Custom Microarray Printing Services, eChips

Microarray Services - eChips Peptide and Oligonucleotide Microarrays Manufactured to Customer Specifications for Basic Research, Life Sciences, Microarray Testing and Agriculture

Arrayit eChips Microarray Services provide unprecedented access to oligonucleotide and peptide microarray content. By uniting the power of microarray technology with the universality of sequence databases, Arrayit makes microarrays affordable, versatile and easy to use. Every microarray is manufactured using our contact printing technology, advanced robotics, surfaces and coupling chemistries to provide premium microarray quality. Our adherence to minimizing particulates, ribonucleases and other contaminants improves microarray data quality. Arrayit eChips allow customers to mine existing databases for sequences of interest and send them by electronic mail for printing. Synthesized oligonucleotides and peptides are printed on optically smooth glass slides, allowing researchers to create a nearly infinite variety of microarrays for basic research, clinical, pharmaceutical and agricultural applications. Because the customer performs all of the steps downstream of manufacturing, the data remain completely confidential. Imagine any nucleic acid or peptide molecule, from any organism, for any application on a pristine surface and you are beginning to understand the breadth and depth of our Custom Microarray Services. Arrayit eChips set a new standard in custom microarray services.

Table of Contents

• Introduction
• Quality Control and Use
• Description of Services
• Short Protocols
• Complete Protocols
• Tips for Design and Use
• Product Contents
• Equipment Requirements
• Technical Support
• Scientific Publications
• Ordering Information
• Storage Conditions
• Warranty

Introduction
Congratulations on taking a big step towards improving the affordability, quality and speed of your genomics, biomedical, pharmaceutical and agricultural research. This booklet contains all the information required to take full advantage of Arrayit eChips microarray services.

Quality Control and Use
Arrayit takes every measure to assure the quality of our eChips microarray services. The finest microarray technology was used to develop these services. Rigorous quality control monitoring on a slide-by-slide basis guarantees that each microarray slide conforms to the highest industry standards.

Description of Services
Arrayit eChips microarray services can provide a virtually unlimited variety of microarrays to customers at an affordable price. All of our microarrays are manufactured using advanced robotics with filtered air and humidity control. These advanced manufacturing methods provide a custom microarray manufacturing environment that affords consistent high quality. Users will appreciate the following product features:

• Pristine, optically smooth glass printing substrate slides
• Proprietary, covalent coupling chemistries that are stable to 100°C
• Substrate slides (1 x 25 x 76 mm) fit all commercial microarray scanners
• Substrate corner chamfer enables unambiguous slide orientation
• Barcoding allows automated slide identification
• Any sequence, any organism, any application
• Microarrays of DNA, RNA and peptides
• Utilize a wide range of parallel analysis applications
• Examine both hybridization and protein interactions
• Advanced robotics sets a new standard for microarray printing
• Robotics with micron positional accuracy
• Duplicate printing assures high data precision and low CVs
• Low reaction volumes (2-30 µl) speed kinetics and maximize signals
• Arrayit's microarray printing technology assures high microarray quality
• Total confidentiality of all results
• Develop new assays, publish, discover and patent results
• Electronic services leverage oligo and peptide sequence databases
• Reasonable turnaround time of 1-2 weeks (larger orders for oligo design, synthesis and arraying may take longer)

Short Protocols
1. Contact Arrayit Corporation with your project information to obtain a quote.
2. Email ID numbers or sequences by email to arrayit@arrayit.com as Excel or tab delimited text file. 
3. Place order based on quote, wait 1-2 weeks depending on the details of your order.
4. Obtain eChips by UPS shipping.
 

Table 1. Synthetic sequences for eChips.

Complete Protocols
1. Contact Arrayit with your project information to obtain a quote. Our eChip services are divided into three components: oligonucleotide or peptide design, oligonucleotide or peptide synthesis, and custom microarray printing. Contact arrayit@arrayit.com with your project information so that we can provide you with a quote. Our staff of highly trained scientists and engineers can provide design, content and application assistance if you have any questions. The cost per microarray depends primarily on the number of microarrays ordered and the number of elements printed. There are additional charges for oligonucleotide and peptide design and synthesis.

