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To determine how a specific gene is covered by the Mouse Diversity Genotyping Array, please visit the NetAffx Analysis Center. Query the gene of interest in the genotyping search field and select the Mouse Diversity Array to return the list of SNPs and their annotations to the gene.

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Yes.

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Our experts do not recommend running samples from species other than the one the GeneChip expression array was designed for. Although high homology may exist between species, the sequence differences may be sufficient to interfere with hybridization, and more importantly, data interpretation.

Although we have not validated the use of the GeneChip expression arrays with alternate species, some customers have explored this approach. The following article is an example of this type of study:

Kayo, T., Allison, D.B., Weindruch, R., and Prolla, T.A. Influences of aging and caloric restriction on the transcriptional profile of skeletal muscle from rhesus monkeys. Proceedings of the National Academy of Sciences of the USA. 98:5093-5098, 2001

Please Note: This reference is listed for the convenience of our customers and is not endorsed or supported by the company.

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For a whole chromosome or a region, go to the Graphs tab in ChAS 3.x and use the “copy to clipboard” or “export to txt” functions.

For the whole genome, using ChAS 2.1 or later versions, go to the analysis manager/analysis dashboard and select the “QC results” tab. Then open and/or select the file(s) to export, press the “Generate Report” button, and select the “Export probe level data function.” Data will be exported in .txt format.

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Approximately 190 unprocessed human microRNA sequences from the Sanger MicroRNA Registry are represented on this array. Although the probe sets are present, the current WT Sense Target Labeling Assay has not been tested or optimized to efficiently label the very small RNA molecules. Therefore, the utility of the system to measure microRNA expression is uncertain at this moment.

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It takes approximately 35 minutes to scan each Exon Array.

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In many cases the Genechip probes do overlap quite heavily. Multiple probes, although overlapping, are utilized as they still provide separate physical measures of expression and add to the robustness of the platform. Care was taken to ensure that probes from the same probe set, however similar in sequence composition, are spatially separated on the array. In addition, the annotation library file contains information regarding how many independent probes there are, as well as the number of nonoverlapping probes, in each probe set. Independent probes are defined as those that have less or equal to 13 base overlaps with other probes in the probe set. This information provides additional insight and may be helpful to users when interpreting unexpected results.

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We provideTranscriptome Analysis Console Software for normalization, summarization,  differential expression analysis and visualization free of charge. Due to the presence of multiple organisms on the miRNA arrays, the chromosomal location feature in Transcriptome Analysis Console Software will not give accurate results.

For analysis in Transcriptome Analysis Console Software, array type-specific configuration and annotation files are required. Use the “Download Array Type Files” button in the Preferences tab to download and install array type-specific library files.

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If metric and control information is not included in the header of the CHP file, Expression Console Software will not display that information. This occurs for two reasons: (1) an application other than Expression Console Software created the CHP file and did not write the information to the header or (2) the control probes were not identified prior to the analysis run and were not included in the header. To solve this issue in either case, rerun the analysis within Expression Console Software.

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QC Call Rate is available for the 100K Set, 500K Array Set, and the SNP Array 5.0. Contrast QC (recommended) and QC Call Rate is available for the SNP Array 6.0.

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The Human Genome U133 (HG-U133) Set, consisting of two GeneChip arrays, contains almost 45,000 probe sets representing more than 39,000 transcripts derived from approximately 33,000 well-substantiated human genes.

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The Two-Cycle cDNA Synthesis Kit contains all necessary reagents (see the following table) to carry out the two cycles of cDNA synthesis for thirty samples. Note that the reagents for the intermediary in vitro transcription (IVT) amplification using un-labeled ribonucleotides, between the two cDNA synthesis reactions, is not included in the kit. The Ambion MEGAscript T7 Kit is recommended.

Component Name: Concentration: Volume: Quantity
T7-Oligo(dT) Primer, 50 µM: 50 µM: 120 µL: 1
5X 1st Strand Reaction Mix: 5X: 180 µL: 1
DTT, 0.1M: 0.1M: 90 µ:L 1
dNTP, 10 mM: 10 mM: 200 µL: 1
SuperScript II: 200 U/µL: 60 µL: 1
RNase Inhibitor: 40 U/µL: 45 µL: 1
5X 2nd Strand Reaction Mix: 5X: 900 µL: 1
Random Primers: 3 µg/µL: 60 µL: 1
MgCl2, 1M: 1M: 60 µL: 1
E.coli DNA Polymerase I: 10 U/µL: 200 µL: 1
RNase H: 2 U/µL: 55 µL: 1
T4 DNA Polymerase: 5 U/µL: 60 µL: 1
RNase-free Water: n/a: 9.5 mL: 1

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Using cRNA generated from the IVT reaction at the end of the first cycle of the assay as a template, single-stranded DNA is synthesized using random primers and the dUTP + dNTP mix. The resulting single-stranded DNA (ss-DNA) containing the unnatural uracil base is then treated with Uracil DNA Glycosylase, which specifically removes the uracil residue from the ss-DNA molecules. In the same reaction, the APE 1 enzyme then cleaves the phosphodiester backbone where the base is missing, leaving a 3'-hydroxyl and a 5'-deoxyribose phosphate terminus.

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For Genotyping, in general more samples are better for SNP calling; 44 unique samples per batch is recommended.
For Copy Number, there is no minimum sample requirement since the analysis is a single analysis meaning they are analyzed one by one.

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Betaine increases the hybridization stringency. It equalizes the GC Tm and AT Tm, so the background, non-specific, non-rRNA hybridization to the RiboMinus probes due to high GC content may be reduced.

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