Transcriptome Profiling Strategies

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

doi:10.1007/978-3-319-31350-4_4

Transcriptome Profiling Strategies

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

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Abstract

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 language	English (US)
Title of host publication	Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing
Publisher	Springer International Publishing
Pages	69-104
Number of pages	36
ISBN (Print)	9783319313481
DOIs	https://doi.org/10.1007/978-3-319-31350-4_4
State	Published - Jun 3 2016

Access to Document

10.1007/978-3-319-31350-4_4

Cite this

@inbook{1425ad61e7704b498dad7c5cadcd71ac,

title = "Transcriptome Profiling Strategies",

abstract = "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",

author = "Khamis, {Abdullah M.} and Bajic, {Vladimir B.} and Matthias Harbers",

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.",

year = "2016",

month = jun,

day = "3",

doi = "10.1007/978-3-319-31350-4_4",

language = "English (US)",

isbn = "9783319313481",

pages = "69--104",

booktitle = "Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing",

publisher = "Springer International Publishing",

}

TY - CHAP

T1 - Transcriptome Profiling Strategies

AU - Khamis, Abdullah M.

AU - Bajic, Vladimir B.

AU - Harbers, Matthias

N1 - 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.

PY - 2016/6/3

Y1 - 2016/6/3

N2 - 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

AB - 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

UR - http://hdl.handle.net/10754/656337

UR - https://link.springer.com/chapter/10.1007%2F978-3-319-31350-4_4

U2 - 10.1007/978-3-319-31350-4_4

DO - 10.1007/978-3-319-31350-4_4

M3 - Chapter

SN - 9783319313481

SP - 69

EP - 104

BT - Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing

PB - Springer International Publishing

ER -

Transcriptome Profiling Strategies

Abstract

Access to Document

Other files and links

Fingerprint

Cite this