FFPE RNA Sequencing Protocol

Total RNA was isolated from one or two 5-micron slide-mounted FFPE sections using the RNeasy FFPE kit (Qiagen). cDNA synthesis and library preparation were performed using the SMARTer Universal Low Input RNA Kit for Sequencing (Clontech) and the Ion Plus Fragment Library Kit (Life Technologies) as previously described [17 (link)]. Sequencing was performed using the Ion Proton and Ion S5/XL systems (Life Technologies) in the Analytical and Translational Genomics Shared Resource at the University of New Mexico Comprehensive Cancer Center. RNA sequencing data is available for download from the NCBI BioProject database using study accession number PRJNA287156.

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Frerich C.A., Brayer K.J., Painter B.M., Kang H., Mitani Y., El-Naggar A.K, & Ness S.A. (2017). Transcriptomes define distinct subgroups of salivary gland adenoid cystic carcinoma with different driver mutations and outcomes. Oncotarget, 9(7), 7341-7358.

Publication 2017

RNeasy FFPE kit SMARTer Universal Low Input RNA Kit for Sequencing Ion Plus Fragment Library Kit Ion Proton Ion S5/XL

Cancer Cdna Library Proton Synthesis Translational

Corresponding Organization : New Mexico Cancer Center

Other organizations : The University of Texas MD Anderson Cancer Center

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Variable analysis

independent variables

RNA isolation method (RNeasy FFPE kit)
CDNA synthesis and library preparation method (SMARTer Universal Low Input RNA Kit for Sequencing, Ion Plus Fragment Library Kit)
Sequencing platform (Ion Proton and Ion S5/XL systems)

dependent variables

RNA sequencing data

control variables

Number of 5-micron slide-mounted FFPE sections (one or two)
Location of experiment (Analytical and Translational Genomics Shared Resource at the University of New Mexico Comprehensive Cancer Center)

controls

Positive control: Not specified
Negative control: Not specified

Annotations

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