Custom Microarray Printing Services Flex-Chips

Arrayit manufactures custom Flex-Chips microarrays using customer-supplied samples and processes the microarrays (if required) to customer specifications. Total custom microarray printing and processing costs depend on the number of customer samples, the number of elements printed per microarray, the number of microarrays per slide, the number of slides requested and any post-manufacturing proceessing required including hybridization, staining, scanning and data analysis. Listed is an average per slide price for manufacturing only (processing can be performed at an additional fee). Please contact our technical staff by email (arrayit@arrayit.com) for exact pricing and lead times.

Services - Arrayit Flex-Chips Microarray Services Utilize Customer Samples to Print Microarrays Containing Virtually Any Biomolecule

Custom Microarray Services from Arrayit Corporation provide unprecedented access to the microarray revolution at an unbeatable price. Every microarray is manufactured in one of our cleanroom environments, with the most advanced robotics, surfaces and coupling chemistries in the industry.  Our particle- and ribonuclease-free manufacturing environments provide microarrays of dazzling quality. Flex-Chips allow customers to retain confidentiality of their samples by allowing the customers to prepare and send samples of their choice in a 384 well format. Arrayit then prints the customer samples on atomically flat SuperAmine, SuperAldehyde, SuperEpoxy, SuperProtein or another surface. The result is a virtually unlimited variety of microarray biochips for biomedical, pharmaceutical and agricultural research applications. Because the customer prepares the samples, the all results are completely confidential. Imagine any 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 leads the way in custom microarray manufacturing.

Table of Contents

• Introduction
• Quality Control and Use
• Description of Services
• Technical Assistance
• Short Protocols
• Complete Protocols
• Equipment Requirements
• Publications
• Tips for Design and Use
• Product Contents
• 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 Flex Chips.

Quality Control and Use
Arrayit Corporation takes every measure to assure the quality of our Flex Chips.  The finest microarray cleanroom technology was used to develop these products. Rigorous quality control monitoring guarantees that each microarray biochip conforms to the highest industry standards.  Please be aware that certain types and uses of microarrays may be patent protected. Arrayit Corporation does not endorse the improper use of its Custom Microarray Services.  Please consult your intellectual property expert to assure that your particular application is licensed properly.

Description of Services
Flex Chips from Arrayit Corporation provide a virtually unlimited variety of microarray biochips at an affordable price.  All of our microarrays are manufacrured in a custom cleanroom environment, with 0.1 µm filtered air and temperature and humidity control.  This pristine setting provides a custom microarray manufacturing environment that ensures high quality microarrays.  Users will appreciate the following product features:

• Customer provides the samples (up to twenty-five 384 well microplates)
• Pristine, optically flat glass printing substrates
• Proprietary, covalent coupling chemistries that are stable to 100°C
• Substrates (25 x 76 x 0.96 mm) fit all commercial microarray detection systems
• Substrate corner chamfer enables unambiguous slide orientation
• Barcoding allows automated chip identification
• Any sequence, any organism, any application
• Arrays of DNA, RNA and peptides
• Utilize a wide range of parallel analysis applications
• Examine both hybridization and protein interactions
• Cleanroom environment sets a high standard for microarray fabrication
• Robotics with ±10 µm positional accuracy
• Triplicate* spotting assures high data precision and low CVs
• Arrayit's advanced printing technology assures highest microarray quality
• Total confidentiality of all results!
• Develop new assays, publish, discover and patent results
• Complete plating, hybridization, scanning and data analysis services also available

*Replicates spotted depend on the number of samples printed. Larger number of samples may be double spotted or single spotted please inquire for more details.

Reasonable turnaround time of 1-2 weeks (larger orders or complete services work may take longer).

Technical Assistance
Please contact us if you have any comments, suggestions, or if you need technical assistance. By electronic mail: arrayit@arrayit.com (under the subject heading please type "Arrayit technical assistance"). Please remember that we want to hear about your successes!

Short Protocol (Flex-Chips)
1. Please email us at arrayit@arrayit.com with the number of samples, replicates, microarrays and slides requested.
2. Arrayit will send 384-well microplates with foil seals, environmental proof shipping bags and appropriate print buffer.
3. Re-suspend samples in appropriate Arrayit Printing Buffer (see Table 1) and transfer 10 µl per well to the 384 well microplates.
4. Seal 384 well microplates with foil covers (seal every well completely!).
5. Mail sealed microplates back to Arrayit.
6. Receive printed and bar-coded Flex-Chips (2-6 weeks depending on the details of your order).
7. Process the Flex Chips to remove unbound target sequences.
8. Label and purify probes.
9. Perform a hybridization or biochemical reaction.
10. Wash Flex Chips to remove unbound probe molecules.
11. Detect the fluorescent signals.Quantify and model the data.

