Agilent Gene Expression Microarray Analysis



  • – All works from sample QC to data analysis are carried out in-house.
  • – Well equipped with genuine devices and an ozone-free environment to obtain high-quality data.
  • – Shared plan, convenient for small-scale experiments, is available for Human / Mouse microarray.


Service Contents

Your samples are subject to quality check using NanoDrop and Bioanalyzer (or TapeStation) in order to obtain the best results. Basic charge covers up to twice of sample QC.
Entire microarray experiments such as fluorescent dye labeling of nucleic acid samples, hybridization to array slides and raw data acquisition are acceptable.
Data is subject to normalization to extract differentially expressed genes by comparison between samples or groups. The normalization method and threshold in the analysis will be adjusted according to each experimental data.
Please refer to the Agilent Technologies web site for details about Agilent microarray;
For product information, click here.
For gene list, click here.


Analysis Plan

For Human (SurePrint G3 Human GE 8x60K Ver.3.0) or Mouse (SurePrint G3 Mouse GE 8x60K Ver. 2.0) analysis, please select from the following two analysis plans.

Analysis is performed on per-slide. Delivery date will be determined soon after the sample passes the QC and the microarray to be used arrives, so the analysis results are delivered quickly. In case of using made-to-order arrays, it takes time to manufacture the slides, so please contact us at the earliest.
8 arrays on one slide will be shared with some customers for analysis, so even a small number of samples can be analyzed at a reasonable price. It is required to wait for starting the analysis until the required number of samples have been collected.



Item Contents Format Details
Analysis Report
Recording Media
– CD-R
Microarray raw data
txt Signal data generated from microarray system (digitalization software)
Microarray scanned image
tif, bmp Images obtained by scanner, from which raw data is obtained
Signal table
xlsx Signal value(Raw, Normalized, Baseline transformed), LogFC and list of differentially expressed genes in sample comparison
Visual summary
html Box plot, Scatter plot, Correlation, Principal component analysis, Clustering, Sample information
Reference guide
pdf Reference guide for raw data and analyzed data
pdf Protocol for microarray experiments, condition value of the works from experiments to data analysis
Sample QC report
pdf Data of sample quality control
Analysis Report
pdf PDF data of the analysis report document
  • * Our data storing period is 6 months after delivery. Please keep the data in a safe place as we may ask you to provide the data in case of inquiry or additional analysis request after the storing period has been expired.


Price and Domestic Lead-Time

Service Price Domestic Lead-time*2
Microarray Analysis*1
1 color
(Shared plan)*3
Open price 3 weeks (up to 3 months) after
meeting the below requirements;
– Sample QC passed
– Number of samples required for
the share plan
2 colors
(Shared plan)*3
1 color
(Normal Plan)
3 weeks after meeting the below
– Analysis slide delivered
– Sample QC passed
2 colors
(Normal Plan)
Scanning & Digitalization approx. 1 week
Option for Scanning
& Digitalization
Normalization approx. 1 week
Sample Comparison
includes normalization
  • *1 Sample QC fee (twice incl. sample reshipment) is included in the price.
  • *2 The lead-time may vary according to each order specifications such as the number of analyses.
  • *3 Shared plan is only available for analyses with “SurePrint G3 Human 8x60K v3” or “SurePrint G3 Mouse 8x60K v2“.


Ordering (Domestic)

Order Flow

Step 01
Please inquire from the inquiry form.
Step 02
After confirming the order requirement, we will provide a quotation.
Step 03
Please fill the order sheet for your required analysis and send it to by E-mail.

Step 04
Sample shipment
Please ship your sample to deliver to us during week days.
For details on sample shipping, please see “How to ship your sample“.


Sample Requirements

Sample Type Required Amount Purity and Conditions
Total RNA*1 Total amount:500ng or more*2
Concentration:50ng/µL or more
Volume: 10uL or more
OD260/OD280: 1.8~2.1*3
OD260/OD230: 2.0 or more*3
Please dilute in Nuclease Free water.*4
For RNA extraction service order, click here.
  • *1 HSS recommends RNA extraction using RNeasy Mini Kit (QIAGEN) and DNase treatment using RNase-Free DNase Set (QIAGEN).
  • *2 Required sample amount may differ depend on the array format.
  • *3 For samples extracted by spin-column method or of low concentration, OD ratio may not be taken into consideration.
  • *4 DEPC water may inhibit reactions. Please make sure to dissolve RNA to Nuclease Free water.
For details about sample quality conditions, please click the below link.
 How to check
your sample quality


How to ship your sample

RNA sample (for gene expression array analysis service)
To prevent a sample tube from breakage, please put it in another container such as 50mL tube or tube box and pack it together with a printed order sheet and approx. 5kg of dry ice to dispatch under refrigerated or frozen state.

Slide glass (for scanning and digitalization service)
Please use a slide case, wrap it in aluminum foil to block the light, protect it with cushioning material to prevent it from breakage, and pack it with a printed order sheet to dispatch at room temperature (no refrigeration or dry ice required).

 Please send your order form to: 
Attn. Microarray Analysis Section
Analysis Team
Hokkaido System Science Co., Ltd.
2-1, Shinkawa Nishi 2-1, Kita-ku, Sapporo
001-0932, Japan
Tel: +81-11-768-5903
  • * For any sample/slide glass shipping, please let us know the below information by e-mail.
    1. delivery schedule 2. courier 3. tracking number.
  • * Please make sure that your package will be delivered to us on working days.
  • * Remnants of samples will be stored for three months for RNA samples and one week for slide glasses, then be discarded.If sample return is required, please describe so on your order sheet at the order placement.
  • * Please note that samples are returned free of shipping charge only when they are returned with data delivery.



  • – Description and scope of the service are subject to changes without notice.
  • – Cancellation of an order will be rejected after production start. If cancellation is due to force majeure, the client will be asked to pay the service up to the cancellation point.
  • – Samples are limited to the P1 level defined in “the Law concerning the Conservation and Sustainable Use of Biological Diversity through Regulations on the Use of Living Modified Organisms” (Cartagena Protocol) issued by Ministry of Education, Culture, Sports, Science and Technology.
  • – Infective samples such as HCV or HIV are not acceptable. In case of using human clinical sample, please confirm if the informed consent is obtained.
  • – The result of this custom analysis service should be used for the purpose of investigation.The result should not be used for purposes such as production/quality control of a medical product or food, diagnosis, etc.
  • – HSS will not be responsible for losses a client may incur as a result of the custom analysis service output.
  • – HSS will not be responsible for troubles related to industrial property rights or safety whose origin is in the sample submitted by a client or the methods used.


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