Microorganism & Insect Expression Profiling Arrays & Assays

GeneChip™ Plasmodium/Anopheles Genome Array (Applied Biosystems™)

The GeneChip™ Plasmodium/Anopheles Genome Array includes probe sets to over 4,300 Plasmodium falciparum transcripts and approximately 14,900 Anopheles gambiae transcripts. The Plasmodium/Anopheles Genome Array was developed in collaboration with the Malaria Research Institute at the Johns Hopkins Bloomberg School of Public Health.

P. falciparum sequence information for this array was collected primarily from PlasmodB (version 4.1, June 2003) and augmented with sequence information from GenBank™ and dbEST. Sequence information for A. gambiae was drawn primarily from Ensembl (Build 2, 2003) and augmented with sequence information from GenBank and dbEST.

Note: The DsRed probe set is provided with permission from BD Biosciences, and BD Biosciences grants users a limited license to utilize this probe set only on the Plasmodium/Anopheles Genome Array. Other uses of the probe set, or other DsRed sequence or sequences, require a license from BD Biosciences.

GeneChip™ C. elegans Genome Array (Applied Biosystems™)

This whole genome array represents 22,500 transcripts from Caenorhabditis elegans, a model organism for developmental biology and functional genomics.

Sequence information used to select these probe sets came from the December 05, 2000 Sanger Center database release and GenBank™ release 121. All sequences were functionally re-annotated by us for improved descriptions.

For more information, please review the package insert.

GeneChip™ S. aureus Genome Array (Applied Biosystems™)

This GeneChip™ array is available through our Made-to-Order Program, which enables you to purchase selected custom array designs and previous-generation GeneChip arrays no longer available as catalog products. Learn more about ordering and support of GeneChip Custom Arrays.

For comprehensive monitoring of the relative mRNA abundance of S. aureus sequences.
The GeneChip S. aureus Genome Array is useful for studying the expression of sequences in the following four strains of Staphylococcus aureus: N315 (National Institute of Technology and Evaluation, Japan), Mu50 (National Institute of Technology and Evaluation, Japan), NCTC 8325 (University of Oklahoma), and COL (TIGR).

The array contains probe sets to over 3,300 S. aureus open reading frames. Additionally, the array also contains probes to study both forward and reverse orientation of over 4,800 intergenic regions throughout the S. aureus genome.

For more information, please review the data sheet (pdf, 114 KB).

GeneChip™ C. elegans Gene 1.0 ST Array (Applied Biosystems™)

The GeneChip™ C. elegans Gene 1.0 ST Arrays enable you to:
• Measure expression, across the entire gene, with higher resolution and accuracy than with classical 3'-biased microarray solutions
• Get accurate and reproducible data by using multiple independent measurements for each transcript

Background
Model and applied research organisms are valuable for comparative genomics research, evolutionary biology, and continue to play a critical role in deciphering the molecular mechanisms underlying human disease, and agricultural crop improvement. The GeneChip Gene 1.0 ST Arrays have been developed for the analysis of a wide range of model and applied research organisms. These organisms are the latest additions to the growing family of Gene Expression Microarrays offering whole-transcript coverage. The GeneChip Gene 1.0 ST Arrays were designed in collaboration with influential researchers, such as Alan Archibald, Head of the Division of Genetics and Genomics at the Roslin Institute (Porcine Array design), Leonard Zon, Director of Stem Cell Research Program, and Yi Zhou, Genomic Core Director of the Stem Cell Research Program at Children's Hospital Boston and Harvard Medical School in Boston (Zebrafish Array design).

Key benefits
Highest transcript coverage – get confident expression measurements of well-annotated content with up to 26 probes per transcript
Whole-transcriptome analysis – capture the transcript isoforms you may miss with 3'-biased expression designs
High data correlation – achieve high inter- and intra-array strip signal correlation (R >0.99)

Proven performance from the industry standard
GeneChip Gene 1.0 ST Arrays offer whole-transcriptome coverage for selected model and applied research organisms. All designs are based on the most recent genomic content and offer the highest probe coverage (up to 26 probes across the full length of the gene). This allows for accurate detection for whole-transcriptome microarray analysis and provides higher resolution and accuracy than other classical 3'-biased microarray solutions on the market. The whole-transcriptome analysis approach enables researchers to detect multiple transcript isoforms, including those that might be missed using a 3'-biased expression design, such as splice variants, non-polyadenylated transcripts, transcripts with alternative polyadenylation sites, and truncated transcripts.