Table 1. Sample Preparation Guide for Flex-Chips DNA microarrays.

Sample	Volume (per 384-well)	Concentration	Comments
bacterial cells	5-10 µl of sample in 1X MSP
cDNAs	5-10 µl of sample in 1X MSP	0.2-1.0 µg/µl	C6-amino modification
genomic DNA	5-10 µl of sample in 1X MSP	0.2-1.0 µg/µl	C6-amino modification
oligonucleotides	5-10 µl of sample in 1X MSP	30-50 pmoles/µl	C6-amino modification recommended
peptides	5-10 µl of sample in 1X MSP	50 pmoles/µl	Terminal lysine
proteins and protein extracts	5-10 µl of sample in 1X MSP	0.2-1.0 µg/µl	Clarification preferred
mammalian cells	5-10 µl of sample in 1X MSP	105 cells/µl
yeast cells	5-10 µl of sample in 1X MSP	106 cells/µl
bacterial cells	5-10 µl of sample in 1X MSP	107 cells/µl

Complete Protocols (Flex-Chips)
1. The per chip cost is dependent on the number of chips ordered and the number of elements printed. The customer would send a purchase order and down payment for 50% of the order referencing the quote number to arrayit@arrayit.com. Upon receipt of the order and PO number or down payment, Arrayit will send the customer the required number of 384 well plates, foil plate covers, information labels and Arrayit Printing Buffer (buffer choice of the customer is also possible.  The 50% down payment is required for all orders to defray the upfront costs associated with completely custom work.

2. Upon receipt of the plates, re-suspend samples in 2X printing buffer as described in Table 1. Make sure samples are in the appropriate concentration and are re-suspended completely. Samples that are mixed well give superior results in printing. Arrayit cannot be is not responsible for poor printing quality that results from the use of sample buffers other than those made by Arrayit, or poor quality results due to inappropriate concentrations of material.

3. Transfer 10.0 µl per well to provided 96 or 384 well microplates provided by Arrayit. It is recommended to use only these plates.

4. Seal the 96 or 384 well microplates with the foil covers provided such that every well is sealed completely. This is done manually by pressing down on the foil cover over each microplate well. If properly sealed, samples are stable against dehydration for >30 days at room temperature. This allows users to prepare a large number of samples over a period of days or weeks for simultaneous shipping. Arrayit is not responsible for improperly sealed plates. Dehydrated or desiccated samples will be returned to the customer for re-plating. Note that our services team can also prepare the 384-well plates from 96-well plates provided by the customer. If you wish to have us prepare the 384-well plates from your 96-well plates, please indicate this when placing your order.

5. Fill out the information labels provided then freeze plates at -20°C overnight prior to shipping.  All samples should be shipped frozen to prevent sample leakage.

6. Mail sealed and frozen microplates to Arrayit Corporation. Place plates inside a box with dry or wet ice to maintain appropriate temperature and include packing materials (bubbles or peanuts) to minimize agitation.

7. Receive printed and bar-coded Flex-Chips after a period of 2-6 weeks, customer samples will be returned with the printed Flex Chips. Once your plates are received 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 Corporation will make every attempt to process your order as quickly as possible.  Microarrays made from 1 384-well microplate are printed in triplicate with 4 pins at 4.5 mm center-to-center spacing for a total array size of 9 mm x 9 mm. Microarrays printed with 2-25 microplates are printed in triplicate with up to 48 pins at 4.5 mm center-to-center spacing for a total array size of up to 18 mm x 60 mm. Large numbers of samples may require a larger printing area and less than triple spotting. Flex-Chip shipping schedules vary depending on the volume or orders. The shipping time of your Flex Chips will be estimated upon receipt of you samples.

8. Obtain Flex Chips shipped directly to you by Express Mail or by the shipping method that you specify.  All Flex Chips will arrive complete with barcodes and corner chamfer. The barcode contains an identifying number that is unique to each chip 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 substrate.  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 substrate. You will also receive a content file that shows the location of each printed target sequence on the microarray substrate.

9. Process the Flex Chips to remove unbound printed array elements.  Processing protocols vary according to the Substrate used and the target sequences. Detailed protocols are available electronically on the SuperAmine and SuperAldehyde product page.

10. 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 DNA Microarray Protocols, Super Microarray Substrates, Hybridization Products, and Fluorescent Probe Purification.  Scientific Publications provide a wealth of information on labeling and purification procedures. Our specialists are happy to provide advice and feedback on probe labeling and purification.

11. Perform a hybridization or biochemical reaction. Probes should be reacted with the processed Flex Chips 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 substrate 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 UniHybTMand 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 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 2-12 hours.  Information on hybridization reactions can be obtained under Hybridization Products, Super Microarray Substrates, and Microarray Protocols.  Our specialists are happy to provide advice and feedback on hybridization, protein, and other types of biochemical reactions involving Flex Chips.

