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Comprehensive analysis of RNA-seq data reveals the complexity of the transcriptome in Brassica rapa

Chaobo Tong1, Xiaowu Wang2, Jingyin Yu1, Jian Wu2, Wanshun Li3, Junyan Huang1, Caihua Dong1, Wei Hua1* and Shengyi Liu1*

Author Affiliations

1 Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, P.R. China, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China

2 Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, P.R. China, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 10081, China

3 Beijing Genome Institute-Shenzhen, Shenzhen 518083, China

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BMC Genomics 2013, 14:689  doi:10.1186/1471-2164-14-689

Published: 7 October 2013

Additional files

Additional file 1: Figure S1:

Quality for each base in reads viewed by software FastQC. Figure S2. Base composition of reads as visualized by the software FastQC. Figure S3. Evaluation of false mapping reads using duplicated genes. Figure S4. Genome-wide assessment of mapping RNA-seq reads. Figure S5. Sequencing randomness assessment. Figure S6. Gene coverage statistics. Figure S7. Comparison of gene expression in two samples of root and leaf tissues in gene expression. Figure S8. RT-PCR validation of novel transcripts. Figure S9. Cumulative distribution of FPKM values of all and novel transcripts in each sample. Figure S10. Expression profile of B. rapa genome displayed in Integrative Genomics Viewer (IGV). Figure S11. Numbers for different types of dinucleotides at the splicing borders. Figure S12. Genes with multiple AS events.

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Additional file 2: Table S1:

Read mapping results under different read filtering criteria. Table S2. Statistic of mapping reads. Table S3. Constructed transcripts across all tissues. Table S4. Identified novel NTRs in B. rapa. Table S5. Identified 5' UTRs and 3' UTRs in B. rapa. Table S6. The uORFs in the 5' UTRs of B. rapa genes. Table S7. The FPKM values of B. rapa genes. Table S8. The 867 constitutively expressed genes whose FPKM values were greater than 50 in each tissue. Table S9.B. rapa genes specifically expressed in silique and flower tissues. Table S10. The co-expressed gene groups (modules) from weighted gene correlation network analysis (WGCNA). Table S11. Numbers of identified splice junction reads in each tissue. Table S12. Alternative splicing events of B. rapa genes. Table S13. The enriched GO categories of B. rapa genes with alternative splicing events. Table S14. Alternative splicing events in B. rapa TFs genes.

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