Reagents - Microarray Labeling - HighSeq™ Whole Genome Fluorescent DNA Labeling Kits for Human, Plant and Animal Genomic Microarray Analysis

Arrayit HighSeq™ Whole Genome Fluorescent DNA Labeling Kits provide the market’s most rapid and accurate solutions for genome-wide fluorescence labeling. HighSeq™ kits provide high-quality single color and dual color fluorescent probes directly from genomic DNA using direct fluorescence labeling and random primers for simplicity, precision and ease-of-use. HighSeq™ probe mixtures can be used for genome-wide association studies (GWAS), single nucleotide polymorphism (SNP) analysis, microbial and viral detection, comparative genomic hybridization (CGH) and all other applications requiring high quality fluorescent probes for research, genomics, pharmaceuticals and molecular.

Table of Contents

• Introduction
• Product Description
• Kit Contents
• HighSeq™ Labeling Protocols
• Technical Assistance
• Recommended Equipment
• Ordering Information
• Warranty

Introduction
Congratulations on taking an important step towards improving the economies of scale, quality and speed of your genomics research. This booklet contains a complete set of protocols outlining the steps and principles needed to use HighSeq™ Whole Genome Fluorescent DNA Labeling Kits.

Product Description
Arrayit HighSeq™ Whole Genome Fluorescent DNA Labeling Kits set a new standard in genomic research by providing high-efficiency genomic sequence (“HighSeq”) labeling in rapid and ease-to-use methods. HighSeq™ customers will appreciate the following product features:

• Whole genome labeling kits
• Fluorescent green 540 nm, red 640 nm and dual-color green 540 nm and red 640 nm labeling
• Complete and uniform labeling of the human genome
• Ideal for labeling genomic DNA from plants, animals, fungi, bacteria and viruses
• 1.0 µg of total genomic DNA required
• 2.0-4.0 fluorescent probe material produced from 1.0 µg of total genomic DNA
• Rapid 4 hour labeling and purification time
• Easy to use 10-step labeling methods
• Strong signal intensity and low fluorescence background
• Supports all microarray applications
• Enhances single nucleotide polymorphism (SNP) detection
• Enhances comparative genomic hybridization (CGH) assays
• Enhances genome-wide association studies (GWAS)
• Labeling kits stable for 6 months at -20°C
• Fluorescent probes stable one year at -70°C
• Support microarrays manufactured by Arrayit and other suppliers
• Support scanners manufactured by Arrayit InnoScan® and other suppliers
• Set a new standard for whole genome labeling

HighSeq™ Whole Genome DNA Labeling Kit Contents and Protocols
The following HighSeq™ protocols produce high-quality, purified single- and dual-color fluorescent probes from total genomic DNA as the starting material.

HighSeq™ Whole Genome Fluorescent DNA Green 540 nm Labeling Kits

Kit Contents, Green 540 nm, 24 reactions

• 2.5X Reaction buffer, 250 μl
• Random primer mix, 125 μl
• Green 540 nm dNTP mix, 125 μl
• Enzyme mix, 25 μl
• Reaction stop solution, 70 μl
• Nuclease-free water, 1 ml

Store in laboratory (non frost-free) freezer at -20°C

HighSeq™ Whole Genome Labeling Protocol Green 540 nm

1. To a PCR tube, add 4 µl DNA (1.0 µg), 10 μl of 2.5X Reaction buffer and 5 μl of Random primer mix for a total volume of 19 μl. Mix gently and spin briefly.
2. Place the tube in a thermal cycler with a heated lid incubated at 99°C for 10 min to denature the DNA, then cool to 4°C and incubate for 5 min to anneal the random primers.
3. Spin the tube briefly, and add 5 μl of Green 540 dNTP mix and mix gently.
4. Add 1 μl of Enzyme mix and mix gently for a total reaction volume of 25 µl.
5. Spin the tube briefly and incubate in a thermal cycler with a heated lid for 4 hours at 37°C to label the genomic DNA.
6. After the 4 hour labeling step, spin the tube briefly.
7. Add 2.5 µl Reaction stop solution to stop the labeling reaction.
8. Add 72.5 µl of Nuclease-free water to each 27.5 µl labeled sample and proceed to purification.

Arrayit HighSeq™ Whole Genome Fluorescent DNA Green 540 nm Labeling Kits will yield 2.0-4.0 µg of fluorescent DNA with 100 pmoles of incorporated Green 540 dye from 1.0 µg of genomic DNA startiing material.

