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GeneChip® Human Gene 1.0 ST Array

Affymetrix GeneChip® Human Gene 1.0 ST Array

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.


Array Format 169
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

More Information

Details about the complete system for expression analysis with the Gene 1.0 ST Array

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.

Performance

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.

Latin Square spike-in experiments
Latin Square spike
Latin Square spike-in experiments

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.

GeneChip® Human Gene 1.0 ST Array

Part # Description Details
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

Part # Description Details
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

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