Design and Analysis of Epigenetics and ChIPSequencing Data
12
Melanie Kappelmann-Fenzl
Contents
12.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
12.2 DNA Quality and ChIP-Seq Library Preparation . . . . . . . . . . . . .. . .. . .. . .. . .. . .. . . .. . .. . .. . .. 178
12.3 Quality Check (QC) and Sequencing Pre-processing . .... .... .... .... .... .... ..... .... .... 180
12.4 Copy Number Variation (CNV) of Input Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
12.5 Peak/Region Calling ...... ........ ....... ........ ........ ....... ........ ........ ....... ...... 184
12.6 Further ChIP-Seq Analysis . . ....... ...... ....... ...... ....... ...... ...... ....... ...... ...... 186
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
What You Will Learn in This Chapter
In this chapter the theoretical background, the experimental requirements, and some
ways to evaluate Chromatin Immunoprecipitation followed by NGS (ChIP-Seq) are
represented and explained using practical examples. You will learn about the main
differences between sequencing DNA regions with certain histone modifications or
transcription factor binding sites. Moreover, we will introduce a software tool
HOMER, which offers a variety of (epigenetic) sequencing data analysis options.
(continued)
M. Kappelmann-Fenzl (*)
Deggendorf Institute of Technology, Deggendorf, Germany
Institute of Biochemistry (Emil-Fischer Center), Friedrich-Alexander University Erlangen-Nürnberg,
Erlangen, Germany
e-mail: melanie.kappelmann-fenzl@th-deg.de
# Springer Nature Switzerland AG 2021
M. Kappelmann-Fenzl (ed.), Next Generation Sequencing and Data Analysis, Learning
Materials in Biosciences, https://doi.org/10.1007/978-3-030-62490-3_12
177
12
Melanie Kappelmann-Fenzl
Contents
12.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
12.2 DNA Quality and ChIP-Seq Library Preparation . . . . . . . . . . . . .. . .. . .. . .. . .. . .. . . .. . .. . .. . .. 178
12.3 Quality Check (QC) and Sequencing Pre-processing . .... .... .... .... .... .... ..... .... .... 180
12.4 Copy Number Variation (CNV) of Input Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
12.5 Peak/Region Calling ...... ........ ....... ........ ........ ....... ........ ........ ....... ...... 184
12.6 Further ChIP-Seq Analysis . . ....... ...... ....... ...... ....... ...... ...... ....... ...... ...... 186
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
What You Will Learn in This Chapter
In this chapter the theoretical background, the experimental requirements, and some
ways to evaluate Chromatin Immunoprecipitation followed by NGS (ChIP-Seq) are
represented and explained using practical examples. You will learn about the main
differences between sequencing DNA regions with certain histone modifications or
transcription factor binding sites. Moreover, we will introduce a software tool
HOMER, which offers a variety of (epigenetic) sequencing data analysis options.
(continued)
M. Kappelmann-Fenzl (*)
Deggendorf Institute of Technology, Deggendorf, Germany
Institute of Biochemistry (Emil-Fischer Center), Friedrich-Alexander University Erlangen-Nürnberg,
Erlangen, Germany
e-mail: melanie.kappelmann-fenzl@th-deg.de
# Springer Nature Switzerland AG 2021
M. Kappelmann-Fenzl (ed.), Next Generation Sequencing and Data Analysis, Learning
Materials in Biosciences, https://doi.org/10.1007/978-3-030-62490-3_12
177