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.

The Human Gene 1.0 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.

Data Sheets

Gene 1.0 ST Array System for Human, Mouse and Rat (pdf, 436 KB)

Technical Notes

Gene 1.0 ST Array Design (pdf, 324 KB)

Application Notes

Whole-transcript Expression Analysis (pdf, 557 kb)

White Papers

Human Gene 1.0 ST Array Performance (pdf, 620 KB)

Quality Assessment of Exon and Gene Arrays (pdf, 180 KB)

Whole Transcript (WT) Sense Target Labeling Assay Performance (pdf, 652 KB)

Publications

Publications and Reference for Affymetrix® GeneChip® Exon and Gene Arrays (pdf, 74 KB)

FAQs

Gene 1.0 ST Array

Manuals

Whole Transcript (WT) Sense Target Labeling Assay (pdf, 1.12 MB)

Quick Reference Cards

QC Metrics for Exon and Gene Design Expression Arrays (pdf, 123 KB)

Sample Data

Gene 1.0 ST Array Data Set

Array Comparisons

Comparison Spreadsheets User's Guide (pdf, 82 KB)

HG-U133 Plus to Human Gene 1.0 ST, Best Match (zip, 651 KB)

HG-U133 Plus to Human Gene 1.0 ST, Complex Match (zip, 2.7 MB)

HG-U133 Plus to Human Gene 1.0 ST, Good Match (zip, 658 KB)

HG-U133 Plus to Human Gene 1.0 ST, No Match (zip, 38 KB)

Human Exon 1.0 ST to Human Gene 1.0 ST, Best Match (zip, 485 KB)

Human Exon 1.0 ST to Human Gene 1.0 ST, Complex Match (zip, 29 MB)

Human Exon 1.0 ST to Human Gene 1.0 ST, Good Match (zip, 521 KB)

Human Exon 1.0 ST to Human Gene 1.0 ST, No Match (zip 500 B)

Library Files

Human Gene 1.0 ST Array, Analysis (zip, 17 MB)

Human Gene 1.0 ST Array, GCOS (2.18 MB)

Probe BED File

Unsupported Human Gene 1.0 ST Array CDF Files (zip, 13 MB)

Note: Unsupported CDF files are provided for the Human Exon 1.0 ST Array. The corresponding supported files are the PGF and CLF files in the ExACT library file set.

Package Inserts

Human Gene 1.0 ST Array (pdf, 527 KB)

Alignment, Annotation, and Sequence Files

Information about using Alignment, Annotation, and Sequence files

NetAffx Alignment Files

HuGene-1_0-st-v1 BED File (3.7 MB, 3/23/07)

Design Time Annotation Files

HuGene-1_0-st-v1 Design Time Annotations, Full, GFF Format (23 MB, 3/23/07)

Note: For gene level analysis you will need to download one of the probeset level annotation zip files (CSV) to get the meta-probeset lists. None of these files contain textual biological annotations such as gene name or GO annotations; textual biological information can be found in the NetAffx Transcript CSV file. The design time Probeset CSV file provides information about the probeset such as genome coordinate and supporting annotation types. This is a subset of information found in the NetAffx Probeset CSV file. The Probeset CSV file is also a subset of the Full GFF files which contain transcript cluster, exon cluster, probeset, and probe level annotations. The GFF files also contain information about the specific annotations supporting each of the probesets. For example, use the Full GFF files for pulling design time information into a local database. The Mappings TSV file contains mappings between other arrays and annotations.

Current NetAffx Annotation Files

HuGene-1_0-st-v1 Annotations CSV README (27 KB, 11/24/08)

HuGene-1_0-st-v1 Transcript Cluster Annotations, CSV (10 MB, 11/24/08)

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

HuGene-1_0-st-v1 Probe Sequences, FASTA format (25 MB, 7/13/07)

HuGene-1_0-st-v1 Probe Sequences, tabular format (20 MB, 7/13/07)

HuGene-1_0-st-v1 Sequence Files README (8.8 KB, 7/13/07)

HuGene-1_0-st-v1 Transcript Cluster Sequences, FASTA format (21 MB, 3/29/07)

Archived NetAffx Annotation Files

HuGene-1_0-st-v1 Annotations CSV README (27 KB, 3/28/07)

HuGene-1_0-st-v1 Annotations CSV README (26 KB, 7/15/07)

HuGene-1_0-st-v1 Annotations CSV README (26 KB, 11/12/07)

HuGene-1_0-st-v1 Annotations CSV README (26 KB, 3/19/08)

HuGene-1_0-st-v1 Annotations CSV README (27 KB, 7/8/08)

HuGene-1_0-st-v1 Transcript Cluster Annotations, CSV (11 MB, 6/11/07)

HuGene-1_0-st-v1 Transcript Cluster Annotations, CSV (11 MB, 9/17/07)

HuGene-1_0-st-v1 Transcript Cluster Annotations, CSV (8.3 MB, 11/12/07)

HuGene-1_0-st-v1 Transcript Cluster Annotations, CSV (8.7 MB, 3/20/08)

HuGene-1_0-st-v1 Transcript Cluster Annotations, CSV (11 MB, 7/17/08)

Archived Sequence Files

HuGene-1_0-st-v1 Probe Sequences, FASTA format (22 MB, 3/29/07)

HuGene-1_0-st-v1 Probe Sequences, tabular format (21 MB, 3/29/07)

Additional Support

Fluidics Scripts

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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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	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