Complete Reagents, Software and Instrumentation Solution for Optimal Array Performance
For convenience and complete support, the Gene 1.0 ST Array is provided as part of a comprehensive solution that includes GeneChip reagents and instrumentation:
• GeneChip WT Sense Target Labeling and Control Reagents. For detailed information on the procedure of the assay and performance information, please refer to the WT Sense Target Labeling Assay Manual
• GeneChip Fluidics Station 450 for complete walk-away array processing to obtain the highest levels of reproducibility
• GeneChip Scanner 3000 7G with the optional Autoloader for array image acquisition

We offer several tools to help you in your data analysis, including GeneChip Expression Console; software, the NetAffx Analysis Center, and the Integrated Genome Browser (IGB).

Expression Console Software is an easy-to-use application that enables probe set summarization as well as preliminary data quality evaluation. A simple workflow enables the user to quickly analyze the data (see figure). The resulting data can be further analyzed using software applications from GeneChip-compatible™ software providers.

The NetAffx Analysis Center, with regularly updated biological and functional annotations of probe sets, is the most comprehensive resource for array annotations and probe sequence information. Flexible query tools and external links allow researchers to drill down into genes and annotations of interest. This resource makes it easy to interpret microarray results and quickly design downstream studies.

Workflow
Researchers can also use IGB to visualize results in a genomic context. Genomic annotations including RefSeq sequences, SNPs and genomic locations from various sources can be viewed alongside microarray gene expression signal data.

The Gene 1.0 ST Array data analysis workflow is similar to the workflow for 3' gene expression analysis, utilizing Expression Console 1.1, third-party GeneChip-compatible software and annotation tools in the NetAffx Analysis Center and IGB.

Content profile
GeneChip Gene 1.0 ST Arrays provide the latest coverage of the transcribed genome. We use a comprehensive collection of information sources to design probes that interrogate up to 26 unique sequences of each transcript. Together these 26 unique 25-mer probes interrogate up to 650 bases per transcript. This high probe coverage across the entire transcript results in superior performance and data confidence as well as the ability to update your experimental data as the understanding of each genome and transcriptome grows.

GeneChip™ Drosophila Tiling 2.0R Array (Applied Biosystems™)

The GeneChip™ Drosophila Tiling 2.0R Array is our second-generation Drosophila Tiling Array. GeneChip Drosophila Tiling Arrays are versatile, whole-genome tools that researchers have successfully used to map novel areas of transcription and to interpret chromatin IP results on a genome-wide level.

The Drosophila Tiling 2.0R Array builds on the content of its predecessor and includes additional sequences that have since become available through the Berkeley Drosophila Genome Project (BDGP). The majority of the new sequences are located in the heterochromatin regions of the Drosophila genome.

Array Features
• Up-to-date sequence content
   -Based on BDGP genome release 5
   -Release 5 improvements include heterochromatin regions, which contain several hundred known and predicted genes
• Newer design strategy enables a complete representation of the genome
   -Includes repetitive regions
   - No repeat masking used in chip design
   - Novel tiling array design (see White Paper, Drosophila Tiling 2.0R Array Design and Library files)
   - 25-mer oligonucleotide probes interrogate the entire genome with an average 38-base-pair resolution
• Flexible analysis options
   - Default analysis library file (bpmap file) excludes repetitive regions as defined by FlyBase 5.2 and UCSC Genome Browser repeat annotations
   - Entire array content analysis library file available upon request through Customer Support

Note: Due to the different content, design strategy and analysis library file content, direct comparisons of results between the discontinued Drosophila Tiling 1.0R Array and the Drosophila Tiling 2.0R Array are not recommended.

