5. Byron SA, Van Keuren-Jensen KR, Engelthaler DM, Carpten JD, Craig DW. Translating RNA
sequencing into clinical diagnostics: opportunities and challenges. Nat Rev Genet. 2016;17
(5):257–71.
6. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev
Genet. 2009;10(1):57–63.
7. Becker-Andre M, Hahlbrock K. Absolute mRNA quantification using the polymerase chain
reaction (PCR). A novel approach by a PCR aided transcript titration assay (PATTY). Nucleic
Acids Res. 1989;17(22):9437–46.
8. Hoheisel JD. Microarray technology: beyond transcript profiling and genotype analysis. Nat Rev
Genet. 2006;7(3):200–10.
9. Bumgarner R. Overview of DNA microarrays: types, applications, and their future. Curr Protoc
Mol Biol. 2013;101:22-1.
10. Russo G, Zegar C, Giordano A. Advantages and limitations of microarray technology in human
cancer. Oncogene. 2003;22(42):6497–507.
11. Zhao S, Fung-Leung WP, Bittner A, Ngo K, Liu X. Comparison of RNA-Seq and microarray in
transcriptome profiling of activated T cells. PLoS One. 2014;9(1):e78644.
12. Schuierer S, Carbone W, Knehr J, Petitjean V, Fernandez A, Sultan M, et al. A comprehensive
assessment of RNA-seq protocols for degraded and low-quantity samples. BMC Genomics.
2017;18(1):442.
13. Holik AZ, Law CW, Liu R, Wang Z, Wang W, Ahn J, et al. RNA-seq mixology: designing
realistic control experiments to compare protocols and analysis methods. Nucleic Acids Res.
2017;45(5):e30.
14. Kukurba KR, Montgomery SB. RNA sequencing and analysis. Cold Spring Harb Protoc.
2015;2015(11):951–69.
15. Scholes AN, Lewis JA. Comparison of RNA isolation methods on RNA-Seq: implications for
differential expression and meta-analyses. BMC Genomics. 2020;21(1):249.
16. Ali N, Rampazzo RCP, Costa ADT, Krieger MA. Current nucleic acid extraction methods and
their implications to point-of-care diagnostics. Biomed Res Int. 2017;2017:9306564.
17. Gallego Romero I, Pai AA, Tung J, Gilad Y. RNA-seq: impact of RNA degradation on transcript
quantification. BMC Biol. 2014;12:42.
18. Bivens NJ, Zhou M. RNA-Seq library construction methods for transcriptome analysis. Curr
Protoc Plant Biol. 2016;1(1):197–215.
19. Wang L, Felts SJ, Van Keulen VP, Pease LR, Zhang Y. Exploring the effect of library
preparation on RNA sequencing experiments. Genomics. 2019;111(6):1752–9.
20. Liu L, Li Y, Li S, Hu N, He Y, Pong R, et al. Comparison of next-generation sequencing
systems. J Biomed Biotechnol. 2012;2012:251364.
21. Kovaka S, Zimin AV, Pertea GM, Razaghi R, Salzberg SL, Pertea M. Transcriptome assembly
from long-read RNA-seq alignments with StringTie2. Genome Biol. 2019;20(1):278.
22. Hwang B, Lee JH, Bang D. Single-cell RNA sequencing technologies and bioinformatics
pipelines. Exp Mol Med. 2018;50(8):96.
23. Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, et al. A tale of three next
generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina
MiSeq sequencers. BMC Genomics. 2012;13:341.
24. Mohorianu I, Bretman A, Smith DT, Fowler EK, Dalmay T, Chapman T. Comparison of
alternative approaches for analysing multi-level RNA-seq data. PLoS One. 2017;12(8):
e0182694.
25. Andrews S. FASTQC. A quality control tool for high throughput sequence data. 2010.
26. Planet E, Attolini CS, Reina O, Flores O, Rossell D. htSeqTools: high-throughput sequencing
quality control, processing and visualization in R. Bioinformatics. 2012;28(4):589–90.
