Tissue expression profile:
941 RNA-seq libraries of B. juncea, covering 15 tissues were collected in this module. The transcriptomics clean reads were mapped to the T84-66.V2.0 genome by software Hisat2 (v.2.2.1) (Kim et al., 2019), and the expression level of each gene was identified by stringtie (v.2.1.4) (Pertea et al., 2015). "Tissue expression profile" interface provides queries for gene expression profiles cross tissues. Additionally, users can also observe the gene expression level under different lines, treatments and stages, such as B. juncea lines with different seed size (Mathur et al., 2022), B. juncea lines with different leaf colors (Liu et al., 2022), treatments with different nitrogen concentrations (Goel et al., 2018), different seed development stages (Gao et al., 2022). eFP:
Electronic Fluorescent Pictographic (eFP) provides color-coded pictograms of tissues to intuitively visualize temporal dynamic changes in gene expression level. In this module, there are 3 models for users to choose.
Absolute: The absolute expression level for a given gene.
Relative: The relative expression of any given gene is compared to a control data (the median expression value of that gene for all samples that were measured), which can be used to study where the gene is the most prominently expressed (Winter et al., 2007).
Compare: The relative expression of any given gene (primary gene) can be compared to any other gene (reference gene).
Co-expression:
The co-expression networks of gene-gene/lncRNA-mRNA are generated by calculating the Pearson correlation coefficient and the output is decided by the threshold of a Pearson coefficient that is settled by users.
Population expression profile:
A total of 204 B. juncea accessions with RNA-seq data were used to develop the "Population expression profile" (Harper et al., 2020). The transcriptomics clean reads were mapped to the T84-66.V2.0 genome by software Hisat2 (v.2.2.1) (Kim et al., 2019), and the expression level of each gene was identified by stringtie (v.2.1.4) (Pertea et al., 2015).
Differential expression:
Six bioprojects were used in the "Differential expression" module, and five traits of B. juncea were studied in these bioprojects, including leaf color, leaf shape, leaf vein color, seed size, seed development. The R package "DEseq2" (Love et al., 2014) was used for identifying differently expressed genes (DEGs). Before running DEseq2, low expressed (rowSums < 1) genes were removed, and the cut-off criterion for identifying DEGs was as follows: A false discovery rate (FDR) < 0.05 and | log2 (Fold Change) |> 1.

References
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