Instrument and Software Requirements
• GeneChip Scanner 3000, enabled for High-Resolution Scanning* or GeneChip Scanner 3000 7G
• GeneChip Operating Software (GCOS) v1.1.1, which contains the High-Resolution Scanning Update

* GeneChip Scanner 3000 High-Resolution Update is standard on all instruments shipped starting in September 2003 with serial number series 502. Previous versions, such as serial number series 501, will require the GeneChip Scanner 3000 High-Resolution Update, Catalog Number 00-0110, to be installed.

GeneChip™ Xenopus laevis Genome 2.0 Array (Applied Biosystems™)

The GeneChip™ Xenopus laevis Genome 2.0 Array can be used to study the whole genome of Xenopus laevis on a single array. The array is comprised of more than 32,400 probe sets representing more than 29,900 X. laevis transcripts, and was designed in close collaboration with the Xenopus research community as part of the GeneChip Consortia Program. Sequences used in the design of the array were selected from the X. laevis UniGene build 69 (July 2006) and GenBank™ mRNAs (through September 12, 2006).

X. laevis is one of the most important model organisms in developmental biology. Much of the current understanding of early embryonic development derives from experiments performed in the Xenopus embryo.

The GeneChip Xenopus laevis Genome 2.0 Array is designed specifically to monitor gene expression in X. laevis, providing significant utility in developmental studies, such as induction and over-expression. This array is especially useful for researchers interested in identifying the genetic mechanisms critical to the following processes:

• Primordial germ cell migration
• Oocyte maturation
• Programmed cell death
• Pluripotency and lineage specificity
• Nuclear transport
• Patterning events
• Chromosome replication
• Chromatin assembly
• Cell cycle progression
• Intracellular signaling
• Organogenesis
• Oncogenesis

Array Annotations (Interim File)
The GeneChip Xenopus laevis Genome 2.0 Array annotation file contains design-time annotations, using both the original probe-set names and new probe-set names. New probe-set names were assigned to differentiate the probe-set identifiers for GeneChip Xenopus laevis Genome 2.0 Array from the older, version-1.0 array. The new naming convention for the version 2.0 array contains the prefix "Xl2" for all probe-set identifiers, while the original probe-set IDs contain the prefix "Xl."

Please see the Documents Section below for related Manuals, Annotation Files and Data Sheets.

GeneChip™ Drosophila Genome 2.0 Array (Applied Biosystems™)

The GeneChip™ Drosophila Genome 2.0 Array is a microarray tool for studying expression of Drosophila melanogaster transcripts.

• Provides comprehensive coverage of the transcribed Drosophila genome on a single array
• Comprised of 18,880 probe sets, analyzing over 18,500 transcripts
• Sophisticated bioinformatics tools available through the NetAffx™ Analysis Center to rapidly obtain biologically meaningful results

Array Profile
Sequences used in the design of the GeneChip Drosophila Genome 2.0 Array were selected from Flybase version 3.1. Oligonucleotide probes complementary to each corresponding sequence are synthesized in situ on the arrays. Fourteen pairs of oligonucleotide probes are used to measure the level of transcription of each sequence.

Instrument Software Requirements
• GeneChip Scanner 3000, enabled for High-Resolution Scanning*
• GeneChip Operating Software (GCOS) v1.1.1, which contains the High-Resolution Scanning Update
*GeneChip Scanner 3000 High-Resolution Update is standard on all instruments shipped starting in September 2003 with serial number series 502. Previous versions, such as serial number series 501, will require the GeneChip Scanner 3000 High-Resolution Update, Catalog Number 00-0110, to be installed.

For more information, please review the data sheet (pdf, 700 KB).

GeneChip™ E. coli Genome 2.0 Array (Applied Biosystems™)

The GeneChip™ E. coli Genome 2.0 Array contains probe sets to detect transcripts from the K12 strain of E. coli and three pathogenic strains of E. coli. Using the E. coli Genome 2.0 Array, researchers can gain a comprehensive view of three pathogenic forms of E. coli while continuing ongoing research projects with the K12 strain.

The GeneChip E. coli Genome 2.0 Array includes approximately 10,000 probe sets for all 20,366 genes present in four strains of E. coli. Due to the high degree of similarity between the E. coli strains, whenever possible, a single probe set is tiled to represent the equivalent ortholog in all four strains. The GeneChip E. coli Genome 2.0 Array tiles probe sets over the entire open reading frame (ORF) of E. coli, includes over 700 intergenic regions, probes for various antibiotic resistance markers, and incorporates additional control and reporter genes from the previous generation E. coli array.

