RNA Methodologies

Dr. Robert Farrell is a bench-current scientist who has 35 years of experience working with RNA in the study of transcriptional and posttranscriptional regulation of gene expression in a variety of model systems. He is also experienced in animal cell culture methods. Prior to joining the faculty at Penn State University, he operated a biotech education and service firm, winning the 1998 Small Business Contractor of the Year award from the U.S. Department of Agriculture. He is the recipient of campus- and college-wide awards for excellence in teaching, and has extensive experience running RNA and specialized biotechnology hands-on laboratory training programs all over the world. He often serves as a consultant within the pharmaceutical and biotech industries. Dr. Farrell received his Ph.D. and M.S. degrees from The Catholic University of America and his B.S. in Biology from Providence College. Dr. Farrell currently serves as the campus academic officer at Penn State York.

1. RNA and the cellular biochemistry revisited
2. Creating a ribonuclease-free environment 000
3. Stringency: conditions that influence nucleic acid structure
4. Ribonucleic acid isolation strategies
5. Isolation of polyadenylated RNA
6. The truth about tissues
7. Going green: RNA and the molecular biology of plants
8. Quality control for RNA preparations
9. cDNA: a permanent biochemical record of the cell
10. RT-PCR: a science and an art form
11. Quantitative polymerase chain reaction techniques
12. miRNA and other noncoding RNAs
13. RNA interference and gene editing
14. Electrophoresis of RNA
15. Photodocumentation and image analysis
16. Northern analysis
17. Nucleic acid probe technology
18. Quantification of specific mRNAs by nuclease protection
19. Analysis of nuclear RNA
20. RNA in situ hybridization
21. Array analysis of gene expression
22. Subtractive and nonsubtractive methods for the analysis of gene expression
23. Transcriptomes and bioinformatics
24. RNA-seq: the premier transcriptomics tool
25. RNA biomarker discovery and validation
26. Functional genomics strategies
27. A few RNA success stories
Epilogue
Appendix A: Maintaining complete and accurate records
Appendix B: Converting mass to moles
Appendix C: Removal of DNA from an RNA sample
Appendix D: Removal of RNA from a DNA sample
Appendix E: Electrophoresis: principles, parameters, and safety
Appendix F: Disposal of ethidium bromide and SYBR Green solutions
Appendix G: Deionization of formamide, formaldehyde, and glyoxal
Appendix H: Silanizing centrifuge tubes and glassware
Appendix I: Centrifugation as a mainstream tool for the molecular biologist
Appendix J: Dot blot analysis
Appendix K: Useful stock solutions for the molecular biologist
Appendix L: Genomes and proteomes
Appendix M: Common SI prefixes
Appendix N: Common abbreviations
Appendix O: Select suppliers of equipment, reagents, and services
Appendix P: Trademark citations
Glossary