Custom_Human_Microarrays

Services - Custom H25K

Custom Long Oligo Human Microarrays
Getting the exact human biomarker microarray of interest is as easy as selecting specific genes from our fully annotated set of 25,509 human gene target sequences. Each oligonucleotide has been designed for optimal microarray use. All oligos have been well tested in the FDA’s phase I MAQC study and each custom made microarray is guaranteed. These custom microarrays are highly affordable and can be used for a wide variety of applications such as validating microarray data from other platforms. Oligos will be custom synthesized, prepared for microarray manufacturing and microarrays will be manufactured in class 100 clean rooms. Oligos are archived at ArrayIt® for future microarray manufacturing runs or sent back to the end user by request. Practice microarrays are included free of charge with each order to dial in processing conditions.

Ordering and Microarray Format Information

Step 1. Download our complete human genome gene list (hint; right click on link and save as). Edit the list to select the genes that you desire to have on your microarray (including controls). Every gene in the human genome is available and already designed for optimal use on microarrays. Your own sequence designs can be added to the microarray and we do provide oligo design services. Control sequences from mouse, plant and other sources can be added. Control oligos supplied by Ambion and Stratagene can be considered good choices. Predesigned controls can be selected from the gene list by using the search term “control” to find them in the downloaded tab delimited text file.

Step 2. Decide on the number of microarrays desired, the format for the microarrays and the number of technical replicates. Microarrays can be printed in a multiplexed format to accommodate various hybridization and washing systems. Both manual systems made by ArrayIt® and automated systems such as those provided by Genomic Solutions, BioTray, Miltenyi, BioMicro, Advalytics, Ventana and Tecan can all be accommodated. Test microarrays for optimizing protocols are provided free since any new microarray requires some testing, validation and optimization prior to running real experimental sample sets.

Step 3. E-mail the details above to us at services@arrayit.com for a quotation. At the quotation step, your custom microarray will be assigned a project number to track your order. Turn around time depends on the size of the project, but most projects are completed in 2-3 weeks.

To find information on our H25K, Complete Human Genome microarray click here.

Oligonucleotide Design Information

The oligonucleotide designs contain SENSE strand information, and therefore nucleic acid probe mixtures reacted with the custom microarray must contain ANTI-SENSE molecules to hybridize to the SENSE oligonucleotides present on the microarray. The designs contain no pseudogenes, redundant or chimeric sequences. The long oligonucleotide sequences present are annotated across the AceView, Entrez, RefSeq, UniGene, KnownID, and GenBank databases. Each oligonucleotide also includes a unique MicroarrayID, which identifies the sequence. Gene descriptions are based on the best descriptions available from GenBank and AceView. A complete description of the annotation information is provided in Table 1 below.

1. Select 60-mers from any organism of choice
2. Oligos should also include the appropriate controls (i.e. different organism).
3. All oligos should map to the 3' end of cDNAs
4. All oligos should map to within 1,000 nt of the 3' cDNA end
5. All oligos should correspond to the coding strand (protein strand)
6. Avoid sequence repeats and stretches of polyA, G, C and T
7. Avoid extremes of Tms (mixed sequence composition best)
8. Run against the database to avoid cross-reactivity (<70% sequence identity).

Microarray Compatibility Technical Information

These custom microarrays are compatible with all slide based microarray scanners, microarray labeling and hybridization systems. ArrayIt© can recommend amplification and labeling kits known to work well, or your own kits can be used. If you are concerned about compatibility, e-mail us your questions at services@arrayit.com Practice microarrays are provided free of charge to assist in dialing in processing and hybridization protocols.

H25K Annotation

Description

MicroarrayID

Microarray specific identifier for H25K. Use the last 5 digits to order H25K oligonucleotide sequences (see Ordering Information)

GeneName

AceView name from the Nov 04 build. See the website below (http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/) for more information

S

Some AceView genes have more than one expressed region, and different expressed regions are distinguished using S numbers. The gene name and the S number define a unique expressed region

GeneID

Identifier from Entrez Gene, NCBI

RefSeqID

Identifier from the RefSeq (Reference Sequence) database, NCBI

UniGeneID

Identifier from the UniGene database, NCBI

KnownID

Gene name from Known Gene table, UCSC Genome Browser, May 2004 build

GenBank

Best GenBank record, NCBI

Description

Best description of the gene from GenBank and/or AceView, NCBI

Table 1. Provided are descriptions of the H25K annotation information from which to choose your genes. Download the list here, edit for the genes you wish to have on our microarray and email in the list for a quotation to arrayit@arrayit.com.