Additional file 1.

Supplemental Figures. Figure S1. Modified NlaIII-DGE Tag-seq protocol. Figure S2. Transcription at rRNA loci observed with EXPRSS and NlaIII-DGE tag sequencing. Figure S3. Correlation between sense and anti-sense transcript expression. Figure S4. Novel transcription detection using EXPRSS Tag-seq. Figure S5. Cumulative frequency distribution multi-matching reads. Figure S6. Pair-wise scatter plots of gene counts from flg22 treated replicates. Figure S7. Pair-wise correlation of fold changes between three methods tested. Figure S8. Pair-wise scatter plots of gene counts from 60 minutes flg22 treatment replicates from two independent experiments. Figure S9. Pair-wise scatter plots of gene counts from Col-0 flg22 time course replicates. Figure S10. Pair-wise scatter plots of gene counts from npr1-1 flg22 time course replicates. Figure S11. Pair-wise scatter plots of gene counts from jar1-1 flg22 time course replicates. Figure S12. Pair-wise scatter plots of gene counts from ein2-5 flg22 time course replicates. Figure S13. Hierarchical clustering of genes differentially expressed during flg22 time course of four genotypes. Figure S14. Heat maps of log2 fold changes from all data points of genes that are differentially expressed at least from one time point of flg22 time course. Figure S15. Hierarchical clustering of genes differentially expressed during flg22 time course of four genotypes compared to Col-0. Figure S16. Frequency distribution of Read1 and Read2 from paired end sequencing. Figure S17. Examples showing Read1 and Read2 from paired end sequencing. Figure S18. Length distribution of genes detected in EXPRSS. Figure S19. Cartoon depicting tag assignment to genes.

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Rallapalli et al. BMC Genomics 2014 15:341   doi:10.1186/1471-2164-15-341