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. 2024:2822:245-262.
doi: 10.1007/978-1-0716-3918-4_17.

Short-Read RNA-Seq

Rong Hu  1 , Md N Islam  1 , Rency S Varghese  1 , Habtom W Ressom  2
Affiliations

Short-Read RNA-Seq

Rong Hu et al. Methods Mol Biol. 2024.

Abstract

RNA sequencing (RNA-Seq) has emerged as a powerful and versatile tool for the comprehensive analysis of transcriptomes and has been widely used to investigate gene expression, copy number variation, alternative splicing, and novel transcript discovery. This chapter outlines the methodology for conducting short-read RNA-Seq, starting from RNA enrichment to library preparation and sequencing. Throughout the chapter, practical tips and best practices are provided to guide researchers in order to optimize each step of the RNA-Seq workflow. Multiple quality control steps throughout the workflow that are critical to obtain high-quality RNA-Seq data are also discussed.

Keywords: Library preparation; RNA-Seq; Short-read sequencing.

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References

    1. Bainbridge MN, Warren RL, Hirst M et al (2006) Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach. BMC Genomics 7:246 - DOI - PubMed - PMC
    1. Nagalakshmi U, Wang Z, Waern K et al (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320:1344 - DOI - PubMed - PMC
    1. Wilhelm BT, Marguerat S, Watt S et al (2008) Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 453:1239 - DOI - PubMed
    1. Oshlack A, Robinson MD, Young MD (2010) From RNA-seq reads to differential expression results. Genome Biol 11:220 - DOI - PubMed - PMC
    1. Martin JA, Wang Z (2011) Next-generation transcriptome assembly. Nat Rev Genet 12:671 - DOI - PubMed

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