GeneChip™ Human Exon 1.0 ST Array, 30 arrays - FAQs

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10 product FAQs found

Are pseudogene databases included in the design of expression arrays?

Pseudogene databases were not included in the design of expression arrays.

How long can I store labeled cDNA when working with expression microarrays?

Labeled material can be stored for 2 weeks at -20 degrees C.

What is the scan time for GeneChip Human Exon 1.0 ST Array?

The scan time for GeneChip Human Exon 1.0 ST Array is 35 min.

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For my GeneChip Human Exon 1.0 St Array, how can I find the probe set location on the genome?

The probe set start and stop locations can be found in the following downloadable annotation file for the array: http://www.affymetrix.com/Auth/analysis/downloads/na32/wtexon/HuEx-1_0-st-v2.na32.hg19.probeset.csv.zip
Additionally, the following sequence file can be used to get the coordinates for the probes: http://www.affymetrix.com/Auth/analysis/downloads/na25/wtexon/HuEx-1_0-st-v2.probe.tab.zip

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Why is Detection Above Background (DABG) only available on Exon array?

DABG is statistical algorithm that assumes that each probe in the probe set is used. If each probe is not used, the statistics are skewed or biased to create a false negative situation. A transcript-level probe set on a WT array consists of all possible exon probe sets for that isoform and some may not be used due to alternative splicing. For this reason, it is always appropriate to determine if an exon is detectable. It is not always appropriate to assume all exon probe sets at the transcript level are detectable.

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Is the protocol same for Exon 1.0 St and Gene 1.0 St arrays?

The protocols for the Gene 1.0 ST and Exon 1.0 ST arrays are the same until the fragmentation and labeling steps.
Depending on the input amount, please refer to the GeneChip WT Pico Reagent Kit or the GeneChip WT PLUS Reagent Kit for the protocol:
- WT Pico: 50 - 500ng of total RNA
- WT PLUS: ≥ 100pg of total RNA (approx. 10 cells)
From the hybridization step onwards, the differences in protocol are due to the format of the arrays. The Exon array is a 49 format array, whereas the Gene 1.0 ST array is a 169 format array.
For the fluidics step the following scripts should be used depending upon which array you are using:
- Gene 1.0 St array: FS450_0001
- Exon 1.0 St array: FS450_0007

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How is this array design principle different from the GeneChip Human Genome U133 type of arrays?

The GeneChip Exon Arrays represent a new array design philosophy for the most comprehensive and informative coverage with the exon as the basic unit of expression analysis. Such an inclusive design enables discovery of new and novel splicing events not previously observed experimentally. Some of the key differences are summarized below using the human arrays as an example; refer to the “GeneChip Exon Array Design” Technical Note and the “Design and Performance of the GeneChip Human Genome U133 Plus 2.0 and Human Genome U133A 2.0 Array” Technical Note for more details.

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Can I compare Exon Array results with those obtained on the GeneChip Human Genome U133 (HG-U133) Array?

Signal and detection values from the exon arrays cannot be directly compared to that of the HG-U133 arrays. Major differences in array design and assay prevent meaningful comparisons at the signal level. Splice variation and polyadenylation variation can confound comparisons at the biological level (i.e., direction of change) due to differences in probe placement and bias in the target preparation assays.

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What Fluidics protocol do I use for the GeneChip Human Exon Array?

A new Fluidics Protocol has been developed for this assay, FS450_0001.

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Why is there no pre-hybridization step for the arrays using the targets from the WT Assay?

The pre-hybridization step was required for the 3' target in the GeneChip IVT Assays.

No pre-hybridization step is necessary for the WT targets. There are many differences between the WT targets and the 3' targets in terms of the nature of the molecules (DNA vs. RNA), as well as labeling molecule and hybridization cocktail makeup. It has been found that pre-hybridization is not necessary for the WT targets.

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