The 'TranSeq'3′‐end sequencing method for high‐throughput transcriptomics and gene space refinement in plant genomes

O Tzfadia, S Bocobza, J Defoort… - The Plant …, 2018 - Wiley Online Library
High‐throughput RNA sequencing has proven invaluable not only to explore gene
expression but also for both gene prediction and genome annotation. However, RNA …

RNA‐Seq library construction methods for transcriptome analysis

NJ Bivens, M Zhou - Current Protocols in Plant Biology, 2016 - Wiley Online Library
Next‐generation sequencing (NGS) technologies have revolutionized the study of genomics
with an ever‐expanding list of applications. RNA‐Seq has emerged as a powerful method …

Plant Transcriptome Analysis with HISAT–StringTie–Ballgown and TopHat–Cufflinks Pipelines

X Rao - Transcriptome Data Analysis, 2024 - Springer
The development of next-generation sequencing technology has led to a burst of data in a
single assay. Management of a large dataset requires high demands on bioinformatic skills …

[HTML][HTML] Tools for building de novo transcriptome assembly

M Geniza, P Jaiswal - Current Plant Biology, 2017 - Elsevier
The availability of RNA-Seq method allows researchers to capture the spatial or temporal
profile of transcriptomes from various types of biological samples. The transcriptome data …

MP3RNA‐seq: Massively parallel 3′ end RNA sequencing for high‐throughput gene expression profiling and genotyping

J Chen, X Zhang, F Yi, X Gao, W Song… - Journal of Integrative …, 2021 - Wiley Online Library
Transcriptome deep sequencing (RNA‐seq) has become a routine method for global gene
expression profiling. However, its application to large‐scale experiments remains limited by …

Analysis of RNA-Seq data using TopHat and Cufflinks

S Ghosh, CKK Chan - Plant Bioinformatics: Methods and Protocols, 2016 - Springer
The recent advances in high throughput RNA sequencing (RNA-Seq) have generated huge
amounts of data in a very short span of time for a single sample. These data have required …

RNA-Seq for transcriptome analysis in non-model plants

R Garg, M Jain - Legume Genomics: Methods and Protocols, 2013 - Springer
Sequencing of mRNA using next-generation sequencing (NGS) technologies (RNA-seq)
has the potential to reveal unprecedented complexity of the transcriptomes. The …

Genomic limitations to RNA sequencing expression profiling

CD Hirsch, NM Springer, CN Hirsch - The Plant Journal, 2015 - Wiley Online Library
The field of genomics has grown rapidly with the advent of massively parallel sequencing
technologies, allowing for novel biological insights with regards to genomic, transcriptomic …

Genomics and transcriptomics advance in plant sciences

B Pucker, HM Schilbert - Molecular Approaches in Plant Biology and …, 2019 - Springer
Recent progress in sequencing technologies facilitates plant science experiments through
the availability of genome and transcriptome sequences. Genome assemblies provide …

An 'eFP‐Seq Browser'for visualizing and exploring RNA sequencing data

A Sullivan, PK Purohit, NH Freese, A Pasha… - The Plant …, 2019 - Wiley Online Library
Improvements in next‐generation sequencing technologies have resulted in dramatically
reduced sequencing costs. This has led to an explosion of '‐seq'‐based methods, of which …