Perform QIAseq UPXome RNA Gene Expression (ODT-RT primer)
The Perform QIAseq UPXome RNA Gene Expression (ODT-RT primer) template workflow supports reads captured using the ODT-RT primer protocol, where a tag of TTTV is used to capture a fragment. The short length of the polyT tag enables capture of exons as well as the polyA tail. This can be an advantage for low input samples or exosomes where exon usage can be of interest. Note that a 3' bias is not necessarily expected in the data, and only around 50% of reads may map to exons (though this depends on the sample).
The workflow provides two main outputs. The gene expression tracks, which can be used for conducting differential expression analysis, and the Genome Browser View of the mappings, useful for investigating exon usage. Note, however, that although the protocol can be used for differential expression analysis (preferably between samples with similar levels of input RNA), it does not allow for analysis of RNA abundance. This is because the measured expression is higher for genes with more polyT regions.
The Perform QIAseq UPXome RNA Gene Expression (ODT-RT primer) workflow can be found here:
Template Workflows | Biomedical Workflows (
) | QIAseq Sample Analysis (
) | QIAseq RNA Workflows (
) | Perform QIAseq UPXome RNA Gene Expression (ODT-RT primer) (
)
Or run directly from the Analyze QIAseq Samples guide:
Template Workflows | Biomedical Workflows () | QIAseq Sample Analysis () | Analyze QIAseq Samples (
)
where it is available in the the UPXome RNA tab, under QIAseq UPXome Library Kit, and setting analysis to ODT-RT primer.
The workflow is identical to the Perform QIAseq FastSelect RNA Gene Expression (ODT-RT primer) workflow described in Perform QIAseq FastSelect RNA Gene Expression (ODT-RT primer). The only difference is that the Perform QIAseq UPXome RNA Gene Expression (ODT-RT primer) workflow starts by demultiplexing the input into samples that correspond to plate wells.
The workflow is run as described in Running the QIAseq UPXome workflows.
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