GeneChip™ Drosophila Gene 1.1 ST Array Plate (Applied Biosystems™)

The GeneChip™ Drosophila Gene 1.1 ST Array Plate enables you to:
• Measure expression, across the entire gene, with higher resolution and accuracy than with classical 3'-biased microarray solutions
• Get accurate and reproducible data by using multiple independent measurements for each transcript
• Process up to 96 samples on a single array plate with the GeneTitan™ Instrument

Development of the Gene Expression Microarrays

Model and applied research organisms are valuable for comparative genomics research, evolutionary biology, and continue to play a critical role in deciphering the molecular mechanisms underlying human disease, and agricultural crop improvement. Gene 1.1 ST Array Plates have been developed for the analysis of a wide range of model and applied research organisms. These organisms are the latest additions to the growing family of Gene Expression Microarrays offering whole-transcript coverage. The Gene 1.1 ST Array Plates were designed in collaboration with influential researchers, such as Alan Archibald, Head of the Division of Genetics and Genomics at the Roslin Institute (Porcine Gene 1.1 ST Array design), Leonard Zon, Director of Stem Cell Research Program, and Yi Zhou, Genomic Core Director of the Stem Cell Research Program at Children's Hospital Boston and Harvard Medical School in Boston (Zebrafish Gene 1.1 ST Array design).

Key benefits
Highest transcript coverage — get confident expression measurements of well-annotated content with up to 26 probes per transcript
Whole-transcriptome analysis — capture the transcript isoforms you may miss with 3'-biased expression designs
High data correlation — achieve high inter- and intra-array strip signal correlation (R >0.99)
Convenient format — process up to 96 samples at the same time with minimal manual array handling

Proven performance from the industry standard
Gene 1.1 ST Array Plates offer whole-transcriptome coverage for selected model and applied research organisms. All designs are based on the most recent genomic content and offer the highest probe coverage (up to 26 probes across the full length of the gene). This allows for accurate detection for whole-transcriptome microarray analysis and provides higher resolution and accuracy than other classical 3'-biased microarray solutions on the market. The whole-transcriptome analysis approach enables researchers to detect multiple transcript isoforms, including those that might be missed using a 3'-biased expression design, such as splice variants, non-polyadenylated transcripts, transcripts with alternative polyadenylation sites, and truncated transcripts.

Content profile
Gene 1.1 ST Array Plates provide the latest coverage of the transcribed genome. We use a comprehensive collection of information sources to design probes that interrogate up to 26 unique sequences of each transcript. Together these 26 unique 25-mer probes interrogate up to 650 bases per transcript. This high probe coverage across the entire transcript results in superior performance and data confidence as well as the ability to update your experimental data as the understanding of each genome and transcriptome grows.

GeneChip™ S. cerevisiae Tiling 1.0R Array (Applied Biosystems™)

The GeneChip™ S. cerevisiae Tiling 1.0R Array is a versatile whole-genome research tool:
• Most comprehensive S. cerevisiae microarray offering high-density 5 base pair probe resolution
• High-density array design is compatible with many research applications
• 25-mer probes yield the most specific hybridization results available

Array Profile
The GeneChip S. cerevisiae Tiling 1.0R Array is designed for identifying novel transcripts, mapping sites of protein/DNA interaction in chromatin immunoprecipitation (ChIP) experiments, and other whole-genome experiments.* The S. cerevisiae 1.0R Array is a single array comprised of over 3.2 million perfect match/mismatch probe pairs tiled through the complete Saccharomyces cerevisiae genome. Genome sequence information for the design of the S. cerevisiae Tiling 1.0R Array was drawn from the October 2003 Stanford Yeast Genome Database files (www.yeastgenome.org). The array also contains probes to interrogate a 2-µm circle plasmid (NCBI Accession J01347).

Probes are tiled at an average of 5 base pair resolution, as measured from the central position of adjacent 25-mer oligos, creating an overlap of approximately 20 base pairs on adjacent probes.

