Hg-U133 Plus 2.0 Probe Set

Question

[Zhisheng]

Hi,

Has someone used the Affy U133Plus2 gene expression data on 'UCSC Genome Browser on Human' database? How can I know the sequence information of a particular probe set I am interested in? Is the cDNA in option ' View details of parts of alignment within browser window ' the sequence of the probe set or from the human genomes? Many thanks for help.

Best regards,

Answer 1

[David Quigley]

If you only want one probeset, the easiest way to get the sequence of an U133 probeset is via the affymetrix website affymetrix.com). The netaffx section of their site is a searchable front-end to the annotation files that describe the probes. You can easily get the target sequences, and on each probeset's summary page there is a small link labeled UCSC that takes you to the location of the probesets on the genome browser with the Affymetrix track turned on. This identifies the intended targets of the probes. Beware of cases where the probes map to multiple loci due to cross-hybridization or incorrect probe design.

If you want to know the sequences of many probesets at once, your best bet is to download and parse the transcript files available through the Support section of affymetrix.com.