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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What is an example of using ERCC controls in the PrimeView Human Gene Expression Array?
The following link is an example of how the ERCC control probes on the Primeview Human Gene Expression Array can be used: https://pubmed.ncbi.nlm.nih.gov/23101621/.
Please note that the ERCC controls, while tiled on the array itself, are not visible in the commercial library files. A CDF file does exist with these made visible, however. Please contact Technical Support to access a copy of this.
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Does the GeneChip miRNA 3.1 Array Strip require a different hyb/wash/stain kit than the GeneChip 3' IVT arrays and GeneChip ST array strips?
The hyb/wash/stain kit for the GeneChip miRNA 3.1 Array Strips is different than that for the 3' IVT arrays and GeneChip ST array strips. Additional wash A steps have been added to ensure adequate washing after the array strips have been stained.
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Are the PrimeView Human Genome U219 Array Strip and PrimeView Human Genome U219 Array Plate the same as the PrimeView Human Gene Expression Array?
Yes, the PrimeView Human U219 Array and the Primeview Human Gene Expression Array are indeed the same array (including strip and plate).
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