12. Wash Flex Chips to remove unbound probe molecules. Once the Flex Chips 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 Cassettesand 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 Microarray Protocols, Super MicroarraySubstrates, Hybridization Products, and Microarray Wash Buffers.  Scientific Publications provide a wealth of information on microarray wash procedures. Spin the substrates dry by centrifugation for 10 seconds in a Microarray High-Speed Centrifuge.  Our specialists are happy to provide advice and feedback on Flex Chip washing strategies.

13. Detect the fluorescent signals.  Once the Flex Chips 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 PE (Packard Bioscience), Axon, Applied Precision and several 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.

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

Table 2. Many different types of Flex-Chips are possible. The different types allow the user to explore a vast array of molecular interactions and a multitude of applications. Please note that our services team can provide additional services on microarrays manufactured using your samples including processing, hybridization, wsshing, rinsing, scanning and data analysis.

Sample Type	Interaction	Application
antibodies	antibody-antigen, antibody-RNA, antibody-DNA, antibody-cell surface, antibody-organelle	epitope mapping, evolution, gene expression, genotyping, post-translational analysis, proteomics, structure-function
Bacterial Artificial Chromosomes (BACs)	DNA-DNA, DNA-RNA, DNA-protein	contig assembly, evolution, genotyping, mapping, syntenic analysis
carbohydrates	sugar-protein, sugar-antibody, sugar-receptor	docking, signaling
cell extracts	general biochemical	general biochemical
enzymes	enzyme-substrate, enzyme-effector, enzyme-inhibitor	kinetics, substrate specificity, inhibitor analysis
oligonucleotides (DNA, RNA)	DNA-DNA, DNA-protein, RNA-DNA, RNA-RNA, RNA-protein	evolution, gene expression, genotyping, mapping, SNP detection, structure-function, two hybrid analysis
PCR products	DNA-DNA, DNA-RNA, DNA-protein	evolution, gene expression, genotyping, mapping, SNP detection, two-hybrid analysis
peptides	protein-protein, protein-RNA, antigen-antibody	epitope mapping, evolution, gene expression, genotyping, post-translational analysis, proteomics, structure-function
Phage Artificial Chromosomes (PACs)	DNA-DNA, DNA-RNA, DNA-protein	contig assembly, evolution, genotyping, mapping
proteins	protein-DNA, protein-small molecule, protein-RNA, protein-protein, protein-receptor	drug discovery, epitope mapping, evolution, gene expression, genotyping, post-translational analysis, proteomics, structure-function, two-hybrid analysis
small molecules	small-molecule-protein	binding kinetics, drug discovery
tRNAs, rRNAs, mRNAs	RNA-DNA, RNA-RNA, RNA-protein	evolution, gene expression, genotyping, mapping, SNP detection, structure-function
whole cells	receptor-hormone, receptor-antibody, sugar-antibody	cell typing, secretion studies, clonal analysis
Yeast Artificial Chromosomes (YACs)	DNA-DNA, DNA-RNA, DNA-protein	contig assembly, evolution, genotyping, mapping, syntenic analysis

Product Contents
Flex Chips are manufactured and packaged in a cleanroom environment, bar-coded and shipped in a rigid substrate box enclosed in sealed plastic shipping envelope. To open the Flex Chips box, push downward firmly on the top of the box and pull gently upward on the packaging cloth. Our Flex Chip services provide extraordinary quality Custom Microarray Printing.

Custom Microarray Printing
Total custom microarray printing costs depend on the number of elements printed per microarray and the number of microarrays requested. Additional services including hybridization, processing, staining, scanning, quantification and data analysis can be performed for an additional fee.  Prices per microarray are available by email (arrayit@arrayit.com).

Scientific Publications
Click here and here for recent scientific publications using Arrayit brand microarray products from Arrayit Corporation for custom microarray experimentation.

Recommended Equipment and Reagents
NanoPrint™ 2 Microarrayers
SpotBot® 4 Personal Microarrayers
InnoScan® Microarray Scanners
SpotLight™ 2 Microarray Scanners
Microarray Slides
Microarray Hybridization Cassettes
High Throughput Wash Station
Microarray High-Speed Centrifuge
Protein Printing Buffer
BlockIt Blocking Buffer
Microarray Air Jet
Microarray Cleanroom Wipes
PCR Purification Kits
BlockIt Blocking Buffer
Micro-Total RNA Extraction Kit
MiniAmp mRNA Amplification Kit
Indirect Amino Allyl Fluorescent Labeling Kit
Universal Reference mRNA
Green540 and Red640 Reactive Fluorescent Dyes
Hybridization Buffers