HighSeq™ Whole Genome Fluorescent DNA Red 640 nm Labeling Kits

Kit Contents, Red 640 nm, 24 reactions

• 2.5X Reaction buffer, 250 μl
• Random primer mix, 125 μl
• Red 640 nm dNTP mix, 125 μl
• Enzyme mix, 25 μl
• Reaction stop solution, 70 μl
• Nuclease-free water, 1 ml

Store in laboratory (non frost-free) freezer at -20°C

HighSeq™ Whole Genome Labeling Protocol Red 640 nm

1. To a PCR tube, add 4 µl DNA (1.0 µg), 10 μl of 2.5X Reaction buffer and 5 μl of Random primer mix for a total volume of 19 μl. Mix gently and spin briefly.
2. Place the tube in a thermal cycler with a heated lid incubated at 99°C for 10 min to denature the DNA, then cool to 4°C and incubate for 5 min to anneal the random primers.
3. Spin the tube briefly, and add 5 μl of Red 640 dNTP mix and mix gently.
4. Add 1 μl of Enzyme mix and mix gently for a total reaction volume of 25 µl.
5. Spin the tube briefly and incubate in a thermal cycler with a heated lid for 4 hours at 37°C to label the genomic DNA.
6. After the 4 hour labeling step, spin the tube briefly.
7. Add 2.5 µl Reaction stop solution to stop the labeling reaction.
8. Add 72.5 µl of Nuclease-free water to each 27.5 µl labeled sample and proceed to purification.

Arrayit HighSeq™ Whole Genome Fluorescent DNA Red 640 nm Labeling Kits will yield 2.0-4.0 µg of fluorescent DNA with 100 pmoles of incorporated Red 640 dye from 1.0 µg of genomic DNA startiing material.

HighSeq™ Whole Genome Fluorescent DNA Green 540 nm and Red 640 nm Labeling Kits

Kit Contents, Greeen 540 nm and Red 640 nm, 2 x 12 reactions

• 2.5X Reaction buffer, 250 μl
• Random primer mix, 125 μl
• Green 540 nm dNTP mix, 65 μl
• Red 640 nm dNTP mix, 65 μl
• Enzyme mix, 25 μl
• Reaction stop solution, 70 μl
• Nuclease-free water, 1 ml

Store in laboratory (non frost-free) freezer at -20°C

HighSeq™ Whole Genome Labeling Protocol Green 540 nm and  Red 640 nm

1. To a PCR tube, add 4 µl DNA (1.0 µg), 10 μl of 2.5X Reaction buffer and 5 μl of Random primer mix for a total volume of 19 μl. Mix gently and spin briefly.
2. Place the tube in a thermal cycler with a heated lid incubated at 99°C for 10 min to denature the DNA, then cool to 4°C and incubate for 5 min to anneal the random primers.
3. Spin the tube briefly, and add 5 μl of Green 540 dNTP mix or 5 μl of Red 640 dNTP mix and mix gently.
4. Add 1 μl of Enzyme mix and mix gently for a total reaction volume of 25 µl.
5. Spin the tube briefly and incubate in a thermal cycler with a heated lid for 4 hours at 37°C to label the genomic DNA.
6. After the 4 hour labeling step, spin the tube briefly.
7. Add 2.5 µl Reaction stop solution to stop the labeling reaction.
8. Add 72.5 µl of Nuclease-free water to each 27.5 µl labeled sample and proceed to purification.

Arrayit HighSeq™ Whole Genome Fluorescent DNA Green 540 nm and Red 640 nm Labeling Kits will yield 2.0-4.0 µg of fluorescent DNA with 100 pmoles of incorporated Green 540 dye or Red 640 dye from 1.0 µg of genomic DNA startiing material.

Figure 1. Single nucleotide polymorphism (SNP) microarray image containing 60,000 SNPs hybridized with 2.0 µg of Arrayit HighSeq™ Green 540 nm probe produced from 1.0 µg of plant total genomic DNA. The SNP microarray was scanned with an Arrayit InnoScan® 710AL Microarray Scanner set at 3 µm scan resolution, laser power low and 30% photomultiplier tube (PMT). The 16-bit TIFF data were converted to a JPEG image for rapid loading of the HighSeq™ web page. Click here to download the 56 MB TIFF.