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Pipeline publication

[…] –3 with TSS’s connected to bins surrounding random regions to calculate a randomized average and subtracting these average values from the matrix. Z-axis values and color scores are then plotted from these values obtained, as a relative score from the minimum and maximum. Interaction overlaps between promoters of differential genes and distal nrpe1 DMRs was taken using an interaction score > = 5 to obtain as many overlapping high quality interactions as possible., RNA from ago4 seedlings was isolated and rRNA-depleted in three biological repeats as described [] and libraries were prepared by the University of Michigan Sequencing Core. Reads were mapped to the TAIR10 genome assembly using Tophat [] and differential expression was called using EdgeR []. Previously published RNA-seq datasets from seedlings (Col-0 wild-type and the nrpe1 mutant) [] (GSE38464) were obtained from plants grown, harvested, isolated, rRNA-depleted, and sequenced in parallel to the ago4 dataset. Overlaps in differential expression were calculated from EdgeR and plotted as a weighted Venn diagram using the Venneuler package in R., DAP-seq transcription factor binding sites came from the GEO accession GSE60141 []. was generated by taking interactions overlapping promoters (1kb upstream of TSS) on one end and DAP-seq transcription factor peaks on the other or no DAP-seq peak for each transcription factor tested. The median RPKM values of genes interacting in each transcription factor DAP-seq reaction were then plotted as a boxplot and provided in . The genome-wide median was produced from total genes., SVP ChIP-seq data were downloaded from GEO accession GSE33120 []. Reads were then mapped to the TAIR10 genome and immunoprecipitation vs. control were counted in 250bp windows for comparison to H […]

Pipeline specifications

Software tools TopHat, edgeR, venneuler
Organisms Arabidopsis thaliana
Diseases RNA Virus Infections