Abstract
Transcriptomics, the study of RNA molecules, provides in-depth understanding of cellular functions and the genomic landscape of transcription. Transcriptomics refers to the study of all classes on RNA molecules including mRNA, tRNA, and siRNA. In this chapter, we specifically focus on mRNA, which encodes the protein-coding portion of the genomic DNA. We discuss the use of mRNA in annotation of genomes and in studying differential regulation of genes under experimental conditions.
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References
Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63. https://doi.org/10.1038/nrg2484
Wilhelm BT, Marguerat S, Watt S et al (2008) Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 453:1239–1243
Nagalakshmi U, Wang Z, Waern K et al (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320:1344–1349
Grigoriev IV, Nikitin R, Haridas S et al (2013) MycoCosm portal: gearing up for 1000 fungal genomes. Nucleic Acids Res 42(D1):D699–D704
Mortazavi A, Williams BA, McCue K et al (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628
Illumina, Inc. https://support.illumina.com/sequencing/sequencing_kits/truseq_stranded_mrna_ht_sample_prep_kit/documentation.html. Accessed 22 Aug 2017
Grabherr MG, Haas BJ, Yassour M et al (2011) Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat Biotechnol 29(7):644–652. https://doi.org/10.1038/nbt.1883
Kim D, Langmead B, Salzberg SL (2015) HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12:357–360. https://doi.org/10.1038/nmeth.3317
Li H, Handsaker B, Wysoker A et al (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics 25:2078–2079. https://doi.org/10.1093/bioinformatics/btp352
Liao Y, Smyth GK, Shi W (2014) featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30(7):923–930
Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:550
Simão FA, Waterhouse RM, Ioannidis P et al (2015) BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31(19):3210–3212. https://doi.org/10.1093/bioinformatics/btv351
Acknowledgments
The work conducted by the US Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported under Contract No. DE-AC02-05CH11231.
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Singan, V.R., Kuo, R.C., Chen, C. (2018). Fungal Transcriptomics. In: de Vries, R., Tsang, A., Grigoriev, I. (eds) Fungal Genomics. Methods in Molecular Biology, vol 1775. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7804-5_8
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DOI: https://doi.org/10.1007/978-1-4939-7804-5_8
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