Clariom™ D Array, mouse, 2 arrays - FAQs

查看更多产品信息 Clariom™ D Array, mouse - FAQs (902511, 902512)

9 个常见问题解答

What reagent kit should I use with my array?

Please refer to the Microarray Reagent Guide for Arrays and Expression Kits to match the correct reagents your array.

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Which fluidics script should I run with Clariom D arrays?

We recommend using Fluidics Script FS450_0001 for Clariom D arrays (Human, Mouse, Rat).

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Why is it important to use Tough-Spots® labels when using GeneChip cartridge arrays?

Tough-Spots® labels are small adhesive stickers used to temporarily seal the backs of cartridge arrays during the overnight hybridization step. They are required to prevent loss of volume due to evaporation through the septa. We recommend using Tough-Spots® labels on Rolls from USA Scientific (Item No. 9185-0000)

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What are the respective hybridization volumes based on array format for Affymetrix gene expression arrays?

Proper hybridization volume is critical to obtaining an even signal across a given array. Too little volume can lead to black circles in the middle of the array. Too much volume can leak out of the back of the array. The correct hybridization volume leaves enough room for a small air bubble to circulate around the array surface during the overnight hybridization. Here are the recommended hybridization and fill volumes based on the array format:
Array Format; Hybridization Volume; Fill Volume
- 49 Format (Standard); 200 µL; 250 µL
- 64 Format; 200 µL; 250 µL
- 100 Format (Midi); 130 µL; 160 µL
- 169 Format (Mini); 80 µL; 100 µL
- 400 Format (Micro); 80 µL; 100µL

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How are transcript IDs assigned for WT arrays if a gene has multiple transcript IDs?

The first assigned mRNA/gene that is listed in the annotation file for a given probe set or transcript cluster is considered the "best" assignment based on data source quality ranking and assignment scoring system. To get a single best mRNA/gene assignment you can simply take the first one in the list in the annotation file.

Sometimes, there might be multiple best hits between transcript clusters (or probe set) and a mRNA/gene, with identical score and data source quality. In that case, the transcript assignments are ranked based on their descriptions (e.g., title from the GenBank record).

For transcript clusters that detect genes that are alternatively spliced, the different spliced forms will be ranked by length with the longest ones listed first.

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Why do Clariom D arrays require a WT reagent for target preparation in order to deliver alternative splicing data?

WT Pico and WT Plus reagent generate single stranded (ss)-cDNA targets for hybridization onto arrays; this is what makes the kit "strand-specific". The use of ss-cDNA labeled target with arrays that provide alternative splicing information results in better data quality where probes may detect RNA transcribed from both the (+) and (-) DNA strands.

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Why do Clariom S arrays use the (IVT) Pico kit, but Clariom D arrays use the WT Pico kit for challenging samples?

The GeneChip WT Pico kit is a strand-specific reagent, which must be used with Clariom D (and HTA 2.0) to obtain strand-specific information as these arrays having probes on regions overlapping from both strands. Strand-specificity is important for identifying antisense transcripts, determining the transcribed strand of ncRNAs, and demarcating the boundaries of closely situated or overlapping genes.
Strand-specificity is less important for gene-level expression analysis (i.e., when using Clariom S). Probes within regions of overlapping transcription from both strands are avoided in the Clariom S array design; i.e., the array is "stranded" meaning it does not necessarily need a strand-specific reagent kit.

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Which fluidics script should I use with Clariom D and Clariom S arrays?

For the Clariom D arrays, we recommend using the FS450_0001, which is a 49 format array.
For the Clariom S arrays, we recommend using the FS450_0007, which is a 400 format array.

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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.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.