Methods for ChIP-seq Normalization and Their Application for Analysis of Regulatory Elements in Brain Cells

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Abstract

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) has become one of the major tools to elucidate gene expression programs. Similar to other molecular profiling methods, ChIP-seq is sensetive to several technical biases which affect downstream results, especially in cases when material quality is difficult to control, for example, frozen post-mortem human tissue. However methods for bioinformatics analysis improve every year and allow to mitigate these effects after sequencing by adjusting for both technical ChIP-seq biases and more general biological biases like post-mortem interval or cell heterogenity of the sample. Here we review a wide selection of ChIP-seq normalization methods with a focus on application in specific experimental settings, in particular when brain tissue is investigated.

About the authors

F. E. Gusev

Vavilov Institute of General Genetics Russian Academy of Sciences; Center for Genetics and Life Science, “Sirius” University of Science and Technology

Author for correspondence.
Email: gusev@vigg.ru
Russia, 119991, Moscow; Russia, 354340, Krasnodar krai, p. Sirius

T. V. Andreeva

Vavilov Institute of General Genetics Russian Academy of Sciences; Center for Genetics and Life Science, “Sirius” University of Science and Technology

Author for correspondence.
Email: an_tati@vigg.ru
Russia, 119991, Moscow; Russia, 354340, Krasnodar krai, p. Sirius

E. I. Rogaev

Vavilov Institute of General Genetics Russian Academy of Sciences; Center for Genetics and Life Science, “Sirius” University of Science and Technology

Author for correspondence.
Email: evivrog@gmail.com
Russia, 119991, Moscow; Russia, 354340, Krasnodar krai, p. Sirius

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