Cargando…

Construction of transcriptional regulatory networks using total RNA-seq data

Total RNA sequencing allows capturing of long non-coding and circular RNA along with mRNA. Additional sequencing of micro RNA (miRNA), using libraries with shorter fragments, provides the means to characterize miRNA-driven transcriptional regulation. Here, we present a protocol for processing total...

Descripción completa

Detalles Bibliográficos
Autores principales:	Chouvarine, Philippe, Hansmann, Georg
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Elsevier 2021
Materias:	Protocol
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8403681/ https://www.ncbi.nlm.nih.gov/pubmed/34485938 http://dx.doi.org/10.1016/j.xpro.2021.100769

Ejemplares similares

Predicting gene regulatory links from single-cell RNA-seq data using graph neural networks
por: Mao, Guo, et al.
Publicado: (2023)

RNA expression profiles and regulatory networks in human right ventricular hypertrophy due to high pressure load
por: Chouvarine, Philippe, et al.
Publicado: (2021)

Generating transcriptional regulatory networks from time-ordered stem cell differentiation RNA sequencing data
por: Tsai, Yu-Shuen, et al.
Publicado: (2022)

Protocol for integrated analysis of bacterial RNA-seq and ChIP-seq data for establishing a co-expression network
por: Ding, Yiqing, et al.
Publicado: (2023)

A computational approach to generate highly conserved gene co-expression networks with RNA-seq data
por: Arshad, Zainab, et al.
Publicado: (2022)

EU-RNA-seq for in vivo labeling and high throughput sequencing of nascent transcripts
por: Palozola, Katherine C., et al.
Publicado: (2021)

deltaTE: Detection of Translationally Regulated Genes by Integrative Analysis of Ribo‐seq and RNA‐seq Data
por: Chothani, Sonia, et al.
Publicado: (2019)

Transcription Factor Co-expression Networks of Adipose RNA-Seq Data Reveal Regulatory Mechanisms of Obesity
por: Skinkyte-Juskiene, Ruta, et al.
Publicado: (2018)

Protocol to measure ribosome density along mRNA transcripts of Arabidopsis thaliana tissues using Ribo-seq
por: Vélez-Bermúdez, Isabel Cristina, et al.
Publicado: (2023)

SIGNET: single-cell RNA-seq-based gene regulatory network prediction using multiple-layer perceptron bagging
por: Luo, Qinhuan, et al.
Publicado: (2021)

Construction of microRNA and transcription factor regulatory network based on gene expression data in cardiomyopathy
por: Wang, Lei, et al.
Publicado: (2014)

Inferring Gene Regulatory Networks from RNA-seq Data Using Kernel Classification
por: Al-Aamri, Amira, et al.
Publicado: (2023)

Consensus clustering of single-cell RNA-seq data by enhancing network affinity
por: Cui, Yaxuan, et al.
Publicado: (2021)

Protocol for quantitative analysis of RNA 3′-end processing induced by disassociated subunits using chromatin-associated RNA-seq data
por: Huang, Jie, et al.
Publicado: (2023)

Optimized protocols for ChIP-seq and deletion mutant construction in Pseudomonas syringae
por: Yao, Chunyan, et al.
Publicado: (2021)

Protocol for isolation and ATAC-seq library construction of zebrafish red blood cells
por: Ding, Yanyan, et al.
Publicado: (2022)

Reconstructing the maize leaf regulatory network using ChIP-seq data of 104 transcription factors
por: Tu, Xiaoyu, et al.
Publicado: (2020)

Processing single-cell RNA-seq data for dimension reduction-based analyses using open-source tools
por: Chen, Bob, et al.
Publicado: (2021)

Use of scREAD to explore and analyze single-cell and single-nucleus RNA-seq data for Alzheimer’s disease
por: Wang, Cankun, et al.
Publicado: (2021)

iRNA-seq: computational method for genome-wide assessment of acute transcriptional regulation from total RNA-seq data
por: Madsen, Jesper Grud Skat, et al.
Publicado: (2015)

Annotating cell types in human single-cell RNA-seq data with CellO
por: Bernstein, Matthew N., et al.
Publicado: (2021)

Identification of hub genes and transcription factor regulatory network for heart failure using RNA-seq data and robust rank aggregation analysis
por: Tu, Dingyuan, et al.
Publicado: (2022)

Identification of regulatory links between transcription and RNA processing with long-read sequencing
por: Alfonso-Gonzalez, Carlos, et al.
Publicado: (2023)

Prostate Cancer Gene Regulatory Network Inferred from RNA-Seq Data
por: Moore, Daniel, et al.
Publicado: (2019)

Transcript quantification with RNA-Seq data
por: Bohnert, Regina, et al.
Publicado: (2009)

Combining Multiple RNA-Seq Data Analysis Algorithms Using Machine Learning Improves Differential Isoform Expression Analysis
por: Dimopoulos, Alexandros C., et al.
Publicado: (2021)

Measure transcript integrity using RNA-seq data
por: Wang, Liguo, et al.
Publicado: (2016)

Analysis of the translatome in solid tumors using polyribosome profiling/RNA-Seq
por: Adjibade, Pauline, et al.
Publicado: (2016)

AbSeq Protocol Using the Nano-Well Cartridge-Based Rhapsody Platform to Generate Protein and Transcript Expression Data on the Single-Cell Level
por: Erickson, Jami R., et al.
Publicado: (2020)

Defining pervasive transcription units using chromatin RNA-sequencing data
por: Guo, Ziwei, et al.
Publicado: (2022)

Integrated protocol for exitron and exitron-derived neoantigen identification using human RNA-seq data with ScanExitron and ScanNeo
por: Wang, Ting-You, et al.
Publicado: (2021)

Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT
por: Hsu, Che-Wei, et al.
Publicado: (2022)

Quantifying RNA synthesis at rate-limiting steps of transcription using nascent RNA-sequencing data
por: Rabenius, Adelina, et al.
Publicado: (2022)

RNA-seq and ChIP-seq as Complementary Approaches for Comprehension of Plant Transcriptional Regulatory Mechanism
por: Muhammad, Isiaka Ibrahim, et al.
Publicado: (2019)

Processing single-cell RNA-seq datasets using SingCellaR
por: Wang, Guanlin, et al.
Publicado: (2022)

Deconvolution of in vivo protein-RNA contacts using fractionated eCLIP-seq
por: Biancon, Giulia, et al.
Publicado: (2022)

Constructing gene regulatory networks using epigenetic data
por: Sonawane, Abhijeet Rajendra, et al.
Publicado: (2021)

Computational approach to evaluate scRNA-seq data quality and gene body coverage with SkewC
por: Abugessaisa, Imad, et al.
Publicado: (2023)

CapZyme-Seq: A 5′-RNA-Seq Method for Differential Detection and Quantitation of NAD-Capped and Uncapped 5′-Triphosphate RNA
por: Vvedenskaya, Irina O., et al.
Publicado: (2020)

Predicting gene regulatory networks of soybean nodulation from RNA-Seq transcriptome data
por: Zhu, Mingzhu, et al.
Publicado: (2013)

Cannot write session to /tmp/vufind_sessions/sess_nstfhln5gb7j7gt02dtq79ohvd