Transcriptome Profiling Strategies

Abdullah M. Khamis, Vladimir B. Bajic, Matthias Harbers

Research output: Chapter in Book/Report/Conference proceedingChapter


With the rapid development of high-speed DNA sequencing technologies, it became feasible to sequence deeply into cDNA libraries prepared from RNA samples. Such cDNA libraries can benefit from the development of full-length cDNA cloning technologies providing means to obtain sequence information on the entire RNA transcripts or their selected 5′ end. Comprehensive overviews on transcriptomes can be obtained today by combination of those new sequencing technologies with large-scale cDNA library preparation forming the basis to different approaches for transcriptome profiling. In this chapter, we describe the use of full-length cDNA preparations in combination with shotgun sequencing in mRNA profiling (so-called RNA-Seq methods for “RNA sequencing”) and RNA-Seq profiling starting directly from RNA. Moreover, we describe the use of cap analysis gene expression (CAGE) for high-throughput mRNA detection and determination of transcription start sites (TSS) on the genome level. Here we applied “nanoCAGE
Original languageEnglish (US)
Title of host publicationField Guidelines for Genetic Experimental Designs in High-Throughput Sequencing
PublisherSpringer International Publishing
Number of pages36
ISBN (Print)9783319313481
StatePublished - Jun 3 2016

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledgements: We want to express our great thanks to Adam R. Hamilton, Yulia A. Medvedeva, Tanvir Alam, Intikhab Alam, Magbubah Essack, Boris Umylny, Boris R. Jankovic, Nicholas L. Naeger, Makoto Suzuki, and Gene E. Robinson for their great support for our honey bee project, which would have not been possible without working together with them. We further want to thank Charles Plessy and Piero Carninci for their support and encouragement for using CAGE.


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