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.
Annotations derived from Affymetrix CSV file dated 6/23/2004
Evidence of stress in beta cells obtained with laser capture microdisssection from pancreases of brain-dead donor
Data table header descriptions
ID
Affymetrix Probe Set ID
GB_ACC
GenBank Accession Number
SPOT_ID
Species Scientific Name
The genus and species of the organism represented by the probe set.
Annotation Date
The date that the annotations for this probe array were last updated. It will generally be earlier than the date when the annotations were posted on the Affymetrix web site.
Sequence Type
Indicates whether the sequence is an Exemplar, Consensus or Control sequence. An Exemplar is a single nucleotide sequence taken directly from a public database. This sequence could be an mRNA or EST. A Consensus sequence, is a nucleotide sequence assembled by Affymetrix, based on one or more sequence taken from a public database.
Sequence Source
The database from which the sequence used to design this probe set was taken.
Representative Public ID
The accession number of a representative sequence. Note that for consensus-based probe sets, the representative sequence is only one of several sequences (sequence sub-clusters) used to build the consensus sequence and it is not directly used to derive the probe sequences. The representative sequence is chosen during array design as a sequence that is best associated with the transcribed region being interrogated by the probe set. Refer to the "Sequence Source" field to determine the database used.
Transcript ID(Array Design)
Target Description
GenBank description associated with the representative public identifier. Blank for some probe sets.
Gene Title
Title of Gene represented by the probe set.
Gene Symbol
A gene symbol, when one is available (from UniGene).
ENTREZ_GENE_ID
Entrez Gene Database UID
Gene Ontology Biological Process
Gene Ontology Consortium Biological Process derived from LocusLink. Each annotation consists of three parts: "Accession Number // Description // Evidence". The description corresponds directly to the GO ID. The evidence can be "direct", or "extended".
Gene Ontology Cellular Component
Gene Ontology Consortium Cellular Component derived from LocusLink. Each annotation consists of three parts: "Accession Number // Description // Evidence". The description corresponds directly to the GO ID. The evidence can be "direct", or "extended".
Gene Ontology Molecular Function
Gene Ontology Consortium Molecular Function derived from LocusLink. Each annotation consists of three parts: "Accession Number // Description // Evidence". The description corresponds directly to the GO ID. The evidence can be "direct", or "extended".
0006260 // DNA replication // not recorded /// 0006260 // DNA replication // inferred from electronic annotation /// 0006297 // nucleotide-excision repair, DNA gap filling // not recorded
0005634 // nucleus // inferred from electronic annotation /// 0005654 // nucleoplasm // not recorded /// 0005663 // DNA replication factor C complex // inferred from direct assay /// 0005663 // DNA replication factor C complex // inferred from electronic annotation
0000166 // nucleotide binding // inferred from electronic annotation /// 0003677 // DNA binding // inferred from electronic annotation /// 0003689 // DNA clamp loader activity // inferred from electronic annotation /// 0005515 // protein binding // inferred from physical interaction /// 0005524 // ATP binding // traceable author statement /// 0005524 // ATP binding // inferred from electronic annotation /// 0017111 // nucleoside-triphosphatase activity // inferred from electronic annotation
0006810 // transport // inferred from electronic annotation /// 0006811 // ion transport // inferred from electronic annotation /// 0006829 // zinc ion transport // inferred from electronic annotation /// 0030001 // metal ion transport // inferred from electronic annotation
0005886 // plasma membrane // inferred from electronic annotation /// 0016020 // membrane // inferred from electronic annotation /// 0016021 // integral to membrane // inferred from electronic annotation /// 0016323 // basolateral plasma membrane // inferred from electronic annotation
0008270 // zinc ion binding // inferred from electronic annotation /// 0046873 // metal ion transmembrane transporter activity // inferred from electronic annotation
0000187 // activation of MAPK activity // inferred from electronic annotation /// 0001915 // negative regulation of T cell mediated cytotoxicity // inferred from sequence or structural similarity /// 0001916 // positive regulation of T cell mediated cytotoxicity // inferred from electronic annotation /// 0001960 // negative regulation of cytokine mediated signaling pathway // inferred from sequence or structural similarity /// 0002378 // immunoglobulin biosynthetic process // inferred from mutant phenotype /// 0002925 // positive regulation of humoral immune response mediated by circulating immunoglobulin // inferred from electronic annotation /// 0006469 // negative regulation of protein kinase activity // inferred from direct assay /// 0006469 // negative regulation of protein kinase activity // inferred from sequence or structural similarity /// 0006470 // protein amino acid dephosphorylation // inferred from electronic annotation /// 0006470 // protein amino acid dephosphorylation // inferred from sequence or structural similarity /// 0007159 // leukocyte adhesion // inferred from electronic annotation /// 0007166 // cell surface receptor linked signal transduction // traceable author statement /// 0016311 // dephosphorylation // inferred from electronic annotation /// 0016311 // dephosphorylation // inferred from sequence or structural similarity /// 0030217 // T cell differentiation // inferred from sequence or structural similarity /// 0030890 // positive regulation of B cell proliferation // inferred from electronic annotation /// 0030890 // positive regulation of B cell proliferation // inferred from mutant phenotype /// 0031953 // negative regulation of protein amino acid autophosphorylation // inferred from electronic annotation /// 0033261 // regulation of S phase // inferred from mutant phenotype /// 0034113 // heterotypic cell-cell adhesion // inferred from electronic annotation /// 0042098 // T cell proliferation // inferred from electronic annotation /// 0042100 // B cell proliferation // inferred from sequence or structural similarity /// 0042102 // positive regulation of T cell proliferation // inferred from sequence or structural similarity /// 0043065 // positive regulation of apoptosis // inferred from electronic annotation /// 0043410 // positive regulation of MAPKKK cascade // inferred from electronic annotation /// 0045059 // positive thymic T cell selection // inferred from electronic annotation /// 0045060 // negative thymic T cell selection // inferred from electronic annotation /// 0045577 // regulation of B cell differentiation // inferred from electronic annotation /// 0045588 // positive regulation of gamma-delta T cell differentiation // inferred from electronic annotation /// 0045860 // positive regulation of protein kinase activity // non-traceable author statement /// 0046641 // positive regulation of alpha-beta T cell proliferation // inferred from electronic annotation /// 0048304 // positive regulation of isotype switching to IgG isotypes // inferred from electronic annotation /// 0050732 // negative regulation of peptidyl-tyrosine phosphorylation // inferred from electronic annotation /// 0050852 // T cell receptor signaling pathway // inferred from direct assay /// 0050853 // B cell receptor signaling pathway // inferred from sequence or structural similarity /// 0050855 // regulation of B cell receptor signaling pathway // inferred from electronic annotation /// 0050857 // positive regulation of antigen receptor-mediated signaling pathway // inferred from sequence or structural similarity /// 0051209 // release of sequestered calcium ion into cytosol // inferred from sequence or structural similarity /// 0051607 // defense response to virus // inferred from sequence or structural similarity /// 0051726 // regulation of cell cycle // inferred from sequence or structural similarity
0005634 // nucleus // inferred from direct assay /// 0005886 // plasma membrane // not recorded /// 0005887 // integral to plasma membrane // inferred from sequence or structural similarity /// 0005887 // integral to plasma membrane // traceable author statement /// 0005925 // focal adhesion // inferred from sequence or structural similarity /// 0009897 // external side of plasma membrane // inferred from electronic annotation /// 0016020 // membrane // inferred from electronic annotation /// 0016021 // integral to membrane // inferred from electronic annotation /// 0043231 // intracellular membrane-bounded organelle // inferred from direct assay
0004721 // phosphoprotein phosphatase activity // inferred from electronic annotation /// 0004725 // protein tyrosine phosphatase activity // inferred from electronic annotation /// 0004725 // protein tyrosine phosphatase activity // inferred from direct assay /// 0004872 // receptor activity // inferred from electronic annotation /// 0005001 // transmembrane receptor protein tyrosine phosphatase activity // traceable author statement /// 0005515 // protein binding // inferred from electronic annotation /// 0005515 // protein binding // inferred from physical interaction /// 0008201 // heparin binding // inferred from electronic annotation /// 0016787 // hydrolase activity // inferred from electronic annotation /// 0016791 // phosphatase activity // inferred from electronic annotation /// 0019901 // protein kinase binding // inferred from physical interaction /// 0043395 // heparan sulfate proteoglycan binding // inferred from electronic annotation
0006468 // protein amino acid phosphorylation // inferred from direct assay /// 0006468 // protein amino acid phosphorylation // inferred from electronic annotation /// 0006974 // response to DNA damage stimulus // inferred from direct assay /// 0009411 // response to UV // inferred from direct assay /// 0010212 // response to ionizing radiation // inferred from direct assay /// 0030010 // establishment of cell polarity // inferred from sequence or structural similarity /// 0030182 // neuron differentiation // inferred from sequence or structural similarity /// 0031572 // G2/M transition DNA damage checkpoint // inferred from direct assay
0005634 // nucleus // inferred from direct assay /// 0005634 // nucleus // inferred from electronic annotation /// 0005737 // cytoplasm // inferred from direct assay /// 0005737 // cytoplasm // inferred from electronic annotation
0000166 // nucleotide binding // inferred from electronic annotation /// 0000287 // magnesium ion binding // inferred from direct assay /// 0000287 // magnesium ion binding // inferred from electronic annotation /// 0004672 // protein kinase activity // inferred from electronic annotation /// 0004674 // protein serine/threonine kinase activity // inferred from direct assay /// 0004674 // protein serine/threonine kinase activity // inferred from electronic annotation /// 0005524 // ATP binding // inferred by curator /// 0005524 // ATP binding // inferred from electronic annotation /// 0016301 // kinase activity // inferred from electronic annotation /// 0016740 // transferase activity // inferred from electronic annotation /// 0046872 // metal ion binding // inferred from electronic annotation
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