DeLTa-Seq: High-Throughput Targeted RNA-Seq of Rice Leaves Without RNA Purification

Makoto Kashima; Yasuyuki Nomura; Atsushi J Nagano

doi:10.1007/978-1-0716-4204-7_12

DeLTa-Seq: High-Throughput Targeted RNA-Seq of Rice Leaves Without RNA Purification

Methods Mol Biol. 2025:2869:113-121. doi: 10.1007/978-1-0716-4204-7_12.

Authors

Makoto Kashima¹, Yasuyuki Nomura², Atsushi J Nagano^{3

4}

Affiliations

¹ Faculty of Science, Department of Molecular Biology, Toho University, Chiba, Japan.
² Research Institute for Food and Agriculture, Ryukoku University, Shiga, Japan.
³ Faculty of Agriculture, Ryukoku University, Shiga, Japan. [email protected].
⁴ Institute for Advanced Biosciences, Keio University, Yamagata, Japan. [email protected].

PMID: 39499472
DOI: 10.1007/978-1-0716-4204-7_12

Abstract

DeLTa-seq is a high-throughput RNA-seq library preparation method that enables quantification of the expression of hundreds of arbitrarily selected genes without RNA purification. This method involves direct reverse transcription using rice leaf lysate and targeted RNA-seq library preparation. DeLTa-seq enables the precise quantification of gene expression with a small number of sequencing reads. This chapter provides detailed information on the design of gene-specific primers, sampling of rice leaves, preparation of lysates, direct-lysate reverse transcription, targeted RNA-seq library preparation, and bioinformatic analysis of DeLTa-seq data.

Keywords: Direct-lysate reverse transcription; Gene expression analysis; High-throughput RNA-seq; Leaf; Rice; Targeted RNA-seq.

MeSH terms

Computational Biology / methods
Gene Expression Profiling / methods
Gene Expression Regulation, Plant
Gene Library
High-Throughput Nucleotide Sequencing* / methods
Oryza* / genetics
Plant Leaves* / genetics
RNA, Plant* / genetics
RNA, Plant* / isolation & purification
RNA-Seq / methods
Sequence Analysis, RNA / methods

Substances

RNA, Plant