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Obtaining High-Quality Transcriptome Data from Cereal Seeds by a Modified Method for Gene Expression Profiling

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Published on: May 21, 2020

BaRTv2: a highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification.

Max Coulter¹, Juan Carlos Entizne¹, Wenbin Guo²

¹Division of Plant Sciences, University of Dundee, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK.

The Plant Journal : for Cell and Molecular Biology

|June 15, 2022

Summary

This summary is machine-generated.

A new barley reference transcriptome, BaRTv2.18, offers enhanced accuracy for splice junctions and transcription sites. This comprehensive dataset improves transcript quantification and aids in studying gene regulation.

Keywords:

Iso-seq RNA-seq barley reference transcript datasets transcriptomic analysis

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Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

Area of Science:

Plant genomics and transcriptomics
Molecular biology and genetics

Background:

Accurate reference transcriptomes are crucial for precise RNA sequencing (RNA-seq) data analysis.
Understanding transcriptional and post-transcriptional regulation requires detailed characterization of splice junctions (SJs), transcription start sites (TSS), and transcription end sites (TES).

Purpose of the Study:

To generate a highly resolved and comprehensive barley reference transcriptome dataset.
To improve the accuracy of transcript quantification and regulatory analysis in barley.

Main Methods:

Utilized novel computational methods combined with PacBio Iso-seq and Illumina short-read sequencing.
Collected data from 20 diverse barley tissues and conditions.
Applied stringent filtering to ensure the quality of SJs, TSS, and TES.

Main Results:

Developed the Barke barley reference transcriptome version 2 (BaRTv2.18), featuring 39,434 genes and 148,260 transcripts.
BaRTv2.18 demonstrates increased transcript diversity and completeness compared to BaRTv1.0.
Validated the accuracy of transcript quantification, SJs, TSS, and TES using high-resolution reverse transcriptase-polymerase chain reaction and 5'-RACE.

Conclusions:

BaRTv2.18 represents the most comprehensive and resolved barley reference transcriptome to date.
This high-quality resource enables advanced transcriptomic analyses with exceptional precision.
Facilitates detailed investigations into transcriptional and post-transcriptional gene regulation in barley.