Targeted Gene Expression Profiling

Genome-wide targeted amplicon amplification was performed using the Ion AmpliSeq™ Transcriptome Human Gene Expression Kit (Thermo-Fisher, Ottawa, ON, Canada). Total RNA (100 ng) was used to prepare the libraries as per manufacturer’s protocol and described elsewhere [36 (link)]. Prepared libraries were quantified using the Ion Library TaqMan Quantitation kit (Thermo-Fisher, Ottawa, ON, Canada) and then the RNA concentration was adjusted to 100 pM. An Ion Chef instrument (Thermo-Fisher, Ottawa, ON, Canada) was used for loading of Ion 540 chips (Thermo-Fisher, Ottawa, ON, Canada) after which sequencing was performed on an Ion S5 sequencer (Thermo-Fisher, Ottawa, ON, Canada).

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Airo A.M., Felix-Lopez A., Mancinelli V., Evseev D., Lopez-Orozco J., Shire K., Paszkowski P., Frappier L., Magor K.E, & Hobman T.C. (2022). Flavivirus Capsid Proteins Inhibit the Interferon Response. Viruses, 14(5), 968.

Publication 2022

Ion AmpliSeq™ Transcriptome Human Gene Expression Kit Ion Library TaqMan Quantitation kit Ion Chef instrument Ion 540 chips Ion S5 sequencer

Chips Gene expression Genome Human Library Pm 100 Transcriptome

Corresponding Organization : University of Alberta

Other organizations : University of Toronto

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Variable analysis

independent variables

Genome-wide targeted amplicon amplification using the Ion AmpliSeq™ Transcriptome Human Gene Expression Kit

dependent variables

Gene expression

control variables

Total RNA input (100 ng)
Library preparation following manufacturer's protocol
Library quantification using the Ion Library TaqMan Quantitation kit
RNA concentration adjustment to 100 pM
Ion Chef instrument for loading Ion 540 chips
Sequencing on an Ion S5 sequencer

controls

No positive or negative controls were explicitly mentioned in the provided information.

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