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BrassicaEDB: A Gene Expression Database for Brassica Crops

The genus Brassica 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 dif...

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Autores principales: Chao, Haoyu, Li, Tian, Luo, Chaoyu, Huang, Hualei, Ruan, Yingfei, Li, Xiaodong, Niu, Yue, Fan, Yonghai, Sun, Wei, Zhang, Kai, Li, Jiana, Qu, Cunmin, Lu, Kun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7461608/
https://www.ncbi.nlm.nih.gov/pubmed/32823802
http://dx.doi.org/10.3390/ijms21165831
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author Chao, Haoyu
Li, Tian
Luo, Chaoyu
Huang, Hualei
Ruan, Yingfei
Li, Xiaodong
Niu, Yue
Fan, Yonghai
Sun, Wei
Zhang, Kai
Li, Jiana
Qu, Cunmin
Lu, Kun
author_facet Chao, Haoyu
Li, Tian
Luo, Chaoyu
Huang, Hualei
Ruan, Yingfei
Li, Xiaodong
Niu, Yue
Fan, Yonghai
Sun, Wei
Zhang, Kai
Li, Jiana
Qu, Cunmin
Lu, Kun
author_sort Chao, Haoyu
collection PubMed
description The genus Brassica 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) for the research community. In the current BrassicaEDB, we only focused on the transcriptome level in rapeseed. 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 rapeseed 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.
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spelling pubmed-74616082020-09-04 BrassicaEDB: A Gene Expression Database for Brassica Crops Chao, Haoyu Li, Tian Luo, Chaoyu Huang, Hualei Ruan, Yingfei Li, Xiaodong Niu, Yue Fan, Yonghai Sun, Wei Zhang, Kai Li, Jiana Qu, Cunmin Lu, Kun Int J Mol Sci Article The genus Brassica 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) for the research community. In the current BrassicaEDB, we only focused on the transcriptome level in rapeseed. 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 rapeseed 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. MDPI 2020-08-13 /pmc/articles/PMC7461608/ /pubmed/32823802 http://dx.doi.org/10.3390/ijms21165831 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Chao, Haoyu
Li, Tian
Luo, Chaoyu
Huang, Hualei
Ruan, Yingfei
Li, Xiaodong
Niu, Yue
Fan, Yonghai
Sun, Wei
Zhang, Kai
Li, Jiana
Qu, Cunmin
Lu, Kun
BrassicaEDB: A Gene Expression Database for Brassica Crops
title BrassicaEDB: A Gene Expression Database for Brassica Crops
title_full BrassicaEDB: A Gene Expression Database for Brassica Crops
title_fullStr BrassicaEDB: A Gene Expression Database for Brassica Crops
title_full_unstemmed BrassicaEDB: A Gene Expression Database for Brassica Crops
title_short BrassicaEDB: A Gene Expression Database for Brassica Crops
title_sort brassicaedb: a gene expression database for brassica crops
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7461608/
https://www.ncbi.nlm.nih.gov/pubmed/32823802
http://dx.doi.org/10.3390/ijms21165831
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