of results of reverse transcriptase (RT)-PCR (real-time 
   PCR or other quantitative PCR) (single A4-sized page; format of this document corresponds to that of b.)
d. CDs for return of data (three 640-MB discs)
At the time all of the items a-d are sent, enter the required information for the RMOS 
"Microarray System Utilization Form" page, and submit the form on line. 
A password for the "Microarray System Utilization Form" page will be furnished in the e-mail reply. 
Send RNA using an express parcel delivery service especially for frozen 
materials, such as the "Cool Takkyuubin" service, specifying morning delivery 
(Saturdays and Sundays excluded).  Send the four items (a-d) to the address given below.

Address for Submission:
Dr. Shoshi KIKUCHI  (Microarray Center)
Head of Gene Expression Research Team, 
Department of Molecular Genetics, 
National Institute of Agrobiological Resources
Kannondai 2-1-2
Tsukuba, Ibaraki  305-8602 Japan

<Use an express parcel service specifically for delivery of frozen materials, and specify 
morning delivery.>

1-3. Notification from the Microarray Center with the scheduled time for analysis
After the Center receives the four items (a-d, including RNA samples and the data 
information) as specified in the 1-2, the Center set up a hybridization schedule of the 
RNA samples.  Each applicant is informed of the date that the analysis will be performed, 
and then the microarray analysis is carried out.

1-4. Data from Microarray Center is returned on CDs
After the hybridization experiments are carried out, the results are scanned with an FLA-8000 
scanner (Fujifilm) and quantified with ArrayGauge (Fujifilm), and then is copied to 
the CDs and returned to the applicant(s).

2. Guide to Sending RNA Samples

2-1. Tubes to be used (Eppendorf tubes)
Please submit samples in 1.5-ml Eppendorf tubes (non-screw-cap: the type suitable for 
array experiments).

2-2. Instructions for labeling the Eppendorf tubes
Using an oil-based permanent marker, write the "Tube Label" (see note below) both on 
the top of the cap and on the side of the tube.
If also attaching an adhesive label, be sure to use a label that cannot be removed easily. 
Moreover, write the "Tube Label" information on the Eppendorf tube itself before 
attaching the label. Be sure to carry out the step of writing on the tube itself, as this 
information becomes crucial should the label happen to become separated from the tube.
(Note: The "Tube Label" should contain the sample number and a description identifying 
the sample named in the "Tube Label" heading in the "Microarray System Utilization 
Form" described in 1-2)

2-3. Precautions When Sending Samples
Send samples precipitated in ethanol. Before mailing, securely wrap the capped portion 
of the Eppendorf tubes with plastic film (e.g. Parafilm) or other suitable wrapping to 
prevent leakage of the sample (ethanol leakage).
Attention: If upon arrival at the Microarray Center a tube is found to be leaking or to 
have leaked, either the remaining contents in the tube will be analyzed as is, or the 
sample will not be used at all.  

3. RNA Quality Control Guide
Please be sure to perform all of the three following quality checks on all RNA samples 
for which microarray analysis is desired.  Submitting results of all three methods for 
checking the RNA quality are one of the essential conditions for acceptance of the 
application.  Enter the OD value data of the RNA for which analysis is desired in the 
" Microarray System Utilization Form ," send the application on line, and mail the 
documents ("total RNA QC" and "RT-PCR QC") with the photographs of the 
electrophoresis gels to the Microarray Center.

3-1. Measurement of OD values (to be entered on the "Microarray System 
Utilization Form")
Enter numerical values in the "OD260/280," "RNA Density," "t=," and "m=" columns.
"t=" is the column used for indicating total RNA, and "m=" is the column used for 
indicating mRNA.For example, if using total RNA with the one-dye method, no entry need be made in the 
"m-" column. However, if using mRNA with the one-dye method, or if employing the 
two-dye method (when only mRNA is being handled), enter the necessary information in 
both the "t=" and m=" columns.

