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<p>Transcriptome analysis, particularly RNA-sequencing, is an important tool for predicting gene function and investigating the physiology and phenology of organisms. We conducted RNA-sequencing analyses on 35 samples of <i>Cryptomeria japonica</i> collected from 11 specific tissues of 3-year-old trees during the growing season. In addition to these datasets, we retrieved 118 RNA-sequencing datasets from public databases and analyzed gene expression patterns by mapping them to the <i>C. japonica</i> genome sequence. By integrating the read counts and counts per million files from all 153 RNA-sequencing datasets, we constructed a comprehensive repository entitled “SugiExDB: Data repository for <i>Cryptomeria japonica</i> RNA-sequencing read counts” under TogoDB platform (<a href="http://togodb.org/db/index_rnaseq_cj">http://togodb.org/db/index_rnaseq_cj</a>). This repository enables users to see expression patterns for each gene and to download all datasets for further analyses.</p>

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SugiExDB: data repository for Cryptomeria japonica RNA-sequencing read counts in TogoDB

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年6月12日

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  • Naoki Takata,
  • Ryosuke Sato,
  • Soichiro Nagano,
  • Saneyoshi Ueno

摘要

Transcriptome analysis, particularly RNA-sequencing, is an important tool for predicting gene function and investigating the physiology and phenology of organisms. We conducted RNA-sequencing analyses on 35 samples of Cryptomeria japonica collected from 11 specific tissues of 3-year-old trees during the growing season. In addition to these datasets, we retrieved 118 RNA-sequencing datasets from public databases and analyzed gene expression patterns by mapping them to the C. japonica genome sequence. By integrating the read counts and counts per million files from all 153 RNA-sequencing datasets, we constructed a comprehensive repository entitled “SugiExDB: Data repository for Cryptomeria japonica RNA-sequencing read counts” under TogoDB platform (http://togodb.org/db/index_rnaseq_cj). This repository enables users to see expression patterns for each gene and to download all datasets for further analyses.