*Gresham D, et al. Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray. Science 311(5769):1932-6 (2006 Mar 31).

Instrument and Software Requirements
GeneChip Scanner 3000 7G
GeneChip Operating Software (GCOS) version 1.3 or higher

GeneChip™ Yeast Genome 2.0 Array (Applied Biosystems™)

The GeneChip™ Yeast Genome 2.0 Array contains probe sets to detect transcripts from both Saccharomyces cerevisiae and Schizosaccharomyces pombe, which are the two most commonly studied species of yeast. Providing comprehensive coverage of both species, the GeneChip Yeast Genome 2.0 Array includes approximately 5,744 probe sets for 5,841 of the 5,845 genes present in S. cerevisiae and 5,021 probe sets for all 5,031 genes present in S. pombe.

The evolutionary divergence between S. cerevisiae and S. pombe over 500 million years ago caused enough sequence divergence between the two species to require selection of separate probe sets for all genes, even the closest cross-species orthologs. Because both species are included on a single array, the GeneChip Yeast Genome 2.0 Array provides a flexible and affordable platform for researchers studying S. cerevisiae, S. pombe, or both species.

The sequence information for this array was selected from public data sources GenBank™ (May 2004) and Sanger Center (June 2004) for the S. cerevisiae and S. pombe genomes, respectively. Probe sets on the array include 11 oligonucleotide pairs to detect each transcript.

GeneChip™ C. elegans Gene 1.1 ST Array Plate (Applied Biosystems™)

The GeneChip™ C. elegans Gene 1.1 ST Array Plate enables you to:
• Measure expression, across the entire gene, with higher resolution and accuracy than with classical 3'-biased microarray solutions
• Get accurate and reproducible data by using multiple independent measurements for each transcript
• Process up to 96 samples on a single array plate with the GeneTitan™ Instrument

Development of the Gene Expression Microarrays

Model and applied research organisms are valuable for comparative genomics research, evolutionary biology, and continue to play a critical role in deciphering the molecular mechanisms underlying human disease, and agricultural crop improvement. Gene 1.1 ST Array Plates have been developed for the analysis of a wide range of model and applied research organisms. These organisms are the latest additions to the growing family of Gene Expression Microarrays offering whole-transcript coverage. The Gene 1.1 ST Array Plates were designed in collaboration with influential researchers, such as Alan Archibald, Head of the Division of Genetics and Genomics at the Roslin Institute (Porcine Gene 1.1 ST Array design), Leonard Zon, Director of Stem Cell Research Program, and Yi Zhou, Genomic Core Director of the Stem Cell Research Program at Children's Hospital Boston and Harvard Medical School in Boston (Zebrafish Gene 1.1 ST Array design).

Key benefits
Highest transcript coverage — get confident expression measurements of well-annotated content with up to 26 probes per transcript
Whole-transcriptome analysis — capture the transcript isoforms you may miss with 3'-biased expression designs
High data correlation — achieve high inter- and intra-array strip signal correlation (R >0.99)
Convenient format — process up to 96 samples at the same time with minimal manual array handling

Proven performance from the industry standard
Gene 1.1 ST Array Plates offer whole-transcriptome coverage for selected model and applied research organisms. All designs are based on the most recent genomic content and offer the highest probe coverage (up to 26 probes across the full length of the gene). This allows for accurate detection for whole-transcriptome microarray analysis and provides higher resolution and accuracy than other classical 3'-biased microarray solutions on the market. The whole-transcriptome analysis approach enables researchers to detect multiple transcript isoforms, including those that might be missed using a 3'-biased expression design, such as splice variants, non-polyadenylated transcripts, transcripts with alternative polyadenylation sites, and truncated transcripts.

Content profile
Gene 1.1 ST Array Plates provide the latest coverage of the transcribed genome. We use a comprehensive collection of information sources to design probes that interrogate up to 26 unique sequences of each transcript. Together these 26 unique 25-mer probes interrogate up to 650 bases per transcript. This high probe coverage across the entire transcript results in superior performance and data confidence as well as the ability to update your experimental data as the understanding of each genome and transcriptome grows.

