RNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue using Amsbio’s ExpressArt FFPE Clear RNA Ready kit (Amsbio LLC, Cambridge, MA). One case was tested on the TruSight RNA Fusion Panel (Illumina, San Diego, CA), using 100 ng total RNA for RNA-sequencing libraries preparation.9 (link) Fragment length was assessed with an RNA 6000 chip on an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA). The sample was subjected to targeted RNA sequencing on an Illumina MiSeq at eight samples per flow cell (~3 million reads per sample). All reads were independently aligned with STAR (version 2.3) and BowTie2 against the human reference genome (hg19) for Manta-Fusion and TopHat-Fusion analysis, respectively. The second case was tested by Anchored Multiplex RNA sequencing assay using the Archer FusionPlex Solid tumor Kit (Archer, Boulder, CO).10 (link) Anchored Multiplex polymerase chain reaction amplicons were sequenced on Illumina MiSeq, and the data were analyzed using the Archer software.
Protocol detail
FFPE RNA Sequencing for Fusion Analysis
Partial Protocol Preview
This section provides a glimpse into the protocol.
The remaining content is hidden due to licensing restrictions, but the full text is available at the following link:
Access Free Full Text.
Anchored polymerase chain reaction
Assay
Cell
Chip
Embedded paraffin
Formalin
Genome human
Multiplex polymerase chain reaction
Paraffin
Tumor
Corresponding Organization : Memorial Sloan Kettering Cancer Center
Other organizations : Mount Sinai Hospital
Top 5 similar protocols
Variable analysis
independent variables
- RNA extraction method (Amsbio's ExpressArt FFPE Clear RNA Ready kit)
- RNA-sequencing library preparation method (TruSight RNA Fusion Panel, Archer FusionPlex Solid tumor Kit)
- Sequencing platform (Illumina MiSeq)
- Presence and identification of RNA fusions
- Total RNA input amount (100 ng)
- Fragment length assessment (RNA 6000 chip on Agilent Bioanalyzer)
- Bioinformatics analysis methods (STAR, BowTie2, Manta-Fusion, TopHat-Fusion, Archer software)
- Positive control: Not explicitly mentioned
- Negative control: Not 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.
Sign up for free or login to display all annotations
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?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!