Human Gene 1.0 ST Array The GeneChip Human Exon 1.0 ST Array is a single array with over 5 million unique 25-mer oligonucleotide features constituting 1.4 million probe sets Based on annotations against build 34 of the human genome sequence, these 1.4 million probe sets can be grouped into over 1 million exon clusters (1 or more overlapping exons) and over 150,000 transcript clusters (groups of puta- tive alternatively spliced transcripts from the same gene) for the most compre- hensive genome-wide expression profiling at the exon level. The design includes (not mutually exclusive): * 306,583 probe sets with Ensembl transcript support * 289,961 probe sets with putative full-length mRNA support * 665,175 probe sets with EST support * 220,262 probe sets with mouse or rat mRNA support * 883,105 probe sets with gene prediction support The design of the Human Exon 1.0 ST Array adopts an inclusive design strategy by projecting both the publicly available, empirically obtained cDNA-based content and results from gene prediction algorithms on the human genome assembly build 34 from July 2003. Combining all of the input sequence information, boundaries of exons and probe selection regions (PSRs are defined. Probe sets are then selected for the PSRs of 25 bases or more in length. Empirical sequences are obtained from sources such as Human RefSeq (R) mRNAs, and dbEST. Mouse and rat cDNAs are mapped onto the GenBank human genome using genome synteny information from the genome browser group at the University of California, Santa Cruz. Gene predictions include those from published algorithms such as GENSCAN, GENSCAN Suboptimal Ensembl, Vega, geneid, sgp, TWINSCAN, and Exoniphy. Other miscellaneous content on the array includes the microRNA Registry, MITOMAP mitochon- drial transcripts, and structural RNA predictions. The GeneChip® Human Gene 1.0 ST Array provides probe sets for wholegenome gene-level expression studies of known genes. It is a single GeneChip array comprised of more than 750,000 unique 25-mer oligonucleotide features constituting over 28,000 gene-level probe sets. The design of the Human Gene 1.0 ST Array is based primarily on a subset of probes from the GeneChip® Human Exon 1.0 ST Array which map to well-supported exons of known genes. Discovery content, such as transcript regions supported by more speculative sources including Expressed Sequence Tags (ESTs) and gene predictions, are not interrogated by the Human Gene 1.0 ST Array. Design of the array was based on sequences and gene annotations obtained from the following sources and used to group probes from Human Exon 1.0 ST Array into new gene-level probe sets. In some cases these sequences were used to select additional new probes. • The March 2006 human genome sequence (UCSC hg18, NCBI v36) • RefSeq NM (curated and provisional; not predicted) mRNA sequences (24,188 sequences) current to November 3, 2006 • GenBank® complete coding sequence mRNAs current to November 3, 2006 (56,249 sequences) • Ensembl genome annotations from October 2006 (version 41.36c; 56,364 transcripts) Oligonucleotide probes are synthesized in situ complementary to each corresponding sequence. For expression analysis, the samples need to be amplified, and the targets labeled in the sense orientation for hybridization to the arrays.