Working Paper Article Version 1 This version is not peer-reviewed

BrassicaEDB: A Gene Expression Database for Brassica Crops

Version 1 : Received: 11 July 2020 / Approved: 12 July 2020 / Online: 12 July 2020 (15:25:37 CEST)

A peer-reviewed article of this Preprint also exists.

Chao, H.; Li, T.; Luo, C.; Huang, H.; Ruan, Y.; Li, X.; Niu, Y.; Fan, Y.; Sun, W.; Zhang, K.; Li, J.; Qu, C.; Lu, K. BrassicaEDB: A Gene Expression Database for Brassica Crops. Int. J. Mol. Sci. 2020, 21, 5831. Chao, H.; Li, T.; Luo, C.; Huang, H.; Ruan, Y.; Li, X.; Niu, Y.; Fan, Y.; Sun, W.; Zhang, K.; Li, J.; Qu, C.; Lu, K. BrassicaEDB: A Gene Expression Database for Brassica Crops. Int. J. Mol. Sci. 2020, 21, 5831.

Journal reference: Int. J. Mol. Sci. 2020, 21, 5831
DOI: 10.3390/ijms21165831

Abstract

The Brassica family contains several economically important crops, including rapeseed (Brassica napus, 2n = 38, AACC), the second largest source of seed oil and protein meal worldwide. However, research in rapeseed is hampered because it is complicated and time-consuming for researchers to access different types of expression data. We therefore developed the Brassica Expression Database (BrassicaEDB, https://biodb.swu.edu.cn/brassica/) for the research community. We conducted RNA sequencing (RNA-Seq) of 103 tissues from rapeseed cultivar ZhongShuang11 (ZS11) at seven developmental stages (seed germination, seedling, bolting, initial flowering, full-bloom, podding, and maturation). We determined the expression patterns of 101,040 genes via FPKM analysis and displayed the results using the eFP browser. We also analyzed transcriptome data for rapeseed from 70 BioProjects in the SRA database and obtained three types of expression level data (FPKM, TPM, and read counts). We used this information to develop the BrassicaEDB, including eFP, Treatment, Coexpression, and SRA Project modules based on gene expression profiles and Gene Feature, qPCR Primer, and BLAST modules based on gene sequences. The BrassicaEDB provides comprehensive gene expression profile information and a user-friendly visualization interface for Brassica crop researchers. Using this database, researchers can quickly retrieve the expression level data for target genes in different tissues and in response to different treatments to elucidate gene functions and explore the biology of rapeseed at the transcriptome level.

Subject Areas

BrassicaEDB; Brassica napus; gene expression profile; coexpression

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