2. Send a purchase order referencing your quote number to arrayit@arrayit.com.

3. Send sequences by electronic mail as Excel or tab delimited text file. Send the Excel spreadsheet or tab delimited text file as an attachment to an email that identifies the order and has complete contact information. Please remember that due to a high volume of orders, all electronic mail communications must contain complete contact information including name, affiliation, telephone number and FAX number. Failure to provide these details may delay your order. Your oligo sequences or genomic information for oligo design can also be sent to us by overnight mail in an Excel spreadsheet or tab delimited file format on a thumb drive. Please include a letter or email that references your quote number and has complete contact information.

4. Wait 5-10 business days depending on details of your order. Once your order is placed, we will provide a more exact timeline. The time to process orders depends on the volume of orders in the queue and on the size of your order. Arrayit will make every attempt to process your order as quickly as possible.

5. Obtain eChips shipped directly to you by Express Mail or by the shipping method that you specify. All eChips will arrive complete with barcodes and corner chamfer. The barcode contains an identifying number that is unique to each slide in your order. The corner chamfer is provided to allow the user to determine easily which side of the substrate contains the printed microarray and defines the top of the slide. The printed microarray is located on the same side of the substrate as the barcode. The corner chamfer should appear in the upper right corner if the barcode is at the bottom of the slide. You will also receive a content file that shows the location of each printed target sequence on the microarray slide.

6. Process the eChips to remove unbound target sequences. Processing protocols vary according to the slide used and the target sequences. Detailed protocols are available electronically on the corresponding product page.

7. Label and purify probes. There are a myriad of enzymatic and synthetic methods used to label probes derived from RNA, oligonucleotides and proteins. Samples can be labeled using direct labeling whereby fluorescent tags are incorporated into the molecules in the sample. Alternatively, samples can be labeled by indirect means prior to hybridization such that epitopes such as biotin or amino allyl are incorporated into the sample, then the molecules are made fluorescent using fluorescently labeled streptavidin or reactive fluorescent dyes. Post hybridization detection can also be achieved using secondary labeling molecules such as dendrimers (Genisphere, Inc) or antibody-containing fluorescent molecules. Samples can be nucleic acids, proteins or other types of molecules. Users should select the labeling procedure that works best for their application. Labeling procedures and tips are available under Arrayit microarray slides, hybridization cassettes, amplification and labeling, and microarray tools.  Our specialists are happy to provide advice and feedback on probe labeling and purification.

8. Perform a hybridization or biochemical reaction. Probes should be reacted with the processed eChips to allow the molecules to interact with their cognate targets on the chip. This step is best accomplished by reacting the sample to the processed microarray underneath a cover slip positioned over the microarray. The cover slip should extend ~2 mm beyond the edges of the microarray on all sides to ensure that the sample covers all the spots. Sample volumes are typically ~2.0 µl per cm², such that total reaction volumes of 3.0 µl and 20 µl work well for the 12 mm x 12 mm and 22 mm x 40 mm cover slips, respectively. The corner chamfer should be at the upper right side of the slide relative to the user when the microarray is held vertically (with the barcode at the bottom). Buffers suitable for nucleic acid hybridizations include 5X SSC + 0.2% SDS, 1X UniHyb™ and 1X HybIt®.  Other types of buffers such as those containing SSC, SSPE, SDS, and TritonX-100 have also been used successfully. Sample is best added to the microarray by placing the drop at the edge of the cover slip and allowing the sample to spread out between the microarray and the cover slip by capillary action. Once the sample is added, immediately place the microarray slide in an enclosed chamber such as a hybridization cassette and bring the reaction up to temperature as quickly as possible. It is critical to prevent desiccation during the biochemical reactions, as drying is the major source of elevated background fluorescence in microarray experiments. Desiccation is prevented by adding 5-25 µl of buffer to the reaction chamber. Reaction temperatures are typically 37-65°C, though different experiments may require higher or lower reaction temperatures. Reaction times are usually 1-4 hours. Information on hybridization reactions can be obtained under hybridization buffers, microarray slides, and DNA microarray protocols. Our specialists are happy to provide advice and feedback on hybridization, protein, and other types of biochemical reactions involving eChips.

