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Methods for ChIP-seq Normalization and Their Application for the 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 regulation. Similar to other molecular profiling methods, ChIP-seq is sensitive 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 the mitigation of these effects after sequencing by adjusting for both technical ChIP-seq biases and more general biological biases like postmortem 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.

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Funding

This work was supported by the Russian Science Foundation (grant number 19-75-30039).

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Authors and Affiliations

  1. Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991, Moscow, Russia

    F. E. Gusev, T. V. Andreeva & E. I. Rogaev

  2. Center for Genetics and Life Science, Sirius University of Science and Technology, 354340, p. Sirius, Krasnodar krai, Russia

    F. E. Gusev, T. V. Andreeva & E. I. Rogaev

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  1. F. E. Gusev
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Gusev, F.E., Andreeva, T.V. & Rogaev, E.I. Methods for ChIP-seq Normalization and Their Application for the Analysis of Regulatory Elements in Brain Cells. Russ J Genet 59, 745–753 (2023). https://doi.org/10.1134/S1022795423080082

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