Whole Human Genome H25K/BT

Whole Human Genome (Arrayit Corporation®)

Description

First microarray based on the completely sequenced human genome, H25K/BT microarray is designed and manufactured using a fully annotated set of 25 509 human genes.
This next generation microarray offers a significant advantage over competing products consisting of collections of expressed sequences tags (ESTs) from poorly annotated sequence databases.

H25K/BT is a multi-purpose microarray containing 26 304 long oligonucleotides designed to optimize studies of the entire human genome in a single biochemical reaction. Users can utilize samples from genomic DNA, mRNA and proteins. Many problems can be studied, ranging from karyotyping and gene expression profiling to chromatin structure and protein-DNA interactions.

For gene expression, the revolutionary concept one spot-one gene allows the quantitative measurement of more than 300 000 human transcripts in a single hybridization reaction. Researchers have possibility to buy one or more oligonucleotides spotted on H25K/BT microarray.
The most advanced technologies concerning bioinformatics, oligonucleotide manufacturing, microarray printing and surface chemistry bring unprecedented specificity and sensibility, allowing optimized results analysis and exploitation.

Reference Desigantion
H25K:BT Whole Human Genome (25 509 genes - 26 304 long oligonucleotides)

Specifications

The H25K/BT Human Genome microarray contains 26 304 spots representing 25 509 fully annotated human genes and 795 control sequences from mouse, plant or other sources. Nucleic acid probe must correspond to “Anti-Sense” molecules to hybridize to the “Sense” oligonucleotides present on the chip.

Every oligonucleotide present on the microarray is annotated across the Aceveiw, Entrez, RefSeq, UniGene, KnownID, and Genbank databases. Each oligonucleotide has also a unique identifiant (Microarray ID) and allows customers to purchase sequences by specifying the Microarray ID.

The H25K content is printed as 48 sub-grids of 24 x 24 spots spaced at 185 µm centers. The printed H25K microarray occupies an 18 x 54 mm area on the glass substrate, evenly positioned from left to right and top to bottom between the top of the substrate and the barcode. The 12.5 x 19 mm barcode includes the product name, website, barcode, and unique 6 digit tracking number (e.g. 100012). The barcode is on the chip spotted face.

One major advantage of H25K/BT chip comparing to competing human genome microarrays is that patented contact printing method, allowing visual inspection of every printed chip. The process of individual inspection provides the customer with a level of QA and QC that is not possible with competing products.

Protocol

Protocol for Whole Human Genome H25K-BT
Arrayit Corporation® - BioTray®

1. Prepare a labelled target from a biological sample.

Three fundamental principles should be respected for the sample preparation:
• Samples must be pure.
• Labelling targets must be efficient. Controls can be made before the hybridization step.
• Sample integrity must be high. DNA, RNA and protein molecules must be full length.

2. Test of labelling target mixture.

The step is optional and every user has his own technique.

3. Hybridization : putting the target sample on the chip.

The minimal target volume is about 50 μl. The time of hybridization reaction is depending on the target concentration. It should be between 5 minutes and 6 hours. When hybridization reaction is complete, users should process quickly to the washes.

4. Wash the microarray to remove unbound target.

Three washes are required. Washes can be made in solutions containing PBS or SDS and a detergent decreasing gradient (e.g. Triton). Use of ArrayIt Wash Buffer is advised. Prior to washing, remove the cover slide.
Place the slide in the first wash buffer (e.g. Wash Buffer A) for 5 minutes under agitation. Transfer the slide in the second wash buffer (e.g. Wash Buffer B) for 5 minutes. 5 minutes in the third wash solution (e.g. Wash Buffer C) should be sufficient to complete the wash process.
Wash protocol can be optimized by changing temperature and using different washes buffers.
The use of High Speed microarray Centrifuge is required.

5. Detect signals by scanning.

6. Quantify signals.

7. Perform data analysis.