GSR Microarrays Resequencing Services

Affymetrix CustomSeq arrays provide investigators with the ability to quickly and accurately sequence up to 300 kb of their samples against a known sequence. Affymetrix engineers will work directly with you to design the chip so that the data will be most meaningful to your research.

Affymetrix does offer one standard resequencing GeneChip, the Human Mitochondrial Resequencing Array 2.0. This array contains the entire 16 kb mitochondrial genome, and is a convenient way to detect germ-line and heteroplasmic mutations

Resequencing Software

Because GeneChips are so common, most microarray software will read in their raw data easily. A good starting point for users who wish to analyze their own data is the Affymetrix Gene Chip Operating Software, or GCOS. This software will allow you to import, organize, and view your data, and is required for any other Affymetrix analysis software. You can download GCOS from Affymetrix. Please be aware that this software is Windows-only, and will require Administrator access to install

If you'd like to analyze your sequence data, you'll also need the Affymetrix GeneChip Sequence Analysis Software, or GSEQ. This software will allow you to perform sequence analysis of yor data. You can download GSEQ from Affymetrix. Please be aware that this software is Windows-only, and will require Administrator access to install

Resequencing Data

GSR Microarrays will provide the raw data to your experiment in an archive called a DTT. This archive can be imported into your copy of GCOS using the Affymetrix Data Transfer Tool (included with GCOS 1.4, or available from Affymetrix). Data produced before 2006 was exported in CAB format, which can be imported with the same tool. Before you can import data for an array, you must install the Library file for that array.

If you have a large amount of data, your DTT may be broken into several pieces with extensions like DTT, D02, D03, etc. You must have all of the files for a single set in order to read any of the data in them. If you do not have GCOS, you can still extract the individual files in these archives. First, you must rename the files. If you have only a DTT file, rename it to .ZIP. If you have several files for a single archive, rename the last file to .ZIP. That is, if you have three files in your set, rename .D03 to .ZIP. Then proceed through the remaining files - .DTT should become .Z01, .D02 should become .Z02, and so on until you have renamed all of the files. You can now open the .ZIP file with any compressed file software, and you should see the following three files for each sample:

In addition to providing the DTT file, GSR Microarrays will export the sequence calls in the CHP files into a tab-delimited text file. The filename for this file will usually include the words "Table data". Upon request, we can also export the sequences directly into a FASTA file for simple upload into other software.