The GeneChip® Human Gene 1.0 ST Array is the latest product in the family of Affymetrix expression arrays offering whole-transcript coverage. Each of the 28,869 genes is represented on the array by approximately 26 probes spread across the full length of the gene, providing a more complete and more accurate picture of gene expression than 3’ based expression array designs. The small format of the array makes it a cost-effective expression profiling solution for new microarray users.
The Gene 1.0 ST Array is part of a complete solution for gene expression analysis that includes Whole Transcript (WT) Sense Target Labeling and Control Reagents, fluidics and scanning instrumentation and basic analysis software. The array contains the most up-to-date content of well-annotated genes, and data is analyzed using a simple workflow.
The Gene 1.0 ST Array uses a subset of probes from the Human Exon 1.0 ST Array and covers only well-annotated content. Like the Exon 1.0 ST Array, “gene-level” analysis of multiple probes on different exons is summarized into an expression value representing all transcripts from the same gene.
|Feature Size||5 µm|
|Total Number of Distinct Probes||764,885|
|Oligonucleotide Probe Length||25-mer probes|
|Required Orientation of Labeled Targets to be Hybridized to the Array||Sense|
|Gene-level Probe Sets with Ensembl Support||28,132|
|Gene-level Probe Sets with Putative Full-length Transcript Support (GenBank and RefSeq)||19,734|
Comprehensive Coverage of the Entire Gene Locus
The Human Gene 1.0 ST Array interrogates 28,869 well-annotated genes with 764,885 distinct probes. The design of the Human Gene 1.0 ST Array was based on the March 2006 (UCSC hg18, NCBI Build 36) human genome sequence assembly with comprehensive coverage of RefSeq, Ensembl and putative complete CDS GenBank transcripts. The Human Gene 1.0 ST Array has greater than 99 percent coverage of sequences present in the RefSeq database.
The Gene 1.0 ST Array is a perfect match (PM)-only design with probes that hybridize to sense target. Background is estimated using a set of approximately 20,000 generic background probes. Standard poly-A controls and hybridization controls are also represented on the array to allow convenient troubleshooting along the entire experimental process.
The Gene 1.0 ST Array uses a subset of probes from the Exon 1.0 ST Array and covers only well-annotated content. Like the Exon 1.0 ST Array, “gene-level” analysis of multiple probes on different exons are summarized into accumulative expression value representing all transcripts from the same gene.
The Human Gene 1.0 ST Array has shown comparable gene-level performance to classical 3’-based expression arrays, such as the Human Genome U133 Plus 2.0 and Exon 1.0 ST Arrays for genes common to all three platforms (see figure ). Heart and brain tissue mixtures studies, as well as a Latin Square spike-in experiments, have demonstrated high sensitivity and reproducibility. For more detailed information on these experiments please refer to the Human Gene 1.0 ST Array Performance white paper.
The Human Gene 1.0 ST Array has comparable performance to the HG-U133 and Exon 1.0 ST Array as demonstrated by Latin Square spike-in experiments. For each array, multiple comparisons were done for different concentrations (as shown along the x-axis). A t-statistic was computed between the three chips with no spike and the three chips with a concentration listed on the x-axis. From this the percentage of detected spikes (at an empirical false positive rate of 0.01) was determined (as shown along the y-axis). See the Human Gene 1.0 ST Array Performance white paper for more details.
Quick Reference Cards
Material Safety Data Sheets
GeneChip® Human Gene 1.0 ST Array
|901085||GeneChip® Human Gene 1.0 ST Array||Contains 2 Arrays|
|901086||GeneChip® Human Gene 1.0 ST Array||Contains 6 Arrays|
|901087||GeneChip® Human Gene 1.0 ST Array||Contains 30 Arrays|
GeneChip® Human Gene 1.0 ST Arrays and Reagents
|901146||GeneChip® Human Gene 1.0 ST Arrays and Reagents||Contains 30 Arrays and Reagents sufficient for 30 Reactions|
|901147||GeneChip® Human Gene 1.0 ST Arrays and Reagents||Contains 10 Arrays and Reagents sufficient for 10 Reactions|
|Affymetrix® GeneChip® Command Console® Software||Available Via Download|
|Affymetrix® Expression Console™ Software||Available Via Download|
|900652||GeneChip® WT Sense Target Labeling and Control Reagents||Sufficient for 30 reactions|
|900720||GeneChip® Hybridization, Wash, and Stain Kit||Sufficient for 30 reactions|
|00-0211||GeneChip® Scanner 3000 7G with Workstation|
|00-0079||GeneChip® Fluidics Station 450|