Protocol for integrated analysis of bacterial RNA-seq and ChIP-seq data for establishing a co-expression network

Yiqing Ding; Jingwei Li; Tianmin Li; Xin Deng

doi:10.1016/j.xpro.2023.102322

Protocol for integrated analysis of bacterial RNA-seq and ChIP-seq data for establishing a co-expression network

Yiqing Ding, Jingwei Li, Tianmin Li, Xin Deng^*

^*Corresponding author for this work

Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

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Abstract

Transcriptomic data and ChIP-seq data from bacteria are systematically analyzed and efficiently combined. We describe the software environment for analysis and the download and installation methods. Furthermore, we describe the analytical process and present the corresponding mini-test data, which can be conveniently restored and reproduced by users. Moreover, we provide the script for data consolidation, which allows multiple files to be rapidly merged. Overall, this protocol presents software parameters, R codes, and in-house Perl scripts for analyzing bacterial multi-omics data.

For complete details on the use and execution of this protocol, please refer to Xin et al.

Original language	English
Article number	102322
Journal	STAR Protocols
Volume	4
Issue number	2
Online published	19 May 2023
DOIs	https://doi.org/10.1016/j.xpro.2023.102322
Publication status	Published - 16 Jun 2023

Research Keywords

Genetics
Microbiology

Publisher's Copyright Statement

This full text is made available under CC-BY 4.0. https://creativecommons.org/licenses/by/4.0/

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10.1016/j.xpro.2023.102322

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title = "Protocol for integrated analysis of bacterial RNA-seq and ChIP-seq data for establishing a co-expression network",

abstract = "Transcriptomic data and ChIP-seq data from bacteria are systematically analyzed and efficiently combined. We describe the software environment for analysis and the download and installation methods. Furthermore, we describe the analytical process and present the corresponding mini-test data, which can be conveniently restored and reproduced by users. Moreover, we provide the script for data consolidation, which allows multiple files to be rapidly merged. Overall, this protocol presents software parameters, R codes, and in-house Perl scripts for analyzing bacterial multi-omics data. For complete details on the use and execution of this protocol, please refer to Xin et al. {\textcopyright} 2023 The Author(s)",

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author = "Yiqing Ding and Jingwei Li and Tianmin Li and Xin Deng",

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T1 - Protocol for integrated analysis of bacterial RNA-seq and ChIP-seq data for establishing a co-expression network

AU - Ding, Yiqing

AU - Li, Jingwei

AU - Li, Tianmin

AU - Deng, Xin

PY - 2023/6/16

Y1 - 2023/6/16

N2 - Transcriptomic data and ChIP-seq data from bacteria are systematically analyzed and efficiently combined. We describe the software environment for analysis and the download and installation methods. Furthermore, we describe the analytical process and present the corresponding mini-test data, which can be conveniently restored and reproduced by users. Moreover, we provide the script for data consolidation, which allows multiple files to be rapidly merged. Overall, this protocol presents software parameters, R codes, and in-house Perl scripts for analyzing bacterial multi-omics data. For complete details on the use and execution of this protocol, please refer to Xin et al. © 2023 The Author(s)

AB - Transcriptomic data and ChIP-seq data from bacteria are systematically analyzed and efficiently combined. We describe the software environment for analysis and the download and installation methods. Furthermore, we describe the analytical process and present the corresponding mini-test data, which can be conveniently restored and reproduced by users. Moreover, we provide the script for data consolidation, which allows multiple files to be rapidly merged. Overall, this protocol presents software parameters, R codes, and in-house Perl scripts for analyzing bacterial multi-omics data. For complete details on the use and execution of this protocol, please refer to Xin et al. © 2023 The Author(s)

KW - Genetics

KW - Microbiology

UR - http://www.scopus.com/inward/record.url?scp=85159580734&partnerID=8YFLogxK

UR - https://www.scopus.com/record/pubmetrics.uri?eid=2-s2.0-85159580734&origin=recordpage

U2 - 10.1016/j.xpro.2023.102322

DO - 10.1016/j.xpro.2023.102322

M3 - RGC 21 - Publication in refereed journal

C2 - 37210720

SN - 2666-1667

VL - 4

JO - STAR Protocols

JF - STAR Protocols

IS - 2

M1 - 102322

ER -

Protocol for integrated analysis of bacterial RNA-seq and ChIP-seq data for establishing a co-expression network

Abstract

Research Keywords

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GRF: Dissecting Signaling Pathway and Molecular Mechanism of Key Phosphorelay Crosstalk in Pseudomonas Syringae Virulence

GRF: Revealing Signaling Pathway of Novel Two-component System TsiRS in Regulating Virulence of Pseudomonas Syringae

GRF: Elucidating Molecular Mechanism and Signaling Pathway of Novel Protease System RhpPC in Regulating Pathogenicity of Pseudomonas Syringae

Cite this

Protocol for integrated analysis of bacterial RNA-seq and ChIP-seq data for establishing a co-expression network

Abstract

Research Keywords

Publisher's Copyright Statement

Access Output

Other Access Options

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Projects

GRF: Dissecting Signaling Pathway and Molecular Mechanism of Key Phosphorelay Crosstalk in Pseudomonas Syringae Virulence

GRF: Revealing Signaling Pathway of Novel Two-component System TsiRS in Regulating Virulence of Pseudomonas Syringae

GRF: Elucidating Molecular Mechanism and Signaling Pathway of Novel Protease System RhpPC in Regulating Pathogenicity of Pseudomonas Syringae

Cite this