FFPE RNA Extraction and Sequencing

Total RNA was extracted from FFPE slices using the RNeasy FFPE kit (Qiagen) and the manufacture’s protocol. Synthesis of cDNA and library preparation were performed using the SMARTer Universal Low Input RNA Kit for Sequencing (Clontech) and the Ion Plus Fragment Library Kit (ThermoFisher) as previously described [10 (link), 31 (link), 32 (link)]. Sequencing was performed using the Ion Proton S5/XL systems (ThermoFisher) in the Analytical and Translational Genomics Shared Resource at the UNM Comprehensive Cancer Center. RNA sequencing data is available for download from the NCBI BioProject database using study accession number PRJNA940178.

Free full text: Click here

Brayer K.J., Hanson J.A., Cingam S., Martinez C., Ness S.A, & Rabinowitz I. (2023). The inflammatory response of human pancreatic cancer samples compared to normal controls. PLOS ONE, 18(11), e0284232.

Publication 2023

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

Cancer Cdna Library Proton Synthesis Translational

Corresponding Organization : University of New Mexico

Top 5 similar protocols

Variable analysis

independent variables

FFPE slices
RNA extraction using RNeasy FFPE kit (Qiagen)
CDNA synthesis and library preparation using SMARTer Universal Low Input RNA Kit for Sequencing (Clontech) and Ion Plus Fragment Library Kit (ThermoFisher)

dependent variables

RNA sequencing data

control variables

Manufacturer's protocol for RNeasy FFPE kit
Previously described methods for cDNA synthesis and library preparation [10, 31, 32]
Ion Proton S5/XL systems (ThermoFisher) for sequencing

controls

No positive or negative controls explicitly mentioned

Annotations

Based on most similar protocols

Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.

As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!