This GeneChip array is available through the Affymetrix Made-to-Order Program, which enables you to purchase selected custom array designs and previous-generation GeneChip arrays no longer available as catalog products. Learn more about ordering and support of GeneChip Made-to-Order arrays.
The GeneChip® X3P Array was designed specifically for whole-genome expression profiling of formalin-fixed, paraffin-embedded (FFPE) samples, and is now available via the GeneChip Made-to-Order program.
Resulting from a collaboration between Affymetrix and Arcturus, this array is optimized as part of a system solution together with the Paradise™ Reagent System from Arcturus for expression analysis of FFPE samples.
FFPE samples introduce unique challenges for microarray analysis, including potential fragmentation and chemical modification of RNA molecules. In order to overcome these challenges, the Paradise Reagent System was developed to provide RNA isolation and amplification reagents optimized for FFPE samples. In addition, the X3P Array is designed to focus on interrogating sequences located closer to the 3' end of the transcripts compared with standard GeneChip arrays. Together, the reagents and array accommodate the characteristics of the FFPE RNA samples, enabling genome-wide profiling.
The target sequences on the X3P Arrays are identical to those used for designing the Human Genome U133 Plus 2.0 Array, for a total of 47,000 transcripts with 61,000 probe sets, although the probes on the two types of arrays are significantly different.
As a result of the modification to the probe selection criteria, the majority of the probe sets on the X3P arrays are selected from the 300 bases at the most 3' end of the transcripts. This is different from the standard Affymetrix design strategy which selects probe sets within the region of 600 bases proximal to the 3' ends.
To select probes for the 47,000 transcripts, it was not possible to identify high-performance probe sets within the shorter 300 base probe selection region for approximately 4,000 transcripts. For these transcripts, two sets of probes are represented on the arrays: 1) the original probe sets from the standard HG-U133 Plus design are replicated on the X3P arrays, and 2) the new, more 3' probe sets are also included although they fell below the minimum probe score selection threshold.
In addition, fewer than 200 transcripts from the HG-U133 Plus design are only represented by the HG-U133 Plus probe sets, where no probe sets within the smaller (300 bps) probe selection region could be found.
Find individual probe sets on all GeneChip® expression arrays with
Array Finder.
For more information, please review the data sheet (pdf, 114 KB).
