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GeneChip® Human X3P Array

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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).

Part # Description Details
900516 Human X3P Array Contains 6 arrays

Related Products

Part # Description Details
900449 IVT Labeling Kit sufficient for 30 reactions
900375 T7-Oligo(dT) Promoter Primer Kit sufficient for 150 reactions
900433 Poly-A RNA Control Kit sufficient for approximately 100 reactions
900454 Hybridization Control Kit sufficient for 30 reactions

FAQs

Gene Expression Arrays

Manuals

Expression Analysis Technical Manual, with Specific Protocols for Use with the Hybridization, Wash, and Stain Kit (pdf, 1.70 MB)

Probe Set Data in MAGE-ML Format

Library Files

Human X3P Array (zip, 30 MB)

Package Inserts

Human X3P Array (pdf, 67 KB)

Alignment, Annotation, and Sequence Files

Information about using Alignment, Annotation, and Sequence files

NetAffx Alignment Files

X3p Alignments to Genome, PSL (7.4 MB, 9/28/06)

Current NetAffx Annotation Files

U133_X3P Annotations, CSV format, Release 34 (29 MB, 10/24/13)

U133_X3P Orthologs/Homologs, CSV Format, Release 34 (10.0 MB, 10/24/13)

Note: NetAffx annotation files are intended for use in automated analysis. Some are not compatible with all spreadsheet applications. Please use the NetAffx Analysis Center to limit download data to your probe sets of interest. Annotation CSV files for the exon arrays are split into a probe set-level annotation file and a transcript cluster-level annotation file; exon array CSV files are compatible with ExACT.

Sequence Files

X3p Consensus Sequences, FASTA (32 MB, 8/20/08)

X3p Contol Sequences, FASTA (27 KB, 2/5/04)

U133_X3P Probe Sequences, FASTA (11 MB, 8/20/08)

U133_X3P Probe Sequences, Tabular (10 MB, 8/20/08)

X3p Target Sequences, FASTA (5.0 MB, 8/20/08)

Archived NetAffx Annotation Files

U133_X3P Annotations, CSV format, Release 21 (17 MB, 5/31/07)

U133_X3P Annotations, CSV format, Release 22 (18 MB, 5/31/07)

U133_X3P Annotations, CSV format, Release 23 (16 MB, 7/12/07)

U133_X3P Annotations, CSV format, Release 24 (17 MB, 11/6/07)

U133_X3P Annotations, CSV format, Release 25 (17 MB, 3/18/08)

U133_X3P Annotations, CSV format, Release 26 (19 MB, 7/8/08)

U133_X3P Annotations, CSV format, Release 27 (19 MB, 11/30/08)

U133_X3P Annotations, CSV format, Release 28 (19 MB, 3/12/09)

U133_X3P Annotations, CSV format, Release 29 (20 MB, 7/1/09)

U133_X3P Annotations, CSV format, Release 30 (21 MB, 11/15/09)

U133_X3P Annotations, CSV format, Release 31 (20 MB, 8/23/10)

U133_X3P Annotations, CSV format, Release 32 (21 MB, 6/10/11)

U133_X3P Annotations, CSV format, Release 33 (25 MB, 10/30/12)

U133_X3P Annotations, CSV, Release 20 (17 MB, 5/31/07)

U133_X3P Annotations, MAGE-ML XML format, Release 21 (91 MB, 6/15/07)

U133_X3P Annotations, MAGE-ML XML Format, Release 22 (85 MB, 6/15/07)

U133_X3P Annotations, MAGE-ML XML Format, Release 23 (81 MB, 7/12/07)

U133_X3P Annotations, MAGE-ML XML Format, Release 24 (81 MB, 11/6/07)

U133_X3P Annotations, MAGE-ML XML Format, Release 25 (83 MB, 3/18/08)

U133_X3P Annotations, MAGE-ML XML Format, Release 26 (85 MB, 7/8/08)

U133_X3P Annotations, MAGE-ML XML Format, Release 27 (86 MB, 11/24/08)

U133_X3P Annotations, MAGE-ML XML Format, Release 28 (90 MB, 3/12/09)

U133_X3P Annotations, MAGE-ML XML Format, Release 29 (90 MB, 7/1/09)

U133_X3P Annotations, MAGE-ML XML Format, Release 30 (92 MB, 11/15/09)

U133_X3P Annotations, MAGE-ML XML Format, Release 31 (92 MB, 8/23/10)

U133_X3P Annotations, MAGE-ML XML Format, Release 32 (92 MB, 6/9/11)

U133_X3P Annotations, MAGE-ML XML, Release 20 (90 MB, 6/15/07)

U133_X3P BLASTP annotations, CSV format, Release 21 (4.9 MB, 11/15/06)

U133_X3P BLASTP annotations, CSV Format, Release 22 (171 KB, 3/9/07)

U133_X3P BLASTP annotations, CSV Format, Release 23 (175 KB, 7/12/07)

U133_X3P BLASTP annotations, CSV Format, Release 24 (10 KB, 11/6/07)

U133_X3P BLASTP annotations, CSV Format, Release 25 (77 KB, 3/18/08)

U133_X3P BLASTP annotations, CSV Format, Release 26 (13 KB, 7/8/08)

U133_X3P BLASTP annotations, CSV Format, Release 27 (88 KB, 11/24/08)

U133_X3P BLASTP annotations, CSV Format, Release 28 (10 KB, 3/4/09)

U133_X3P BLASTP annotations, CSV Format, Release 29 (9.8 KB, 7/1/09)

U133_X3P BLASTP annotations, CSV Format, Release 30 (53 KB, 11/16/09)

U133_X3P BLASTP annotations, CSV Format, Release 31 (72 KB, 8/11/10)

U133_X3P BLASTP annotations, CSV Format, Release 32 (9.4 KB, 6/9/11)

U133_X3P Orthologs/Homologs, CSV format, Release 21 (8.0 MB, 11/30/06)

U133_X3P Orthologs/Homologs, CSV Format, Release 22 (8.8 MB, 3/9/07)

U133_X3P Orthologs/Homologs, CSV Format, Release 23 (7.5 MB, 7/12/07)

U133_X3P Orthologs/Homologs, CSV Format, Release 24 (7.2 MB, 11/6/07)

U133_X3P Orthologs/Homologs, CSV Format, Release 25 (7.2 MB, 3/18/08)

U133_X3P Orthologs/Homologs, CSV Format, Release 26 (7.8 MB, 7/8/08)

U133_X3P Orthologs/Homologs, CSV Format, Release 27 (8.3 MB, 11/24/08)

U133_X3P Orthologs/Homologs, CSV Format, Release 28 (8.9 MB, 3/12/09)

U133_X3P Orthologs/Homologs, CSV Format, Release 29 (8.8 MB, 7/1/09)

U133_X3P Orthologs/Homologs, CSV Format, Release 30 (8.6 MB, 11/15/09)

U133_X3P Orthologs/Homologs, CSV Format, Release 31 (8.6 MB, 8/11/10)

U133_X3P Orthologs/Homologs, CSV Format, Release 32 (8.6 MB, 6/9/11)

U133_X3P Orthologs/Homologs, CSV Format, Release 33 (9.3 MB, 10/30/12)

Additional Support

Fluidics Scripts

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