9. Wash eChips to remove unbound probe molecules. Once the eChips are reacted with labeled probe samples, the chips must be washed to remove unbound molecules. Following the biochemical reaction, unbound sample should be washed off the surface. For cDNA hybridizations, the following protocol works well. Remove the microarray from the hybridization cassette and place it in a High-Throughput Wash Station and wash according to the protocols provided with the Microarray Wash Buffers. Wash conditions should be modified for different types of reactions and different applications. Make sure the cover slip falls off within 1 minute after transfer into the wash buffer. Wash buffers pre-heated to 42°C can be used to speed the release of the cover slip from the microarray. Failure to remove the cover slip within 1 minute after transfer to the wash buffer may lead to elevated background fluorescence. There are numerous washing protocols available and details are available under DNA microarray protocols, microarray slides, hybridization buffers, and microarray wash buffers. Google scholar contains thousands of Arrayit publications provide a wealth of information on microarray wash procedures. Spin the slidess dry by centrifugation for 5 seconds in a Microarray High-Speed Centrifuge. Our specialists are happy to provide advice and feedback on eChip washing strategies.

10. Detect the fluorescent signals. Once the eChips are reacted and/or stained, and washed, the fluorescent signals must be detected. Detection is best performed using one of the high-quality commercial instruments available. Commercial systems are available from Arrayit, Agilent, and other vendors. Detection should be performed such that the most intense signals on the microarray produce sub-saturating values. Rare species in the probe mixture can be quantified using instrument settings that maximize detectivity. Adjusting the laser power, PMT gain, capture time and other parameters provide enormous detectivity in microarray assays.

11. Quantify and model the data. Data quantification and mining can be performed using a variety of custom and commercial software packages.

Tips for Design and Use
Table 2. A virtually unlimited number of different eChips are possible. Different eChips allow the user to explore diverse molecular interactions and applications.

Product Contents
eChips are manufactured and packaged in a microarray cleanroom, bar-coded and shipped in a slide box enclosed in sealed anti-static shipping envelope. To open the eChips box, push downward firmly on the top of the box and pull gently upward on the packaging cloth.

Arrayit eChips services are divided into three stages, Oligo Design, Oligo synthesis and Custom Microarray Printing.

1. Oligo Design

Oligo Design services are available for an additional fee. Oligo designed is performed using the Arrayit Oligo Design Directive. This Directive ensures that the oligos:

• are mapped to within 1,000 nucleotides of the 3' end of the transcript
• are selected to avoid sequence repeats and long stretches of poly A, G, C and T
• melting temperatures of the oligos are matched within a selected range;
• checked against gene sequence databases to avoid cross-reactivity with related transcripts.

Oligo design services can take 1-2 weeks depending on the number of oligos required. Alternatively, you can design your own oligos using Array Designer Software from Premier Biosoft or a comparable software product.

2. Oligo Synthesis
Arrayit oligos are available in 96- or 384-well formats or you may order your oligos through your own oligo synthesis provider. Oligo synthesis typically requires an additional 1-2 weeks, depending on the number of oligos ordered.

Peptide Synthesis
Arrayit peptides are available in 96- or 384-well formats or you may order your peptides through your own oligo synthesis provider. Peptide synthesis typically requires an additional 1-2 weeks, depending on the number of peptides ordered.

3. Custom Microarray Printing
Total custom microarray printing costs depend on the number of elements printed per microarray and the number of microarrays requested.

Recommended Equipment and Reagents