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Computational protocol for the identification of X-linked genes contributing to X chromosome upregulation from RNA-sequencing datasets.

ABSTRACT: The X chromosome/autosome ratio has been widely used to profile XCU at the chromosomal level. However, this approach overlooks features of inside genes. Here, we present a computational protocol for the identification of X-linked genes contributing to X chromosome upregulation from RNA-sequencing datasets. We describe steps for selecting data, preparing software, processing data, and data analysis. This protocol quantifies the contribution value and contribution increment of each X-linked gene to XCU. For complete details on the use and execution of this protocol, please refer to Lyu et al. (2022).¹.

SUBMITTER: Yang Q

PROVIDER: S-EPMC10628899 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature

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Computational protocol for the identification of X-linked genes contributing to X chromosome upregulation from RNA-sequencing datasets.

Yang Qianying Q Lyu Qingji Q Tian Jianhui J An Lei L

STAR protocols 20231027 4

The X chromosome/autosome ratio has been widely used to profile XCU at the chromosomal level. However, this approach overlooks features of inside genes. Here, we present a computational protocol for the identification of X-linked genes contributing to X chromosome upregulation from RNA-sequencing datasets. We describe steps for selecting data, preparing software, processing data, and data analysis. This protocol quantifies the contribution value and contribution increment of each X-linked gene t ...[more]

PMID: 37897732

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