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GeneChip^® HT Rat Focus Array Plate

HT Array Plate

The GeneChip® HT Rat Focus Array Plate enables researchers to perform large-scale studies by analyzing whole-genome expression for as many as 96 rat samples at a time. Each plate contains 24 or 96 individual HT Rat Focus Arrays measuring gene expression levels for the 16,000 best characterized genes found on the Rat Genome 230 2.0 Array; probe sets found on the HT Rat Focus Array are a subset of those found on the Rat Genome 230 2.0 Array.

The throughput and automated processing of the multi-array plates increases cost-efficiency and accelerates large-scale rat studies by:

Reducing labor costs and time of analysis
Increasing standardization within and across sites
Simplifying management of running multiple microarrays in parallel

Scientists are using the Rat Focus HT Array Plates to generate expression data in large-scale studies including toxicology, neurobiology and other research using the rat as a model organism.

Analyze up to 96 rat samples at a time
Measure gene expression of more than 16,000 well-substantiated rat genes for each sample
Get accurate and reproducible data by using multiple, independent measurements for each transcript, with more than 24,000 probe sets per array

Array Plate Design

Each array plate consists of 96 appendages, to which as many as 96 individual microarrays can be attached. The plates are constructed to be spatially compatible with conventional 96-well plate formats and liquid-handling equipment. This configuration is designed to address the needs of large-scale experiments by greatly simplifying the management of multiple microarrays run in parallel, reducing labor costs and enabling increased standardization within studies and across sites. For each plate, two plate configurations are offered:

24-Array Plate – 24 HT Rat Focus Arrays are positioned on a single plate of 24 arrays for simultaneous processing and analysis
96-Array Plate – 96 HT Rat Focus Arrays are positioned on a single plate of 96 arrays

Content Profile

Probe sets on the GeneChip® HT Rat Focus Array Plate are a subset of those present on the cartridge format Rat Genome 230 2.0 Array. Probe sets for the best characterized genes were prioritized for inclusion on the Rat Focus Array Plate based upon a number of different criteria, including overlap of the probe set target sequence to annotated full-length mRNAs, EnsGene-predicted mRNAs, UniGene clusters containing at least one full-length mRNA or human and mouse full-length mRNA syntenic alignments on the rat genome.

Oligonucleotide probes complementary to each corresponding sequence are synthesized in situ on the arrays. Similar to the cartridge format arrays, 11 pairs of oligonucleotide probes are used to measure the transcription level of each sequence represented on the GeneChip® Rat Focus HT Array Plate.

Data Sheets

HT Array Replacement Guideline (pdf, 179 KB)

Rat Genome 230 2.0 Arrays and HT Rat Focus Array Plates (pdf, 1.0 MB)

White Papers

HT and Cartridge IVT Expression Arrays (pdf, 601 KB)

Performance Evaluation of the GeneChip® HT Array Plate Scanner (pdf, 1.96MB)

GeneChip^® HT Rat Focus Array Plates

Part #	Description	Details
900975	GeneChip® HT Rat Focus 24-Array Plate	Contains 4 HT Rat Focus 24-Array Plates
900974	GeneChip® HT Rat Focus 96-Array Plate	Contains 1 HT Rat Focus 96-Array Plate

GeneChip^® HT Rat Focus Array Plates with Reagents

Part #	Description	Details
900977	GeneChip® HT Rat Focus 24-Array Plate with Reagents*	Contains 4 HT Rat Focus 24-Array Plates Contains 1 HT One-Cycle Target Labeling and Controls Kit, 96 Reactions

GeneChip^® HT Rat Focus 96-Array Plate with Reagents*

Part #	Description	Details
900976	GeneChip® HT Rat Focus 96-Array Plate with Reagents*	Contains 1 HT Rat Focus 96-Array Plate Contains 1 HT One-Cycle Target Labeling and Controls Kit, 96 Reactions
	* All trays necessary for array plate processing are included with HT Plates listed above.

Required Products

Part #	Description	Details
900686	GeneChip® HT One-Cycle Target Labeling and Controls Kit	Sufficient for 96 reactions
00-0162 00-0235	GeneChip® Array Station	See Product Page
00-0332	GeneChip® HT Array Plate Scanner	See Product Page
	GeneChip® HT Software Suite	Composed of: GeneChip® Operating Software (GCOS) v1.2 or higher HT Image Reader HT Data Transfer Tool

Related Products

Part #	Description	Details
	Assays and Reagents	See Product Page

FAQs

Gene Expression Arrays

Manuals

Expression Analysis Technical Manual For HT Array Plates Using the GeneChip® Array Station (pdf, 7.4 MB)

Probe Set Data in MAGE-ML Format

Library Files

HT Rat-Focus Array (zip, 14 MB)

Alignment, Annotation, and Sequence Files

Information about using Alignment, Annotation, and Sequence files

Current NetAffx Annotation Files

HT_Rat-Focus Annotations, CSV format (7.4 MB, 3/12/09)

HT_Rat-Focus Annotations, MAGE-ML XML Format (35 MB, 3/12/09)

HT_Rat-Focus BLASTP annotations, CSV Format (1.7 KB, 3/4/09)

HT_Rat-Focus Orthologs/Homologs, CSV Format (5.9 MB, 3/12/09)

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.