11 Design and Analysis of RNA Sequencing Data
171
sequencing into clinical diagnostics: opportunities and challenges. Nat Rev Genet. 2016;17
(5):257–71.
6. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev
Genet. 2009;10(1):57–63.
7. Becker-Andre M, Hahlbrock K. Absolute mRNA quantification using the polymerase chain
reaction (PCR). A novel approach by a PCR aided transcript titration assay (PATTY). Nucleic
Acids Res. 1989;17(22):9437–46.
8. Hoheisel JD. Microarray technology: beyond transcript profiling and genotype analysis. Nat Rev
Genet. 2006;7(3):200–10.
9. Bumgarner R. Overview of DNA microarrays: types, applications, and their future. Curr Protoc
Mol Biol. 2013;101:22-1.
10. Russo G, Zegar C, Giordano A. Advantages and limitations of microarray technology in human
cancer. Oncogene. 2003;22(42):6497–507.
11. Zhao S, Fung-Leung WP, Bittner A, Ngo K, Liu X. Comparison of RNA-Seq and microarray in
transcriptome profiling of activated T cells. PLoS One. 2014;9(1):e78644.
12. Schuierer S, Carbone W, Knehr J, Petitjean V, Fernandez A, Sultan M, et al. A comprehensive
assessment of RNA-seq protocols for degraded and low-quantity samples. BMC Genomics.
2017;18(1):442.
13. Holik AZ, Law CW, Liu R, Wang Z, Wang W, Ahn J, et al. RNA-seq mixology: designing
realistic control experiments to compare protocols and analysis methods. Nucleic Acids Res.
2017;45(5):e30.
14. Kukurba KR, Montgomery SB. RNA sequencing and analysis. Cold Spring Harb Protoc.
2015;2015(11):951–69.
15. Scholes AN, Lewis JA. Comparison of RNA isolation methods on RNA-Seq: implications for
differential expression and meta-analyses. BMC Genomics. 2020;21(1):249.
16. Ali N, Rampazzo RCP, Costa ADT, Krieger MA. Current nucleic acid extraction methods and
their implications to point-of-care diagnostics. Biomed Res Int. 2017;2017:9306564.
17. Gallego Romero I, Pai AA, Tung J, Gilad Y. RNA-seq: impact of RNA degradation on transcript
quantification. BMC Biol. 2014;12:42.
18. Bivens NJ, Zhou M. RNA-Seq library construction methods for transcriptome analysis. Curr
Protoc Plant Biol. 2016;1(1):197–215.
19. Wang L, Felts SJ, Van Keulen VP, Pease LR, Zhang Y. Exploring the effect of library
preparation on RNA sequencing experiments. Genomics. 2019;111(6):1752–9.
20. Liu L, Li Y, Li S, Hu N, He Y, Pong R, et al. Comparison of next-generation sequencing
systems. J Biomed Biotechnol. 2012;2012:251364.
21. Kovaka S, Zimin AV, Pertea GM, Razaghi R, Salzberg SL, Pertea M. Transcriptome assembly
from long-read RNA-seq alignments with StringTie2. Genome Biol. 2019;20(1):278.
22. Hwang B, Lee JH, Bang D. Single-cell RNA sequencing technologies and bioinformatics
pipelines. Exp Mol Med. 2018;50(8):96.
23. Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, et al. A tale of three next
generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina
MiSeq sequencers. BMC Genomics. 2012;13:341.
24. Mohorianu I, Bretman A, Smith DT, Fowler EK, Dalmay T, Chapman T. Comparison of
alternative approaches for analysing multi-level RNA-seq data. PLoS One. 2017;12(8):
e0182694.
25. Andrews S. FASTQC. A quality control tool for high throughput sequence data. 2010.
26. Planet E, Attolini CS, Reina O, Flores O, Rossell D. htSeqTools: high-throughput sequencing
quality control, processing and visualization in R. Bioinformatics. 2012;28(4):589–90.
11 Design and Analysis of RNA Sequencing Data
171