Rather Fine Books

How can The Power and Versatility of RNA-SEQ in Laboratory Research be used as a companion text?

The author envisions the instructor selecting a publicly available set of RNA-seq samples appropriate to
the class. They can divide the samples among the students and ask them to run a variety of tools on
their assigned samples (i.e. FastQC, OptiType, HISAT2, StringTie, Arriba, Trinity, MMuFLR, etc.) using the
same set of parameters as the rest of the class. This will give each student experience with running the
tools without overtaxing the computer systems with the CPU intensive applications. Then the students
can share the output from all these programs with the rest of the class. From there it would be the
responsibility of each student to consolidate the output and analyze it, using examples from the book or
developing their own. They can compare their conclusions with those of the authors who published the
dataset. It is sure to provide each student with many wonderful “Eureka!” moments as they become
comfortable with the versatility of RNA-seq data and its value to the laboratory researcher.

Can CRISPR cause a transcription-induced chimera (TIC)?

Yes, it is possible, but not common. If there is a gene in close proximity to the start of the target gene
and transcribed in the opposite direction, it can happen. It is easy to detect the presence of the TIC
using Integrative Genomics Viewer (IGV). To avoid this type of unintended consequence, follow the
guidelines presented in Chapter 6 of The Power and Versatility of RNA-SEQ in Laboratory Research.

Have you used RNA-seq in parallel with mass spectrometry?

Yes, just recently, for both protein detection and phosphorylation status. I have found it quite
informative using the technique outlined in the Yang et al article Quantitative Analysis of Differential
Proteome Expression in Bladder Cancer vs. Normal Bladder Cells Using SILAC Method (PloS One 2015)
to look for significance in the protein changes, and then comparing those results back to the DEAPR
results covered in Chapter 10 of The Power and Versatility of RNA-SEQ in Laboratory Research.