GeneChip™ Drosophila (melanogaster) Gene 1.0 ST Array (Applied Biosystems™)

The GeneChip™ Drosophila (melanogaster) Gene 1.0 ST Arrays enable you to:
• Measure expression, across the entire gene, with higher resolution and accuracy than with classical 3'-biased microarray solutions
• Get accurate and reproducible data by using multiple independent measurements for each transcript

Background
Model and applied research organisms are valuable for comparative genomics research, evolutionary biology, and continue to play a critical role in deciphering the molecular mechanisms underlying human disease, and agricultural crop improvement. The GeneChip Gene 1.0 ST Arrays have been developed for the analysis of a wide range of model and applied research organisms. These organisms are the latest additions to the growing family of Gene Expression Microarrays offering whole-transcript coverage. The GeneChip Gene 1.0 ST Arrays were designed in collaboration with influential researchers, such as Alan Archibald, Head of the Division of Genetics and Genomics at the Roslin Institute (Porcine Array design), Leonard Zon, Director of Stem Cell Research Program, and Yi Zhou, Genomic Core Director of the Stem Cell Research Program at Children's Hospital Boston and Harvard Medical School in Boston (Zebrafish Array design).

Key benefits
Highest transcript coverage – get confident expression measurements of well-annotated content with up to 26 probes per transcript
Whole-transcriptome analysis – capture the transcript isoforms you may miss with 3'-biased expression designs
High data correlation – achieve high inter- and intra-array strip signal correlation (R >0.99)

Proven performance from the industry standard
GeneChip Gene 1.0 ST Arrays offer whole-transcriptome coverage for selected model and applied research organisms. All designs are based on the most recent genomic content and offer the highest probe coverage (up to 26 probes across the full length of the gene). This allows for accurate detection for whole-transcriptome microarray analysis and provides higher resolution and accuracy than other classical 3'-biased microarray solutions on the market. The whole-transcriptome analysis approach enables researchers to detect multiple transcript isoforms, including those that might be missed using a 3'-biased expression design, such as splice variants, non-polyadenylated transcripts, transcripts with alternative polyadenylation sites, and truncated transcripts.

Complete Reagents, Software and Instrumentation Solution for Optimal Array Performance
For convenience and complete support, the Gene 1.0 ST Array is provided as part of a comprehensive solution that includes GeneChip reagents and instrumentation:
• GeneChip WT Sense Target Labeling and Control Reagents. For detailed information on the procedure of the assay and performance information, please refer to the WT Sense Target Labeling Assay Manual
• GeneChip Fluidics Station 450 for complete walk-away array processing to obtain the highest levels of reproducibility
• GeneChip Scanner 3000 7G with the optional Autoloader for array image acquisition

We offer several tools to help you in your data analysis, including GeneChip Expression Console; software, the NetAffx Analysis Center, and the Integrated Genome Browser (IGB).

Expression Console Software is an easy-to-use application that enables probe set summarization as well as preliminary data quality evaluation. A simple workflow enables the user to quickly analyze the data (see figure). The resulting data can be further analyzed using software applications from GeneChip-compatible™ software providers.

The NetAffx Analysis Center, with regularly updated biological and functional annotations of probe sets, is the most comprehensive resource for array annotations and probe sequence information. Flexible query tools and external links allow researchers to drill down into genes and annotations of interest. This resource makes it easy to interpret microarray results and quickly design downstream studies.

Workflow
Researchers can also use IGB to visualize results in a genomic context. Genomic annotations including RefSeq sequences, SNPs and genomic locations from various sources can be viewed alongside microarray gene expression signal data.

The Gene 1.0 ST Array data analysis workflow is similar to the workflow for 3' gene expression analysis, utilizing Expression Console 1.1, third-party GeneChip-compatible software and annotation tools in the NetAffx Analysis Center and IGB.

Content profile
GeneChip Gene 1.0 ST Arrays provide the latest coverage of the transcribed genome. We use a comprehensive collection of information sources to design probes that interrogate up to 26 unique sequences of each transcript. Together these 26 unique 25-mer probes interrogate up to 650 bases per transcript. This high probe coverage across the entire transcript results in superior performance and data confidence as well as the ability to update your experimental data as the understanding of each genome and transcriptome grows.