GeneChip™ Human Transcriptome Array 2.0, 10 arrays - FAQs

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

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The GeneChip Human Transcriptome Assay 2.0 takes approximately 35 min to scan.

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Sometimes, there are transcript clusters in the GeneChip Human Transcriptome Array (HTA) 2.0 with multiple associated gene symbols, and it appears that the probes in the cluster span multiple adjacent/overlapping genes.

For example: The transcript TC04000948.hg.1 is associated with the gene symbols ABCA11P//ZNF721 in the GeneChip HTA 2.0 annotation file. This is one of those infrequent cases where multiple genes will co-exist in the same location. In this particular case, one of them is a zinc-finger protein, and the other one is a pseudogene. Pseudogenes are often defined as "not having any known function" or "not expressed". However, as the knowledge of biology progresses, the definition of "function" changes and it may be found that these do have function, just that it is not known. Pseudogenes occasionally are transcribed, and sometimes, they are just artifacts of ancient or recent duplication events.

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HTAv1, also known as Glue Grant Human Transcriptome Array (GG-H), is a custom array made in collaboration with Stanford Genome Technology, Wing Wong's lab at Stanford, and the Inflammation and Host Response to Injury program (“Glue Grant”). The array was designed to interrogate gene expression, alternative splicing, detection of coding SNPs and non-coding transcription. Permissions from the group are required to use this array. HTA 2.0 is one of our catalog arrays. This array follows a similar design as the HTAv1 but focus on the whole transcript gene expression and alternative splicing of coding and non-coding transcripts. We provide assay and software for the processing and analysis of this array.

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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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