3-2. Electrophoretic check of total RNA (Separate Form 1; a single A4-sized sheet)
With all RNA for which array analysis is desired, use 10 g total RNA in agarose gel 
containing 1.1% formaldehyde, perform electrophoresis, and photograph the results. 

After downloading and printing out the form "Total RNA QC" (a separate Form 1; 
a single A4-sized sheet), attach the photograph to the page and mail it in. In this case, 
describe which RNA samples correspond to the RNA in each lane in the photograph 
(i.e., which lane contains each RNA sample entered on the "Microarray System Utilization 
Form") so as to permit us to match each RNA sample shown on the gel with its 
corresponding "Tube Label."

3-3. RT-PCR check (Separate Form 2; a single A4-sized sheet)
Carry out reverse transcriptase PCR using a gene that is commonly expressed in all RNA 
samples, both the RNAs as control and the RNA samples with which you want to 
compare the control RNAs, confirm with electrophoresis, photograph the gel.  Then 

download and print out the form "RT-PCR QC" (Separate Form 2; a single A4-sized 
sheet), attach the photograph, and mail it in.  Before mailing, describe how the RT-PCR 
check was carried out using the gene (e.g. the gene you used; the DNA sequence of the 
gene-specific primers you used, the type of PCR [normal RT-PCR or real-time PCR] you 
used; the PCR condition you used, etc.).    
To discover genes suitable for the RT-PCR quality control check, select a number of 
candidates from among the genes thought to exhibit constant expression (such as 
housekeeping genes) and conduct actual confirmation with RT-PCR.  This procedure 
allows the selection of optimal genes for the purpose.  
However, genes that can be used for the purposes of 3-3 in certain experiments are not 
necessarily suitable for the same purposes in the other experiments, even when for the 
same purposes of 3-3.  

4. Labelling Selection Guide

4-1. Selection of the one-dye or two-dye method
For a single experiment, please select either (not both) the one-dye method or the two-dye 
method (experiments using the two different methods are not conducted simultaneously). 
Refer here for help in selecting the one-dye or two-dye method.
<Related Data>
Differences in Fluorescence Levels for Cy3 and Cy5

4-2. Number of samples
One-dye method:	Up to 12 RNA samples can be submitted for one experiment
Two-dye method:	Up to 6 pairs (12 RNA samples) can be submitted for one experiment.
Please consider allowing for repeated experiments in a single "application" 
(example: experiments conducted twice for each of six different types of samples 
when using the one-dye method). 

4-3. Labeling instructions
Whether selecting the one-dye or two-dye method, use the indirect labeling method. 
The AtlasTM Glass Fluorescent Labeling Kit (Clontech  K1037-1; 
is used for indirect labeling.  For more detailed information on labeling methods (both 
indirect labelling and direct labelling), see here.  For information on the data obtained by 
the Microarray Center using direct labelling and indirect labelling, see here.
<Related Data>
Differences Between Direct Labeling and Indirect Labeling Methods
Differences Between Total RNA and Poly A+RNA

Microarray System Utilization Form
Once you understand the content of this guide to utilization of the system, go to the 
"Microarray System Utilization Form," and enter the necessary information. At the same time 
that you fill out the Utilization Form, send the four following items (1-4) by an 
express parcel service to the address given below.

Address for Submission:
Dr. Shoshi KIKUCHI  (Microarray Center)
Head of Gene Expression Research Team, 
Department of Molecular Genetics, 
National Institute of Agrobiological Resources
Kannondai 2-1-2
Tsukuba, Ibaraki  305-8602 Japan

1. Sample RNA 
2. CDs for return of data (three 640-MB discs)
3. Documentation with attached photograph(s) of the gel electrophoresis for the total 
    RNA for all included RNA samples
4. Documentation with photograph(s) of gel electrophoresis after RT-PCR 

Enter Microarray System Utilization Form