M8K Chip

• Catalog#: AC-0008
• Size: 2 slides

Description: 
M8K-chip is a median-density glass-based slide which contains 8640 40-mer oligonucleotides representing unique sequences of ~8000 experimentally validated promoter regions in the mouse genome. Among these 8640 oligonucleotides, ~6000 correspond to single gene promoter, while the remaining target several alternative promoters of individual genes. The detail information on genes, promoter annotation and probe design is documented in the files of M8K oligo design .pdf and M8K.gal, which are included in this CD. In addition, 768 tiling array probes are printed on the same slide to provide internal controls for data analysis. These probes on the array are identified as TL_ numbers instead of NM_ numbers under the Nucleotide Accession column in the M8K.gal file. A panel of yeast and bacteria plasmid sequences is also included as internal negative controls. These genes are identified using NC_ numbers.

Array Location: 
The oligos are spotted on the top end of the glass slide, opposite from the label. The array occupies an area of 17 x 35mm, beginning ~7mm from the top edge of the slide, with left and right margins of ~3.5mm each. The array consists of 24 blocks, each of which contains 18 rows and 20 columns. The blocks are organized from top to bottom and right to left (see fig. 1) 

Package Size: 
Two slides/package 

Reconstitution and Storage: 
Room temperature for up to 3 months. If not used immediately after opening, store under vacuum condition. 

Application of the Array: 
? Interactions between transcription factors and promoter DNA ? DNA methylation ? DNA modifications ? DNA repairing 

Limitations and Warranty: 
The product is intended for research use only. No products from ASB are to be construed as a recommendation for use in violation of any patent. Our warranty is limited to the price paid for the product. ASB is not liable for any property damage, personal injury, time or effort or economic loss caused by our products. 

Caution: 
This product is not licensed or approved for administration to humans or to animals. Standard Laboratory Practices should be followed when handling this material. 

Quality Control: 
For each lot of chips our QC procedure includes four steps: 1) visual inspection: Each of the slides is subject to a visual-light scan to identify any missed or inadequately deposited samples. 2) Cy3N35 primer hybridization: Representative slides are hybridized with dye-labeled random primers to examine the morphology of features and background of slides. 3) Position control: Representative slides are randomly selected for hybridization with genomic DNA and position control probes to ensure the feature positions. 4) Data analysis: Data from all three QC steps are collected and analyzed. An image of the array, intensity data, and an overall intensity histogram from each representative slide are recorded in the QC report. Slides which passed our 4 steps QC procedure are then carefully packed for shipment. Figure 1 shows the entire slide image and Figure 2 represents an enlarged portion of a slide to show detailed morphology of the spots. Missing or bad spots are controlled less than 2% to pass our QC. 

Assay Procedure and related product: 
The Aviva ChIP-DSL system consists of ChIP-DSL microarray and the assay kit package. The assay kit package can be purchased separately (Cat. No. AK-0508). A detailed assay procedure protocol is included in the kit. The ChIP-DSL assay system includes three kits: ChIP kit, DSL kit and Hybridization kit. Among these kits, DSL kit is the essential component, which provides the oligo pool necessary to use the promoter microarrays. ChIP and Hybridization kits are optimized for ChIP-DSL technology. All kits provide sufficient reagents for at least 10 reactions and have been carefully tested. As an alternative to the complete ChIP-DSL system, the three kits and some key components are also available individually to allow maximum user flexibility. In addition, Aviva Systems Biology provides other products and services for target gene validations. These include customer design and synthesis of validation primers, full-length cDNA cloning for human transcription factors, etc. For more information about our full list of products, please visit our web at www.avivasysbio.com 

Suggested starting concentrations are provided. Optimal dilutions should be determined by end-user. Differences in calculated versus apparent molecular weight may be due to post-translational modifications or protein hydrophobicity. For research use only not for diagnostic, human, or veterinary use.

Fig. 1

The whole image of M8K array. The labels indicate the block number.

Fig. 2

Spot morphology of M8K chip. Position probes are shown as red.